Starting phenix.real_space_refine on Sat Aug 23 15:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pz2_18035/08_2025/8pz2_18035.map" } resolution = 4.2 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= 0.001 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 44 5.16 5 C 8240 2.51 5 N 2258 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 13121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6188 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 29, 'TRANS': 753} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2777 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 440 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1760 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1263 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Time building chain proxies: 3.20, per 1000 atoms: 0.24 Number of scatterers: 13121 At special positions: 0 Unit cell: (138.45, 101.53, 125.67, 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 44 16.00 O 2579 8.00 N 2258 7.00 C 8240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 630.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3086 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 20 sheets defined 29.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.196A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.581A pdb=" N GLN A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.619A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.055A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.609A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.642A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.843A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.102A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 removed outlier: 5.361A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.597A pdb=" N LEU C 42 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.570A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.382A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.562A pdb=" N VAL D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 4.247A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.617A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.701A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.548A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 4.996A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.676A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 49 removed outlier: 4.115A pdb=" N GLN F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.860A pdb=" N GLN F 55 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 88 removed outlier: 3.597A pdb=" N MET F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.704A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 150 removed outlier: 3.680A pdb=" N ILE F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.594A 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 396 through 420 removed outlier: 3.678A pdb=" N ALA F 419 " --> pdb=" O GLN F 415 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.735A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.386A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.668A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 239 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.804A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.804A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 327 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 355 removed outlier: 5.994A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 414 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.615A pdb=" N PHE A 490 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 510 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.461A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.890A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.547A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.147A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.746A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.584A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 286 through 291 removed outlier: 5.154A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.781A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.154A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.523A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.905A pdb=" N VAL F 32 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL F 31 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 424 " --> pdb=" O VAL F 31 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4428 1.34 - 1.46: 2664 1.46 - 1.58: 6210 1.58 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 13385 Sorted by residual: bond pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.15e+00 bond pdb=" CB ASP A 740 " pdb=" CG ASP A 740 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU A 365 " pdb=" CD2 LEU A 365 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG ARG B 195 " pdb=" CD ARG B 195 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CG LEU B 261 " pdb=" CD2 LEU B 261 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17641 1.81 - 3.62: 467 3.62 - 5.42: 62 5.42 - 7.23: 3 7.23 - 9.04: 2 Bond angle restraints: 18175 Sorted by residual: angle pdb=" N ALA C 54 " pdb=" CA ALA C 54 " pdb=" C ALA C 54 " ideal model delta sigma weight residual 109.15 113.73 -4.58 1.44e+00 4.82e-01 1.01e+01 angle pdb=" C VAL A 532 " pdb=" N HIS A 533 " pdb=" CA HIS A 533 " ideal model delta sigma weight residual 122.62 117.84 4.78 1.56e+00 4.11e-01 9.39e+00 angle pdb=" C THR A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.97 116.74 5.23 1.80e+00 3.09e-01 8.45e+00 angle pdb=" N GLY A 429 " pdb=" CA GLY A 429 " pdb=" C GLY A 429 " ideal model delta sigma weight residual 110.63 114.70 -4.07 1.43e+00 4.89e-01 8.10e+00 angle pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " pdb=" CD2 LEU B 261 " ideal model delta sigma weight residual 110.70 102.51 8.19 3.00e+00 1.11e-01 7.46e+00 ... (remaining 18170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7162 17.85 - 35.70: 655 35.70 - 53.55: 118 53.55 - 71.40: 17 71.40 - 89.25: 21 Dihedral angle restraints: 7973 sinusoidal: 3135 harmonic: 4838 Sorted by residual: dihedral pdb=" CA SER B 191 " pdb=" C SER B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N VAL B 387 " pdb=" CA VAL B 387 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1431 0.047 - 0.094: 444 0.094 - 0.140: 108 0.140 - 0.187: 8 0.187 - 0.234: 4 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA PHE A 394 " pdb=" N PHE A 394 " pdb=" C PHE A 394 " pdb=" CB PHE A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PHE A 586 " pdb=" N PHE A 586 " pdb=" C PHE A 586 " pdb=" CB PHE A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1992 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 78 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C GLN F 78 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN F 78 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE F 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 30 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO D 31 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.015 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" CG TRP A 206 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.002 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 183 2.65 - 3.21: 12553 3.21 - 3.78: 19161 3.78 - 4.34: 25300 4.34 - 4.90: 42449 Nonbonded interactions: 99646 Sorted by model distance: nonbonded pdb=" OG1 THR E 94 " pdb=" OD1 ASN E 103 " model vdw 2.090 3.040 nonbonded pdb=" NE2 GLN A 384 " pdb=" OE1 GLU A 521 " model vdw 2.170 3.120 nonbonded pdb=" O GLY F 44 " pdb=" OG SER F 48 " model vdw 2.205 3.040 nonbonded pdb=" O TYR A 548 " pdb=" OG SER A 551 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 608 " pdb=" OE2 GLU A 650 " model vdw 2.229 3.040 ... (remaining 99641 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 13.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 0.049 13385 Z= 0.281 Angle : 0.698 9.039 18175 Z= 0.382 Chirality : 0.048 0.234 1995 Planarity : 0.005 0.056 2399 Dihedral : 14.675 89.251 4887 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % 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: -1.00 (0.20), residues: 1662 helix: 1.29 (0.25), residues: 420 sheet: -0.44 (0.25), residues: 392 loop : -1.84 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 195 TYR 0.028 0.002 TYR E 37 PHE 0.034 0.002 PHE A 586 TRP 0.035 0.002 TRP A 206 HIS 0.010 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00635 (13385) covalent geometry : angle 0.69762 (18175) hydrogen bonds : bond 0.12188 ( 579) hydrogen bonds : angle 5.83918 ( 1620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.526 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 280 HIS cc_start: 0.7408 (m-70) cc_final: 0.7128 (m-70) REVERT: A 667 THR cc_start: 0.8460 (t) cc_final: 0.8225 (m) REVERT: A 780 LEU cc_start: 0.8905 (mt) cc_final: 0.8268 (tt) REVERT: D 52 ILE cc_start: 0.9275 (mt) cc_final: 0.8749 (mt) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1077 time to fit residues: 29.1519 Evaluate side-chains 140 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.083158 restraints weight = 27007.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082111 restraints weight = 31259.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.082495 restraints weight = 35003.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083181 restraints weight = 25570.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083431 restraints weight = 22065.073| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13385 Z= 0.269 Angle : 0.648 7.334 18175 Z= 0.348 Chirality : 0.046 0.170 1995 Planarity : 0.005 0.055 2399 Dihedral : 4.953 26.131 1839 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.35 % Allowed : 7.08 % Favored : 92.57 % 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: -1.14 (0.20), residues: 1662 helix: 1.16 (0.25), residues: 429 sheet: -0.59 (0.25), residues: 393 loop : -1.93 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.023 0.002 TYR E 37 PHE 0.032 0.002 PHE A 586 TRP 0.017 0.002 TRP A 206 HIS 0.008 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00616 (13385) covalent geometry : angle 0.64762 (18175) hydrogen bonds : bond 0.04803 ( 579) hydrogen bonds : angle 5.18686 ( 1620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.491 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 667 THR cc_start: 0.8516 (t) cc_final: 0.8294 (m) REVERT: A 780 LEU cc_start: 0.8888 (mt) cc_final: 0.8234 (tt) REVERT: A 804 PHE cc_start: 0.7895 (t80) cc_final: 0.7620 (t80) REVERT: B 225 GLN cc_start: 0.7518 (tp-100) cc_final: 0.7168 (tp-100) outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.1117 time to fit residues: 30.1393 Evaluate side-chains 144 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 198 GLN A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084202 restraints weight = 27041.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083464 restraints weight = 26992.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084170 restraints weight = 27694.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084509 restraints weight = 21174.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084721 restraints weight = 20287.786| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13385 Z= 0.171 Angle : 0.570 7.989 18175 Z= 0.307 Chirality : 0.044 0.166 1995 Planarity : 0.004 0.051 2399 Dihedral : 4.623 25.177 1839 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.00 (0.20), residues: 1662 helix: 1.38 (0.25), residues: 430 sheet: -0.64 (0.25), residues: 403 loop : -1.83 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.020 0.002 TYR E 37 PHE 0.021 0.001 PHE A 586 TRP 0.023 0.001 TRP A 206 HIS 0.007 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00387 (13385) covalent geometry : angle 0.57050 (18175) hydrogen bonds : bond 0.04162 ( 579) hydrogen bonds : angle 4.87731 ( 1620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.653 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 780 LEU cc_start: 0.8875 (mt) cc_final: 0.8246 (tt) REVERT: C 43 GLU cc_start: 0.7951 (pm20) cc_final: 0.7406 (tt0) REVERT: D 146 ASP cc_start: 0.7993 (m-30) cc_final: 0.7438 (m-30) REVERT: D 207 ASP cc_start: 0.8991 (p0) cc_final: 0.8768 (p0) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1129 time to fit residues: 31.5044 Evaluate side-chains 142 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 93 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 186 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085598 restraints weight = 26873.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.085217 restraints weight = 29421.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086050 restraints weight = 26725.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086195 restraints weight = 21796.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.086839 restraints weight = 19028.639| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13385 Z= 0.142 Angle : 0.546 8.425 18175 Z= 0.293 Chirality : 0.043 0.171 1995 Planarity : 0.004 0.064 2399 Dihedral : 4.454 24.181 1839 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.14 % Allowed : 3.61 % Favored : 96.25 % 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: -0.80 (0.21), residues: 1662 helix: 1.63 (0.25), residues: 424 sheet: -0.52 (0.25), residues: 399 loop : -1.74 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 112 TYR 0.019 0.001 TYR D 184 PHE 0.020 0.001 PHE A 24 TRP 0.013 0.001 TRP A 206 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00317 (13385) covalent geometry : angle 0.54615 (18175) hydrogen bonds : bond 0.03827 ( 579) hydrogen bonds : angle 4.65715 ( 1620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.383 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 420 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8641 (mt-10) REVERT: A 468 TYR cc_start: 0.7847 (t80) cc_final: 0.7609 (t80) REVERT: A 780 LEU cc_start: 0.8895 (mt) cc_final: 0.8247 (tt) REVERT: C 43 GLU cc_start: 0.7847 (pm20) cc_final: 0.7302 (tt0) REVERT: F 87 MET cc_start: 0.7895 (tpt) cc_final: 0.7449 (tpp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1086 time to fit residues: 31.2949 Evaluate side-chains 147 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 160 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 141 optimal weight: 0.0470 chunk 52 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 259 ASN A 561 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087203 restraints weight = 26845.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.086532 restraints weight = 27901.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087376 restraints weight = 29218.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.087615 restraints weight = 21941.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087667 restraints weight = 21533.596| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13385 Z= 0.142 Angle : 0.551 8.184 18175 Z= 0.296 Chirality : 0.044 0.161 1995 Planarity : 0.004 0.057 2399 Dihedral : 4.401 24.651 1839 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % 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: -0.80 (0.21), residues: 1662 helix: 1.59 (0.25), residues: 424 sheet: -0.52 (0.25), residues: 407 loop : -1.72 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.019 0.001 TYR E 37 PHE 0.031 0.001 PHE A 586 TRP 0.009 0.001 TRP B 183 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00323 (13385) covalent geometry : angle 0.55122 (18175) hydrogen bonds : bond 0.03787 ( 579) hydrogen bonds : angle 4.60222 ( 1620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.548 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 420 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 780 LEU cc_start: 0.8892 (mt) cc_final: 0.8255 (tt) REVERT: B 368 GLN cc_start: 0.8797 (pp30) cc_final: 0.8499 (pp30) REVERT: D 52 ILE cc_start: 0.9245 (mt) cc_final: 0.8822 (mt) REVERT: D 146 ASP cc_start: 0.7914 (m-30) cc_final: 0.7635 (m-30) REVERT: F 87 MET cc_start: 0.7889 (tpt) cc_final: 0.7410 (tpp) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1138 time to fit residues: 32.6600 Evaluate side-chains 145 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.083361 restraints weight = 27040.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.082041 restraints weight = 27917.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082496 restraints weight = 32690.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.083125 restraints weight = 24789.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.083559 restraints weight = 21578.378| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13385 Z= 0.230 Angle : 0.630 9.944 18175 Z= 0.336 Chirality : 0.046 0.205 1995 Planarity : 0.005 0.057 2399 Dihedral : 4.717 25.013 1839 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % 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: -0.99 (0.20), residues: 1662 helix: 1.37 (0.25), residues: 429 sheet: -0.64 (0.25), residues: 398 loop : -1.81 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.023 0.002 TYR E 37 PHE 0.028 0.002 PHE A 586 TRP 0.012 0.001 TRP A 206 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00527 (13385) covalent geometry : angle 0.63011 (18175) hydrogen bonds : bond 0.04278 ( 579) hydrogen bonds : angle 4.81320 ( 1620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.536 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 780 LEU cc_start: 0.8917 (mt) cc_final: 0.8252 (tt) REVERT: D 112 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7905 (ttt-90) REVERT: E 66 ASP cc_start: 0.9044 (t0) cc_final: 0.8829 (t0) REVERT: F 87 MET cc_start: 0.7893 (tpt) cc_final: 0.7353 (tpp) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.1130 time to fit residues: 31.2933 Evaluate side-chains 139 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 5 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087282 restraints weight = 26770.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.086288 restraints weight = 28663.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.086785 restraints weight = 28739.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087317 restraints weight = 23003.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087606 restraints weight = 20848.638| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13385 Z= 0.113 Angle : 0.548 9.023 18175 Z= 0.292 Chirality : 0.043 0.154 1995 Planarity : 0.004 0.055 2399 Dihedral : 4.354 24.604 1839 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.14 % Allowed : 1.20 % Favored : 98.66 % 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: -0.77 (0.21), residues: 1662 helix: 1.64 (0.25), residues: 425 sheet: -0.55 (0.25), residues: 405 loop : -1.69 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.021 0.001 TYR A 585 PHE 0.018 0.001 PHE A 586 TRP 0.012 0.001 TRP F 413 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00255 (13385) covalent geometry : angle 0.54797 (18175) hydrogen bonds : bond 0.03548 ( 579) hydrogen bonds : angle 4.50480 ( 1620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.536 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 30 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7236 (m90) REVERT: A 468 TYR cc_start: 0.7640 (t80) cc_final: 0.7422 (t80) REVERT: A 780 LEU cc_start: 0.8906 (mt) cc_final: 0.8253 (tt) REVERT: B 31 LYS cc_start: 0.8107 (pttt) cc_final: 0.7749 (mtmt) REVERT: D 52 ILE cc_start: 0.9210 (mt) cc_final: 0.8747 (mt) REVERT: D 111 MET cc_start: 0.8854 (tpp) cc_final: 0.8319 (tpp) REVERT: D 146 ASP cc_start: 0.7935 (m-30) cc_final: 0.7235 (m-30) REVERT: E 66 ASP cc_start: 0.9021 (t0) cc_final: 0.8752 (t0) REVERT: F 76 MET cc_start: 0.7451 (tpp) cc_final: 0.7217 (tmm) REVERT: F 87 MET cc_start: 0.7834 (tpt) cc_final: 0.7402 (tpp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1186 time to fit residues: 33.5186 Evaluate side-chains 149 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.086974 restraints weight = 26832.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.085408 restraints weight = 27622.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.086079 restraints weight = 31961.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.086642 restraints weight = 24007.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.086863 restraints weight = 22366.281| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13385 Z= 0.137 Angle : 0.558 9.049 18175 Z= 0.296 Chirality : 0.044 0.163 1995 Planarity : 0.004 0.055 2399 Dihedral : 4.348 25.390 1839 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.07 % Allowed : 1.06 % Favored : 98.87 % 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: -0.76 (0.21), residues: 1662 helix: 1.66 (0.25), residues: 424 sheet: -0.54 (0.25), residues: 415 loop : -1.70 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.021 0.001 TYR E 37 PHE 0.023 0.001 PHE A 804 TRP 0.011 0.001 TRP A 206 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00318 (13385) covalent geometry : angle 0.55849 (18175) hydrogen bonds : bond 0.03654 ( 579) hydrogen bonds : angle 4.55823 ( 1620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.546 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 76 CYS cc_start: 0.7902 (m) cc_final: 0.7696 (m) REVERT: A 89 LYS cc_start: 0.8606 (tppt) cc_final: 0.8078 (tppt) REVERT: A 780 LEU cc_start: 0.8905 (mt) cc_final: 0.8262 (tt) REVERT: B 31 LYS cc_start: 0.8090 (pttt) cc_final: 0.7800 (mtmt) REVERT: C 43 GLU cc_start: 0.8128 (pm20) cc_final: 0.7211 (tt0) REVERT: D 109 MET cc_start: 0.8804 (mtt) cc_final: 0.8488 (mtt) REVERT: E 66 ASP cc_start: 0.9026 (t0) cc_final: 0.8748 (t0) REVERT: F 87 MET cc_start: 0.7877 (tpt) cc_final: 0.7496 (tpt) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1166 time to fit residues: 32.6367 Evaluate side-chains 149 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 22 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086889 restraints weight = 26900.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085310 restraints weight = 35544.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085881 restraints weight = 30793.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.086551 restraints weight = 24237.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.086879 restraints weight = 21516.051| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13385 Z= 0.143 Angle : 0.564 9.177 18175 Z= 0.300 Chirality : 0.044 0.167 1995 Planarity : 0.004 0.056 2399 Dihedral : 4.344 24.968 1839 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.14 % Allowed : 0.99 % Favored : 98.87 % 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: -0.76 (0.21), residues: 1662 helix: 1.66 (0.25), residues: 424 sheet: -0.52 (0.25), residues: 413 loop : -1.71 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.021 0.001 TYR E 37 PHE 0.021 0.001 PHE A 586 TRP 0.013 0.001 TRP A 206 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00330 (13385) covalent geometry : angle 0.56443 (18175) hydrogen bonds : bond 0.03667 ( 579) hydrogen bonds : angle 4.54749 ( 1620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.462 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 30 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7221 (m90) REVERT: A 76 CYS cc_start: 0.7897 (m) cc_final: 0.7636 (m) REVERT: A 89 LYS cc_start: 0.8602 (tppt) cc_final: 0.8091 (tppt) REVERT: A 780 LEU cc_start: 0.8940 (mt) cc_final: 0.8265 (tt) REVERT: B 31 LYS cc_start: 0.8093 (pttt) cc_final: 0.7828 (mtmt) REVERT: C 43 GLU cc_start: 0.8158 (pm20) cc_final: 0.7186 (tt0) REVERT: D 52 ILE cc_start: 0.9195 (mt) cc_final: 0.8749 (mt) REVERT: E 66 ASP cc_start: 0.8988 (t0) cc_final: 0.8734 (t0) REVERT: F 87 MET cc_start: 0.7883 (tpt) cc_final: 0.7589 (tpt) outliers start: 2 outliers final: 1 residues processed: 184 average time/residue: 0.1092 time to fit residues: 30.4611 Evaluate side-chains 147 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085541 restraints weight = 26979.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.084738 restraints weight = 29905.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.085578 restraints weight = 28737.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.085999 restraints weight = 22582.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086088 restraints weight = 21374.818| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13385 Z= 0.167 Angle : 0.585 9.075 18175 Z= 0.311 Chirality : 0.045 0.168 1995 Planarity : 0.004 0.055 2399 Dihedral : 4.455 26.017 1839 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % 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: -0.78 (0.21), residues: 1662 helix: 1.61 (0.25), residues: 420 sheet: -0.48 (0.25), residues: 408 loop : -1.71 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.022 0.002 TYR E 37 PHE 0.023 0.002 PHE A 804 TRP 0.017 0.001 TRP A 206 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00385 (13385) covalent geometry : angle 0.58484 (18175) hydrogen bonds : bond 0.03853 ( 579) hydrogen bonds : angle 4.62317 ( 1620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.538 Fit side-chains TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL F 164 " (corrupted residue). Skipping it. REVERT: A 76 CYS cc_start: 0.7915 (m) cc_final: 0.7647 (m) REVERT: A 89 LYS cc_start: 0.8599 (tppt) cc_final: 0.8056 (tppt) REVERT: A 780 LEU cc_start: 0.8931 (mt) cc_final: 0.8280 (tt) REVERT: C 43 GLU cc_start: 0.8147 (pm20) cc_final: 0.7181 (tt0) REVERT: D 111 MET cc_start: 0.8763 (tpp) cc_final: 0.8563 (tpp) REVERT: D 146 ASP cc_start: 0.7933 (m-30) cc_final: 0.7509 (m-30) REVERT: E 66 ASP cc_start: 0.8985 (t0) cc_final: 0.8741 (t0) REVERT: F 76 MET cc_start: 0.7832 (tpp) cc_final: 0.7150 (tmm) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1111 time to fit residues: 31.2337 Evaluate side-chains 148 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 41 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.087593 restraints weight = 27054.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.087393 restraints weight = 30318.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.087889 restraints weight = 27930.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.088352 restraints weight = 22601.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088439 restraints weight = 21196.878| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.003 0.035 13385 Z= 0.120 Angle : 0.563 9.359 18175 Z= 0.298 Chirality : 0.044 0.196 1995 Planarity : 0.004 0.056 2399 Dihedral : 4.283 24.642 1839 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.66 (0.21), residues: 1662 helix: 1.73 (0.25), residues: 420 sheet: -0.38 (0.25), residues: 414 loop : -1.68 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 112 TYR 0.019 0.001 TYR D 185 PHE 0.019 0.001 PHE A 586 TRP 0.013 0.001 TRP A 206 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00272 (13385) covalent geometry : angle 0.56289 (18175) hydrogen bonds : bond 0.03546 ( 579) hydrogen bonds : angle 4.50362 ( 1620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.90 seconds wall clock time: 32 minutes 48.64 seconds (1968.64 seconds total)