Starting phenix.real_space_refine on Mon Aug 25 06:25:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.map" model { file = "/net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pzv_18046/08_2025/8pzv_18046.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 45 5.16 5 C 8357 2.51 5 N 2290 2.21 5 O 2609 1.98 5 H 12738 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26040 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12115 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 5375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5375 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 11, 'TRANS': 357} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 804 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 51} 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: "D" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3485 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1291 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2828 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "I" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH2NOTPRO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 3.60, per 1000 atoms: 0.14 Number of scatterers: 26040 At special positions: 0 Unit cell: (111.93, 133.77, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 Mg 1 11.99 O 2609 8.00 N 2290 7.00 C 8357 6.00 H 12738 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 559.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 18 sheets defined 27.9% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.729A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.678A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.105A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'C' and resid 33 through 39 removed outlier: 3.838A pdb=" N GLU C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.782A pdb=" N VAL D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.848A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 45 Processing helix chain 'F' and resid 62 through 87 removed outlier: 4.691A pdb=" N HIS F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 3.524A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 122 removed outlier: 4.027A pdb=" N TYR F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 148 removed outlier: 3.584A pdb=" N ARG F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'F' and resid 395 through 420 removed outlier: 3.655A pdb=" N ARG F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.243A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 83 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 80 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.213A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.681A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER B 193 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 245 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.808A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA A 343 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN A 276 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.256A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.414A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 454 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL A 456 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A 447 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 458 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN A 445 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY A 460 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLY A 443 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS A 462 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLN A 441 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.270A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 6.531A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.683A pdb=" N GLU B 99 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU B 107 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 101 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 117 removed outlier: 5.542A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.164A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202 removed outlier: 5.959A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.404A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.200A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332 removed outlier: 6.068A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.813A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 35 through 38 627 hydrogen bonds defined for protein. 1773 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: 5.45 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12730 1.03 - 1.23: 19 1.23 - 1.42: 5809 1.42 - 1.61: 7661 1.61 - 1.81: 88 Bond restraints: 26307 Sorted by residual: bond pdb=" CB UX8 I 3 " pdb=" HB2 UX8 I 3 " ideal model delta sigma weight residual 0.970 1.244 -0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" CZ3 UX8 I 3 " pdb=" HZ3 UX8 I 3 " ideal model delta sigma weight residual 0.930 1.130 -0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" CA UX8 I 3 " pdb=" C UX8 I 3 " ideal model delta sigma weight residual 1.525 1.323 0.202 2.10e-02 2.27e+03 9.21e+01 bond pdb=" CE3 UX8 I 3 " pdb=" HE3 UX8 I 3 " ideal model delta sigma weight residual 0.930 1.118 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" CA UX8 I 3 " pdb=" CB UX8 I 3 " ideal model delta sigma weight residual 1.530 1.713 -0.183 2.00e-02 2.50e+03 8.40e+01 ... (remaining 26302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.03: 47249 7.03 - 14.06: 9 14.06 - 21.09: 1 21.09 - 28.12: 2 28.12 - 35.15: 3 Bond angle restraints: 47264 Sorted by residual: angle pdb=" CA UX8 I 3 " pdb=" C UX8 I 3 " pdb=" O UX8 I 3 " ideal model delta sigma weight residual 120.80 142.44 -21.64 1.70e+00 3.46e-01 1.62e+02 angle pdb=" C GLN B 234 " pdb=" CA GLN B 234 " pdb=" HA GLN B 234 " ideal model delta sigma weight residual 109.00 73.85 35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB GLN B 234 " pdb=" CA GLN B 234 " pdb=" HA GLN B 234 " ideal model delta sigma weight residual 109.00 73.87 35.13 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N GLN B 234 " pdb=" CA GLN B 234 " pdb=" HA GLN B 234 " ideal model delta sigma weight residual 110.00 78.28 31.72 3.00e+00 1.11e-01 1.12e+02 angle pdb=" H1 TRP I 1 " pdb=" N TRP I 1 " pdb=" H2 TRP I 1 " ideal model delta sigma weight residual 109.47 87.81 21.66 3.00e+00 1.11e-01 5.21e+01 ... (remaining 47259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 11289 17.62 - 35.25: 870 35.25 - 52.87: 217 52.87 - 70.50: 63 70.50 - 88.12: 20 Dihedral angle restraints: 12459 sinusoidal: 6734 harmonic: 5725 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -138.08 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA THR A 571 " pdb=" C THR A 571 " pdb=" N PHE A 572 " pdb=" CA PHE A 572 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLN F 55 " pdb=" C GLN F 55 " pdb=" N ALA F 56 " pdb=" CA ALA F 56 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 12456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1855 0.083 - 0.167: 159 0.167 - 0.250: 0 0.250 - 0.333: 0 0.333 - 0.417: 2 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CB UX8 I 3 " pdb=" CA UX8 I 3 " pdb=" CG UX8 I 3 " pdb=" O9 UX8 I 3 " both_signs ideal model delta sigma weight residual False -2.38 -2.80 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA GLN B 234 " pdb=" N GLN B 234 " pdb=" C GLN B 234 " pdb=" CB GLN B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA UX8 I 3 " pdb=" N UX8 I 3 " pdb=" C UX8 I 3 " pdb=" CB UX8 I 3 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 2013 not shown) Planarity restraints: 4031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " 0.023 2.00e-02 2.50e+03 1.45e-02 8.37e+00 pdb=" CG TRP A 546 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP A 546 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 546 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 546 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 546 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 546 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 107 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 108 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 45 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO C 46 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 46 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 46 " -0.023 5.00e-02 4.00e+02 ... (remaining 4028 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 724 2.11 - 2.73: 47351 2.73 - 3.35: 78911 3.35 - 3.98: 103787 3.98 - 4.60: 161334 Nonbonded interactions: 392107 Sorted by model distance: nonbonded pdb=" H HIS C 51 " pdb=" OD1 ASN D 241 " model vdw 1.481 2.450 nonbonded pdb=" H LEU B 194 " pdb=" OD2 ASP B 246 " model vdw 1.481 2.450 nonbonded pdb=" O HIS A 677 " pdb=" H THR A 692 " model vdw 1.508 2.450 nonbonded pdb=" O PHE A 347 " pdb=" H LEU A 377 " model vdw 1.538 2.450 nonbonded pdb=" O LEU A 247 " pdb=" H ARG B 195 " model vdw 1.549 2.450 ... (remaining 392102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.170 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.910 Find NCS groups from input model: 0.050 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.202 13572 Z= 0.266 Angle : 0.613 21.643 18421 Z= 0.330 Chirality : 0.046 0.417 2016 Planarity : 0.004 0.046 2427 Dihedral : 13.949 88.120 4956 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.20), residues: 1678 helix: 0.88 (0.24), residues: 442 sheet: -1.71 (0.22), residues: 457 loop : -1.22 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.019 0.001 TYR A 794 PHE 0.010 0.001 PHE D 128 TRP 0.048 0.002 TRP A 546 HIS 0.002 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00556 (13569) covalent geometry : angle 0.61336 (18419) SS BOND : bond 0.00224 ( 1) SS BOND : angle 1.38914 ( 2) hydrogen bonds : bond 0.10101 ( 623) hydrogen bonds : angle 6.49994 ( 1773) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: D 41 GLN cc_start: 0.7149 (mm110) cc_final: 0.6818 (mm110) REVERT: F 76 MET cc_start: 0.5354 (mmm) cc_final: 0.5094 (tpt) REVERT: F 136 MET cc_start: 0.6296 (mmt) cc_final: 0.6053 (mmm) REVERT: F 137 ILE cc_start: 0.4881 (tp) cc_final: 0.4601 (tt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 1.1614 time to fit residues: 283.7485 Evaluate side-chains 178 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 463 ASN A 538 ASN B 225 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN F 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119758 restraints weight = 44307.073| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.39 r_work: 0.3243 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13572 Z= 0.181 Angle : 0.554 5.816 18421 Z= 0.301 Chirality : 0.045 0.399 2016 Planarity : 0.004 0.045 2427 Dihedral : 5.066 20.361 1860 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 1.12 % Allowed : 8.06 % Favored : 90.82 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.20), residues: 1678 helix: 0.96 (0.23), residues: 446 sheet: -1.90 (0.22), residues: 448 loop : -1.16 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 132 TYR 0.014 0.001 TYR D 184 PHE 0.013 0.001 PHE A 426 TRP 0.019 0.002 TRP A 546 HIS 0.006 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00381 (13569) covalent geometry : angle 0.55387 (18419) SS BOND : bond 0.00194 ( 1) SS BOND : angle 2.54888 ( 2) hydrogen bonds : bond 0.04064 ( 623) hydrogen bonds : angle 5.89255 ( 1773) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it. REVERT: B 178 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 253 VAL cc_start: 0.8755 (t) cc_final: 0.8481 (p) REVERT: C 34 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6722 (mm110) REVERT: D 41 GLN cc_start: 0.7495 (mm110) cc_final: 0.6975 (mm110) REVERT: D 84 ASP cc_start: 0.8170 (m-30) cc_final: 0.7902 (m-30) REVERT: F 76 MET cc_start: 0.5255 (mmm) cc_final: 0.5006 (tpt) REVERT: F 136 MET cc_start: 0.6435 (mmt) cc_final: 0.6179 (mmm) REVERT: F 137 ILE cc_start: 0.4816 (tp) cc_final: 0.4591 (tt) outliers start: 16 outliers final: 5 residues processed: 200 average time/residue: 1.0680 time to fit residues: 235.6993 Evaluate side-chains 174 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 463 ASN B 225 GLN F 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119540 restraints weight = 44200.618| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.39 r_work: 0.3240 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13572 Z= 0.177 Angle : 0.535 5.544 18421 Z= 0.289 Chirality : 0.044 0.397 2016 Planarity : 0.004 0.041 2427 Dihedral : 4.983 20.830 1860 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 1.33 % Allowed : 9.74 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.20), residues: 1678 helix: 1.05 (0.24), residues: 447 sheet: -1.89 (0.22), residues: 441 loop : -1.15 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.014 0.001 TYR D 184 PHE 0.009 0.001 PHE A 791 TRP 0.010 0.002 TRP A 546 HIS 0.005 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00373 (13569) covalent geometry : angle 0.53416 (18419) SS BOND : bond 0.00352 ( 1) SS BOND : angle 2.33780 ( 2) hydrogen bonds : bond 0.03895 ( 623) hydrogen bonds : angle 5.67448 ( 1773) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 168 ASN cc_start: 0.7006 (t0) cc_final: 0.6789 (t0) REVERT: B 253 VAL cc_start: 0.8751 (t) cc_final: 0.8478 (p) REVERT: D 41 GLN cc_start: 0.7539 (mm110) cc_final: 0.6998 (mm110) REVERT: F 136 MET cc_start: 0.6441 (mmt) cc_final: 0.6186 (mmm) REVERT: F 137 ILE cc_start: 0.4894 (tp) cc_final: 0.4595 (tt) REVERT: F 143 ASN cc_start: 0.6655 (OUTLIER) cc_final: 0.5850 (t0) outliers start: 19 outliers final: 8 residues processed: 187 average time/residue: 0.9815 time to fit residues: 203.5906 Evaluate side-chains 181 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 538 ASN A 606 ASN E 54 GLN F 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117282 restraints weight = 44003.810| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.38 r_work: 0.3191 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13572 Z= 0.240 Angle : 0.567 6.560 18421 Z= 0.307 Chirality : 0.045 0.388 2016 Planarity : 0.004 0.041 2427 Dihedral : 5.150 20.383 1860 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.81 % Favored : 92.13 % Rotamer: Outliers : 2.03 % Allowed : 11.00 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.20), residues: 1678 helix: 0.90 (0.23), residues: 447 sheet: -1.81 (0.22), residues: 429 loop : -1.26 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 166 TYR 0.014 0.002 TYR A 794 PHE 0.012 0.002 PHE A 737 TRP 0.012 0.002 TRP A 745 HIS 0.005 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00513 (13569) covalent geometry : angle 0.56681 (18419) SS BOND : bond 0.00288 ( 1) SS BOND : angle 2.28430 ( 2) hydrogen bonds : bond 0.04050 ( 623) hydrogen bonds : angle 5.68407 ( 1773) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8296 (tmmt) REVERT: B 253 VAL cc_start: 0.8762 (t) cc_final: 0.8459 (p) REVERT: D 41 GLN cc_start: 0.7578 (mm110) cc_final: 0.6988 (mm110) REVERT: D 84 ASP cc_start: 0.8209 (m-30) cc_final: 0.7886 (m-30) REVERT: F 136 MET cc_start: 0.6445 (mmt) cc_final: 0.6204 (mmm) REVERT: F 137 ILE cc_start: 0.4866 (tp) cc_final: 0.4552 (tt) REVERT: F 143 ASN cc_start: 0.6596 (OUTLIER) cc_final: 0.5810 (t0) REVERT: F 400 MET cc_start: 0.5971 (tpp) cc_final: 0.5349 (tpp) outliers start: 29 outliers final: 16 residues processed: 195 average time/residue: 1.0253 time to fit residues: 222.6100 Evaluate side-chains 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 154 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120061 restraints weight = 43832.934| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.38 r_work: 0.3222 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13572 Z= 0.149 Angle : 0.524 6.008 18421 Z= 0.282 Chirality : 0.044 0.393 2016 Planarity : 0.004 0.044 2427 Dihedral : 4.950 20.148 1860 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 1.75 % Allowed : 11.84 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.20), residues: 1678 helix: 1.13 (0.24), residues: 447 sheet: -1.82 (0.22), residues: 447 loop : -1.15 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.014 0.001 TYR D 184 PHE 0.010 0.001 PHE A 426 TRP 0.010 0.001 TRP B 183 HIS 0.005 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00311 (13569) covalent geometry : angle 0.52383 (18419) SS BOND : bond 0.00191 ( 1) SS BOND : angle 2.02496 ( 2) hydrogen bonds : bond 0.03664 ( 623) hydrogen bonds : angle 5.54125 ( 1773) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 217 GLN cc_start: 0.7277 (pm20) cc_final: 0.6667 (pp30) REVERT: A 417 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7523 (tmtt) REVERT: B 253 VAL cc_start: 0.8715 (t) cc_final: 0.8419 (p) REVERT: D 41 GLN cc_start: 0.7511 (mm110) cc_final: 0.6911 (mm110) REVERT: F 39 GLU cc_start: 0.5203 (tp30) cc_final: 0.3620 (tt0) REVERT: F 136 MET cc_start: 0.6445 (mmt) cc_final: 0.6207 (mmm) REVERT: F 137 ILE cc_start: 0.4804 (tp) cc_final: 0.4476 (tt) REVERT: F 400 MET cc_start: 0.5922 (tpp) cc_final: 0.5346 (tpp) outliers start: 25 outliers final: 12 residues processed: 196 average time/residue: 0.9574 time to fit residues: 208.6258 Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN F 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118243 restraints weight = 44268.236| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.39 r_work: 0.3190 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13572 Z= 0.218 Angle : 0.552 6.437 18421 Z= 0.298 Chirality : 0.044 0.388 2016 Planarity : 0.004 0.044 2427 Dihedral : 5.080 20.600 1860 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.57 % Favored : 92.37 % Rotamer: Outliers : 1.75 % Allowed : 12.89 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.20), residues: 1678 helix: 1.04 (0.24), residues: 447 sheet: -1.75 (0.23), residues: 435 loop : -1.24 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.014 0.002 TYR E 37 PHE 0.020 0.002 PHE D 128 TRP 0.011 0.002 TRP A 745 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00468 (13569) covalent geometry : angle 0.55185 (18419) SS BOND : bond 0.00218 ( 1) SS BOND : angle 2.04198 ( 2) hydrogen bonds : bond 0.03903 ( 623) hydrogen bonds : angle 5.56638 ( 1773) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.7138 (pt0) cc_final: 0.6799 (pt0) REVERT: A 417 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7469 (tmtt) REVERT: B 253 VAL cc_start: 0.8736 (t) cc_final: 0.8428 (p) REVERT: D 41 GLN cc_start: 0.7513 (mm110) cc_final: 0.6885 (mm110) REVERT: F 135 GLU cc_start: 0.5746 (mt-10) cc_final: 0.5505 (mt-10) REVERT: F 136 MET cc_start: 0.6436 (mmt) cc_final: 0.6203 (mmm) REVERT: F 137 ILE cc_start: 0.4841 (tp) cc_final: 0.4520 (tt) REVERT: F 143 ASN cc_start: 0.6533 (OUTLIER) cc_final: 0.5713 (t0) outliers start: 25 outliers final: 18 residues processed: 195 average time/residue: 0.9597 time to fit residues: 208.4568 Evaluate side-chains 190 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN F 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117949 restraints weight = 43982.875| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.38 r_work: 0.3191 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13572 Z= 0.225 Angle : 0.561 6.137 18421 Z= 0.302 Chirality : 0.044 0.392 2016 Planarity : 0.004 0.041 2427 Dihedral : 5.126 20.360 1860 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 1.82 % Allowed : 13.59 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.20), residues: 1678 helix: 0.99 (0.24), residues: 447 sheet: -1.73 (0.23), residues: 421 loop : -1.32 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.014 0.002 TYR D 184 PHE 0.011 0.001 PHE A 791 TRP 0.012 0.002 TRP A 745 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00484 (13569) covalent geometry : angle 0.56017 (18419) SS BOND : bond 0.00218 ( 1) SS BOND : angle 2.03492 ( 2) hydrogen bonds : bond 0.03928 ( 623) hydrogen bonds : angle 5.57730 ( 1773) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7462 (tmtt) REVERT: B 253 VAL cc_start: 0.8729 (t) cc_final: 0.8422 (p) REVERT: D 41 GLN cc_start: 0.7623 (mm110) cc_final: 0.6919 (mm110) REVERT: F 39 GLU cc_start: 0.5291 (tp30) cc_final: 0.3695 (tt0) REVERT: F 135 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5496 (mt-10) REVERT: F 136 MET cc_start: 0.6452 (mmt) cc_final: 0.6221 (mmm) REVERT: F 137 ILE cc_start: 0.4863 (tp) cc_final: 0.4538 (tt) REVERT: F 143 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.5726 (t0) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.9580 time to fit residues: 201.3213 Evaluate side-chains 190 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN E 54 GLN F 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118023 restraints weight = 44177.947| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.39 r_work: 0.3190 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13572 Z= 0.212 Angle : 0.556 6.578 18421 Z= 0.300 Chirality : 0.044 0.394 2016 Planarity : 0.004 0.056 2427 Dihedral : 5.109 20.227 1860 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 1.82 % Allowed : 13.88 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.20), residues: 1678 helix: 0.99 (0.24), residues: 449 sheet: -1.73 (0.23), residues: 433 loop : -1.28 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.015 0.002 TYR D 184 PHE 0.024 0.001 PHE D 128 TRP 0.011 0.002 TRP A 745 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00454 (13569) covalent geometry : angle 0.55583 (18419) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.99267 ( 2) hydrogen bonds : bond 0.03868 ( 623) hydrogen bonds : angle 5.56150 ( 1773) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7509 (tmtt) REVERT: B 253 VAL cc_start: 0.8720 (t) cc_final: 0.8419 (p) REVERT: D 41 GLN cc_start: 0.7627 (mm110) cc_final: 0.6918 (mm110) REVERT: F 39 GLU cc_start: 0.5217 (tp30) cc_final: 0.3647 (tt0) REVERT: F 135 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5530 (mt-10) REVERT: F 136 MET cc_start: 0.6414 (mmt) cc_final: 0.6184 (mmm) REVERT: F 137 ILE cc_start: 0.4824 (tp) cc_final: 0.4505 (tt) REVERT: F 143 ASN cc_start: 0.6517 (OUTLIER) cc_final: 0.5704 (t0) REVERT: F 400 MET cc_start: 0.6057 (tpp) cc_final: 0.5735 (tpp) outliers start: 26 outliers final: 19 residues processed: 189 average time/residue: 1.0117 time to fit residues: 212.7322 Evaluate side-chains 189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118540 restraints weight = 44155.464| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.38 r_work: 0.3201 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13572 Z= 0.191 Angle : 0.547 6.969 18421 Z= 0.295 Chirality : 0.044 0.397 2016 Planarity : 0.004 0.048 2427 Dihedral : 5.067 19.913 1860 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 2.03 % Allowed : 14.02 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.20), residues: 1678 helix: 1.03 (0.24), residues: 450 sheet: -1.74 (0.23), residues: 433 loop : -1.26 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.015 0.001 TYR D 184 PHE 0.010 0.001 PHE A 791 TRP 0.010 0.002 TRP A 745 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00407 (13569) covalent geometry : angle 0.54703 (18419) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.93165 ( 2) hydrogen bonds : bond 0.03783 ( 623) hydrogen bonds : angle 5.53588 ( 1773) Misc. bond : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7533 (tmtt) REVERT: B 253 VAL cc_start: 0.8697 (t) cc_final: 0.8410 (p) REVERT: D 41 GLN cc_start: 0.7657 (mm110) cc_final: 0.6975 (mm110) REVERT: E 57 TYR cc_start: 0.7677 (t80) cc_final: 0.7158 (t80) REVERT: F 39 GLU cc_start: 0.5315 (tp30) cc_final: 0.3742 (tt0) REVERT: F 135 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5558 (mt-10) REVERT: F 136 MET cc_start: 0.6430 (mmt) cc_final: 0.6200 (mmm) REVERT: F 137 ILE cc_start: 0.4865 (tp) cc_final: 0.4579 (tt) REVERT: F 143 ASN cc_start: 0.6571 (OUTLIER) cc_final: 0.5747 (t0) REVERT: F 400 MET cc_start: 0.6106 (tpp) cc_final: 0.5790 (tpp) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 0.9831 time to fit residues: 207.3105 Evaluate side-chains 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 162 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119487 restraints weight = 43903.583| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.37 r_work: 0.3224 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13572 Z= 0.163 Angle : 0.536 7.242 18421 Z= 0.288 Chirality : 0.044 0.402 2016 Planarity : 0.004 0.044 2427 Dihedral : 4.964 19.743 1860 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.57 % Favored : 92.37 % Rotamer: Outliers : 1.75 % Allowed : 14.51 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.20), residues: 1678 helix: 1.13 (0.24), residues: 450 sheet: -1.79 (0.22), residues: 448 loop : -1.19 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.015 0.001 TYR D 184 PHE 0.009 0.001 PHE A 791 TRP 0.010 0.001 TRP B 143 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00344 (13569) covalent geometry : angle 0.53609 (18419) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.90717 ( 2) hydrogen bonds : bond 0.03641 ( 623) hydrogen bonds : angle 5.46544 ( 1773) Misc. bond : bond 0.00092 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLN cc_start: 0.7367 (pm20) cc_final: 0.6671 (pp30) REVERT: A 417 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7526 (tmtt) REVERT: A 598 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8002 (ptmt) REVERT: B 253 VAL cc_start: 0.8685 (t) cc_final: 0.8413 (p) REVERT: D 41 GLN cc_start: 0.7656 (mm110) cc_final: 0.6998 (mm110) REVERT: E 57 TYR cc_start: 0.7670 (t80) cc_final: 0.7180 (t80) REVERT: F 39 GLU cc_start: 0.5387 (tp30) cc_final: 0.3766 (tt0) REVERT: F 135 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5546 (mt-10) REVERT: F 136 MET cc_start: 0.6425 (mmt) cc_final: 0.6201 (mmm) REVERT: F 137 ILE cc_start: 0.4868 (tp) cc_final: 0.4535 (tt) REVERT: F 143 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.5746 (t0) REVERT: F 400 MET cc_start: 0.6078 (tpp) cc_final: 0.5791 (tpp) outliers start: 25 outliers final: 16 residues processed: 187 average time/residue: 1.0158 time to fit residues: 211.3436 Evaluate side-chains 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 159 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 70 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119950 restraints weight = 44223.909| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.37 r_work: 0.3244 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13572 Z= 0.154 Angle : 0.528 7.033 18421 Z= 0.283 Chirality : 0.043 0.403 2016 Planarity : 0.004 0.043 2427 Dihedral : 4.900 19.905 1860 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.67 % Rotamer: Outliers : 1.26 % Allowed : 14.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.20), residues: 1678 helix: 1.22 (0.24), residues: 449 sheet: -1.76 (0.23), residues: 448 loop : -1.17 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.015 0.001 TYR D 184 PHE 0.024 0.001 PHE D 128 TRP 0.010 0.001 TRP B 143 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00325 (13569) covalent geometry : angle 0.52731 (18419) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.90233 ( 2) hydrogen bonds : bond 0.03589 ( 623) hydrogen bonds : angle 5.41883 ( 1773) Misc. bond : bond 0.00093 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7962.21 seconds wall clock time: 135 minutes 16.92 seconds (8116.92 seconds total)