Starting phenix.real_space_refine on Fri Feb 6 08:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mgf_48254/02_2026/9mgf_48254.map" } resolution = 3.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 7552 2.51 5 N 2104 2.21 5 O 2389 1.98 5 H 11258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23338 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 10587 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 29, 'TRANS': 747} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 13, 'HIS:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 10, 'ASN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 264 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5315 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 853 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 7, 'TRANS': 52} 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: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3440 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1370 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "F" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1732 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 3 Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 41 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 23338 At special positions: 0 Unit cell: (110.39, 130.31, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 2389 8.00 N 2104 7.00 C 7552 6.00 H 11258 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=2.04 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: 1.93 Conformation dependent library (CDL) restraints added in 799.2 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 24.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.127A pdb=" N VAL A 208 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.924A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.567A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.670A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.792A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.724A 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 542 through 553 removed outlier: 3.911A pdb=" N ARG A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.877A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG C 33 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 35 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.580A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.534A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.837A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.714A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.733A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 210 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.632A pdb=" N ASP A 28 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL A 86 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.981A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.518A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.161A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.161A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.585A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.707A pdb=" N SER A 778 " --> pdb=" O GLY A 781 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 483 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 485 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 487 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR A 474 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 489 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A 472 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR A 491 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU A 470 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP A 493 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR A 468 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR A 434 " --> pdb=" O GLU F 800 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU F 800 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN F 801 " --> pdb=" O ALA F 788 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR F 735 " --> pdb=" O THR F 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.883A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.938A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118 removed outlier: 5.443A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.564A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.667A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.841A 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: 6.629A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 287 through 292 removed outlier: 5.706A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.502A 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 333 removed outlier: 6.087A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.666A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN E 96 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU E 101 " --> pdb=" O ASN E 96 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1602 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: 5.08 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11257 1.03 - 1.23: 20 1.23 - 1.43: 5388 1.43 - 1.63: 6869 1.63 - 1.82: 67 Bond restraints: 23601 Sorted by residual: bond pdb=" N VAL F 619 " pdb=" CA VAL F 619 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N ILE F 621 " pdb=" CA ILE F 621 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.32e-02 5.74e+03 8.94e+00 bond pdb=" N GLU A 283 " pdb=" CA GLU A 283 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.33e-02 5.65e+03 8.31e+00 bond pdb=" N ASN A 448 " pdb=" H ASN A 448 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" N GLN E 54 " pdb=" H GLN E 54 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 23596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 41046 1.70 - 3.41: 979 3.41 - 5.11: 87 5.11 - 6.82: 14 6.82 - 8.52: 5 Bond angle restraints: 42131 Sorted by residual: angle pdb=" N ASN B 287 " pdb=" CA ASN B 287 " pdb=" C ASN B 287 " ideal model delta sigma weight residual 109.24 116.35 -7.11 1.67e+00 3.59e-01 1.81e+01 angle pdb=" N VAL B 286 " pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 109.34 117.86 -8.52 2.08e+00 2.31e-01 1.68e+01 angle pdb=" C GLU A 689 " pdb=" N CYS A 690 " pdb=" CA CYS A 690 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA GLN E 54 " pdb=" C GLN E 54 " pdb=" O GLN E 54 " ideal model delta sigma weight residual 120.42 116.45 3.97 1.06e+00 8.90e-01 1.40e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" C ASN A 448 " ideal model delta sigma weight residual 110.80 103.57 7.23 2.13e+00 2.20e-01 1.15e+01 ... (remaining 42126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10036 17.96 - 35.91: 769 35.91 - 53.87: 196 53.87 - 71.82: 90 71.82 - 89.78: 20 Dihedral angle restraints: 11111 sinusoidal: 5903 harmonic: 5208 Sorted by residual: dihedral pdb=" CA VAL B 286 " pdb=" C VAL B 286 " pdb=" N ASN B 287 " pdb=" CA ASN B 287 " ideal model delta harmonic sigma weight residual -180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR F 809 " pdb=" C THR F 809 " pdb=" N TRP F 810 " pdb=" CA TRP F 810 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ILE A 260 " pdb=" C ILE A 260 " pdb=" N THR A 261 " pdb=" CA THR A 261 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 11108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1167 0.040 - 0.079: 376 0.079 - 0.119: 144 0.119 - 0.159: 42 0.159 - 0.198: 5 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA ARG A 661 " pdb=" N ARG A 661 " pdb=" C ARG A 661 " pdb=" CB ARG A 661 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ARG C 33 " pdb=" N ARG C 33 " pdb=" C ARG C 33 " pdb=" CB ARG C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PRO A 782 " pdb=" N PRO A 782 " pdb=" C PRO A 782 " pdb=" CB PRO A 782 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1731 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 54 " 0.043 2.00e-02 2.50e+03 4.41e-01 2.91e+03 pdb=" CD GLN E 54 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN E 54 " -0.041 2.00e-02 2.50e+03 pdb=" NE2 GLN E 54 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN E 54 " -0.760 2.00e-02 2.50e+03 pdb="HE22 GLN E 54 " 0.764 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 448 " 0.240 2.00e-02 2.50e+03 2.95e-01 1.31e+03 pdb=" CG ASN A 448 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 448 " -0.237 2.00e-02 2.50e+03 pdb=" ND2 ASN A 448 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 448 " -0.450 2.00e-02 2.50e+03 pdb="HD22 ASN A 448 " 0.454 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 173 " 0.037 9.50e-02 1.11e+02 3.71e-02 2.78e+01 pdb=" NE ARG D 173 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG D 173 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 173 " 0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG D 173 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG D 173 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 173 " -0.065 2.00e-02 2.50e+03 pdb="HH21 ARG D 173 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 173 " 0.028 2.00e-02 2.50e+03 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 498 2.09 - 2.72: 37651 2.72 - 3.34: 64321 3.34 - 3.97: 80819 3.97 - 4.60: 126745 Nonbonded interactions: 310034 Sorted by model distance: nonbonded pdb=" HH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 1.461 2.450 nonbonded pdb="HH21 ARG C 33 " pdb=" OD1 ASP D 121 " model vdw 1.476 2.450 nonbonded pdb=" OE1 GLU B 27 " pdb=" H GLU B 27 " model vdw 1.527 2.450 nonbonded pdb=" OD1 ASN B 350 " pdb=" H GLU B 352 " model vdw 1.560 2.450 nonbonded pdb="HD22 ASN A 422 " pdb=" O TRP F 810 " model vdw 1.563 2.450 ... (remaining 310029 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.190 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.990 Find NCS groups from input model: 0.080 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12344 Z= 0.181 Angle : 0.761 9.409 16726 Z= 0.436 Chirality : 0.048 0.198 1734 Planarity : 0.007 0.095 2248 Dihedral : 14.428 89.780 4345 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.08 % Allowed : 8.59 % Favored : 91.33 % 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 are not related in a simple way. whole: -0.63 (0.20), residues: 1596 helix: -0.22 (0.25), residues: 326 sheet: 0.30 (0.22), residues: 495 loop : -0.92 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG A 767 TYR 0.035 0.004 TYR D 222 PHE 0.027 0.002 PHE A 586 TRP 0.020 0.003 TRP A 576 HIS 0.008 0.003 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00357 (12343) covalent geometry : angle 0.75687 (16724) SS BOND : bond 0.00536 ( 1) SS BOND : angle 7.32198 ( 2) hydrogen bonds : bond 0.17321 ( 579) hydrogen bonds : angle 7.86619 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7767 (ttt-90) REVERT: E 53 GLN cc_start: 0.8893 (tp40) cc_final: 0.8390 (tp40) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2301 time to fit residues: 59.2326 Evaluate side-chains 161 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 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 357 ASN B 255 ASN B 294 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.193278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133601 restraints weight = 36974.067| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.73 r_work: 0.3603 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12344 Z= 0.163 Angle : 0.623 6.457 16726 Z= 0.345 Chirality : 0.045 0.153 1734 Planarity : 0.004 0.054 2248 Dihedral : 6.351 58.355 1760 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.68 % Rotamer: Outliers : 1.16 % Allowed : 9.33 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.25 (0.20), residues: 1596 helix: 1.17 (0.27), residues: 338 sheet: -0.02 (0.21), residues: 494 loop : -0.81 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 212 TYR 0.013 0.001 TYR D 184 PHE 0.015 0.001 PHE A 478 TRP 0.014 0.001 TRP F 739 HIS 0.003 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00353 (12343) covalent geometry : angle 0.62281 (16724) SS BOND : bond 0.00589 ( 1) SS BOND : angle 2.40890 ( 2) hydrogen bonds : bond 0.04370 ( 579) hydrogen bonds : angle 5.73650 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7478 (tppt) REVERT: E 53 GLN cc_start: 0.9016 (tp40) cc_final: 0.8617 (tp40) REVERT: F 717 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7944 (mt-10) outliers start: 14 outliers final: 13 residues processed: 193 average time/residue: 0.2583 time to fit residues: 68.9364 Evaluate side-chains 182 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135732 restraints weight = 36865.235| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.14 r_work: 0.3572 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12344 Z= 0.148 Angle : 0.573 6.720 16726 Z= 0.316 Chirality : 0.044 0.173 1734 Planarity : 0.004 0.068 2248 Dihedral : 5.917 68.650 1760 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 1.32 % Allowed : 9.66 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1596 helix: 1.62 (0.28), residues: 338 sheet: -0.10 (0.21), residues: 498 loop : -0.81 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.013 0.001 TYR D 184 PHE 0.012 0.001 PHE E 95 TRP 0.011 0.001 TRP A 745 HIS 0.007 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00322 (12343) covalent geometry : angle 0.57274 (16724) SS BOND : bond 0.00032 ( 1) SS BOND : angle 1.32984 ( 2) hydrogen bonds : bond 0.03904 ( 579) hydrogen bonds : angle 5.33234 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 THR cc_start: 0.8433 (m) cc_final: 0.7936 (p) REVERT: E 53 GLN cc_start: 0.9006 (tp40) cc_final: 0.8566 (tp40) outliers start: 16 outliers final: 12 residues processed: 186 average time/residue: 0.2458 time to fit residues: 64.8636 Evaluate side-chains 175 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 77 optimal weight: 0.0570 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129836 restraints weight = 36630.749| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.86 r_work: 0.3543 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12344 Z= 0.157 Angle : 0.552 6.631 16726 Z= 0.302 Chirality : 0.044 0.146 1734 Planarity : 0.004 0.061 2248 Dihedral : 5.612 72.919 1760 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 1.73 % Allowed : 10.40 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.03 (0.21), residues: 1596 helix: 1.83 (0.28), residues: 338 sheet: -0.13 (0.21), residues: 504 loop : -0.75 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.014 0.001 TYR A 754 PHE 0.014 0.001 PHE F 724 TRP 0.011 0.001 TRP A 745 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00348 (12343) covalent geometry : angle 0.55211 (16724) SS BOND : bond 0.00358 ( 1) SS BOND : angle 0.86598 ( 2) hydrogen bonds : bond 0.03525 ( 579) hydrogen bonds : angle 5.08651 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8351 (tm-30) REVERT: A 338 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7537 (ttm110) REVERT: A 753 GLN cc_start: 0.8373 (tt0) cc_final: 0.7921 (tm-30) REVERT: B 377 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7321 (tppt) REVERT: B 386 THR cc_start: 0.8511 (m) cc_final: 0.7991 (p) outliers start: 21 outliers final: 19 residues processed: 181 average time/residue: 0.2464 time to fit residues: 64.0193 Evaluate side-chains 177 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 45 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132066 restraints weight = 36763.798| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.17 r_work: 0.3517 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12344 Z= 0.189 Angle : 0.558 6.973 16726 Z= 0.305 Chirality : 0.044 0.148 1734 Planarity : 0.004 0.081 2248 Dihedral : 5.523 72.189 1760 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 2.23 % Allowed : 10.90 % Favored : 86.87 % 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 are not related in a simple way. whole: -0.12 (0.21), residues: 1596 helix: 1.90 (0.28), residues: 337 sheet: -0.21 (0.21), residues: 499 loop : -0.86 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.016 0.001 TYR A 416 PHE 0.012 0.001 PHE E 95 TRP 0.012 0.001 TRP A 745 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00419 (12343) covalent geometry : angle 0.55776 (16724) SS BOND : bond 0.00567 ( 1) SS BOND : angle 1.87371 ( 2) hydrogen bonds : bond 0.03550 ( 579) hydrogen bonds : angle 4.99980 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 LYS cc_start: 0.7414 (ttpt) cc_final: 0.7109 (ttmm) REVERT: A 753 GLN cc_start: 0.8382 (tt0) cc_final: 0.7769 (tt0) REVERT: B 377 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7292 (tppt) REVERT: B 386 THR cc_start: 0.8611 (m) cc_final: 0.8107 (p) outliers start: 27 outliers final: 22 residues processed: 181 average time/residue: 0.2599 time to fit residues: 66.1412 Evaluate side-chains 179 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 615 THR Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 72 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 60.0000 chunk 132 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.190357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130075 restraints weight = 36866.576| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.81 r_work: 0.3542 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12344 Z= 0.141 Angle : 0.532 7.217 16726 Z= 0.288 Chirality : 0.043 0.144 1734 Planarity : 0.004 0.059 2248 Dihedral : 5.323 70.600 1760 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.98 % Allowed : 11.56 % Favored : 86.46 % 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 are not related in a simple way. whole: -0.04 (0.21), residues: 1596 helix: 2.05 (0.29), residues: 337 sheet: -0.26 (0.21), residues: 500 loop : -0.78 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 212 TYR 0.014 0.001 TYR D 79 PHE 0.011 0.001 PHE E 95 TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00310 (12343) covalent geometry : angle 0.53088 (16724) SS BOND : bond 0.00039 ( 1) SS BOND : angle 2.42604 ( 2) hydrogen bonds : bond 0.03278 ( 579) hydrogen bonds : angle 4.82939 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7496 (mm-30) REVERT: A 580 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5834 (pttm) REVERT: A 701 LYS cc_start: 0.7388 (ttpt) cc_final: 0.7105 (ttmm) REVERT: A 753 GLN cc_start: 0.8458 (tt0) cc_final: 0.7832 (tt0) REVERT: B 377 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7248 (tppt) REVERT: B 386 THR cc_start: 0.8560 (m) cc_final: 0.8044 (p) REVERT: D 212 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8456 (mtp85) REVERT: F 717 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7540 (mp0) REVERT: F 792 LYS cc_start: 0.5357 (tptt) cc_final: 0.4964 (tptp) outliers start: 24 outliers final: 20 residues processed: 181 average time/residue: 0.2739 time to fit residues: 69.5571 Evaluate side-chains 177 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 615 THR Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 5 optimal weight: 50.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.190714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132997 restraints weight = 36769.246| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.11 r_work: 0.3542 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12344 Z= 0.118 Angle : 0.514 6.570 16726 Z= 0.277 Chirality : 0.043 0.143 1734 Planarity : 0.004 0.103 2248 Dihedral : 5.127 67.741 1760 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.57 % Allowed : 12.96 % Favored : 85.47 % 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 are not related in a simple way. whole: 0.08 (0.21), residues: 1596 helix: 2.26 (0.29), residues: 337 sheet: -0.27 (0.21), residues: 506 loop : -0.68 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.013 0.001 TYR D 184 PHE 0.012 0.001 PHE A 804 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00260 (12343) covalent geometry : angle 0.51375 (16724) SS BOND : bond 0.00317 ( 1) SS BOND : angle 1.94671 ( 2) hydrogen bonds : bond 0.03091 ( 579) hydrogen bonds : angle 4.68817 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7392 (mm-30) REVERT: A 580 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5915 (pttm) REVERT: A 701 LYS cc_start: 0.7426 (ttpt) cc_final: 0.7156 (ttmm) REVERT: A 753 GLN cc_start: 0.8487 (tt0) cc_final: 0.7896 (tt0) REVERT: B 377 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7332 (tppt) REVERT: B 386 THR cc_start: 0.8612 (m) cc_final: 0.8108 (p) REVERT: D 109 MET cc_start: 0.8317 (mmm) cc_final: 0.7957 (mtp) REVERT: F 717 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7575 (mp0) REVERT: F 792 LYS cc_start: 0.5366 (tptt) cc_final: 0.4990 (tptp) outliers start: 19 outliers final: 17 residues processed: 176 average time/residue: 0.2522 time to fit residues: 63.2104 Evaluate side-chains 174 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.188646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130692 restraints weight = 35806.951| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.66 r_work: 0.3556 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12344 Z= 0.123 Angle : 0.511 7.066 16726 Z= 0.274 Chirality : 0.043 0.143 1734 Planarity : 0.004 0.069 2248 Dihedral : 5.036 67.383 1760 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.82 % Allowed : 13.21 % Favored : 84.97 % 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 are not related in a simple way. whole: 0.10 (0.21), residues: 1596 helix: 2.29 (0.29), residues: 337 sheet: -0.25 (0.22), residues: 506 loop : -0.69 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 212 TYR 0.012 0.001 TYR D 184 PHE 0.010 0.001 PHE A 785 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00271 (12343) covalent geometry : angle 0.51051 (16724) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.54990 ( 2) hydrogen bonds : bond 0.03044 ( 579) hydrogen bonds : angle 4.63133 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5899 (pttm) REVERT: A 701 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7139 (ttmm) REVERT: A 753 GLN cc_start: 0.8486 (tt0) cc_final: 0.7889 (tt0) REVERT: B 292 ASP cc_start: 0.7362 (m-30) cc_final: 0.6677 (t0) REVERT: B 386 THR cc_start: 0.8576 (m) cc_final: 0.8072 (p) REVERT: D 109 MET cc_start: 0.8276 (mmm) cc_final: 0.7916 (mtp) REVERT: D 212 ARG cc_start: 0.8942 (ttm110) cc_final: 0.8412 (mtp85) REVERT: F 792 LYS cc_start: 0.5248 (tptt) cc_final: 0.4918 (tptp) outliers start: 22 outliers final: 18 residues processed: 182 average time/residue: 0.2221 time to fit residues: 58.4463 Evaluate side-chains 181 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.188717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132011 restraints weight = 36868.856| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.02 r_work: 0.3506 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12344 Z= 0.174 Angle : 0.536 7.262 16726 Z= 0.289 Chirality : 0.043 0.146 1734 Planarity : 0.004 0.086 2248 Dihedral : 5.088 67.185 1760 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 1.90 % Allowed : 13.54 % Favored : 84.56 % 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 are not related in a simple way. whole: -0.02 (0.21), residues: 1596 helix: 2.22 (0.29), residues: 337 sheet: -0.30 (0.22), residues: 502 loop : -0.80 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 212 TYR 0.016 0.001 TYR D 79 PHE 0.015 0.001 PHE A 440 TRP 0.010 0.001 TRP A 745 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00387 (12343) covalent geometry : angle 0.53542 (16724) SS BOND : bond 0.00022 ( 1) SS BOND : angle 1.91247 ( 2) hydrogen bonds : bond 0.03212 ( 579) hydrogen bonds : angle 4.69999 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5990 (pttm) REVERT: A 701 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7256 (ttmm) REVERT: B 377 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7261 (tppt) REVERT: B 386 THR cc_start: 0.8600 (m) cc_final: 0.8136 (p) REVERT: D 97 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7203 (ttm-80) REVERT: D 109 MET cc_start: 0.8314 (mmm) cc_final: 0.7951 (mtp) REVERT: D 212 ARG cc_start: 0.9013 (ttm110) cc_final: 0.8503 (mtp85) REVERT: F 717 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7596 (mp0) REVERT: F 792 LYS cc_start: 0.5224 (tptt) cc_final: 0.4914 (tptp) outliers start: 23 outliers final: 19 residues processed: 174 average time/residue: 0.2437 time to fit residues: 60.6496 Evaluate side-chains 172 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 50.0000 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132980 restraints weight = 36836.763| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.82 r_work: 0.3537 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12344 Z= 0.126 Angle : 0.512 6.820 16726 Z= 0.275 Chirality : 0.043 0.143 1734 Planarity : 0.004 0.068 2248 Dihedral : 5.004 67.476 1760 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 1.57 % Allowed : 13.96 % Favored : 84.48 % 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 are not related in a simple way. whole: 0.08 (0.21), residues: 1596 helix: 2.27 (0.29), residues: 339 sheet: -0.21 (0.22), residues: 497 loop : -0.75 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 212 TYR 0.012 0.001 TYR D 184 PHE 0.012 0.001 PHE A 440 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00278 (12343) covalent geometry : angle 0.51162 (16724) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.60599 ( 2) hydrogen bonds : bond 0.03024 ( 579) hydrogen bonds : angle 4.60384 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5832 (pttm) REVERT: A 701 LYS cc_start: 0.7435 (ttpt) cc_final: 0.7166 (ttmm) REVERT: B 31 LYS cc_start: 0.9056 (pttm) cc_final: 0.8616 (mmmt) REVERT: B 292 ASP cc_start: 0.7542 (m-30) cc_final: 0.6688 (t0) REVERT: B 386 THR cc_start: 0.8555 (m) cc_final: 0.8090 (p) REVERT: D 109 MET cc_start: 0.8302 (mmm) cc_final: 0.7939 (mtp) REVERT: D 212 ARG cc_start: 0.8980 (ttm110) cc_final: 0.8478 (mtp85) REVERT: F 792 LYS cc_start: 0.5221 (tptt) cc_final: 0.4906 (tptp) outliers start: 19 outliers final: 17 residues processed: 168 average time/residue: 0.2391 time to fit residues: 58.4075 Evaluate side-chains 170 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain F residue 629 VAL Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 722 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 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 422 ASN E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133163 restraints weight = 36608.042| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.83 r_work: 0.3539 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12344 Z= 0.126 Angle : 0.508 6.851 16726 Z= 0.272 Chirality : 0.043 0.143 1734 Planarity : 0.004 0.051 2248 Dihedral : 4.995 76.280 1760 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 1.57 % Allowed : 14.04 % Favored : 84.39 % 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 are not related in a simple way. whole: 0.12 (0.21), residues: 1596 helix: 2.32 (0.29), residues: 339 sheet: -0.21 (0.22), residues: 497 loop : -0.72 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 212 TYR 0.015 0.001 TYR D 79 PHE 0.013 0.001 PHE A 440 TRP 0.008 0.001 TRP A 745 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00279 (12343) covalent geometry : angle 0.50798 (16724) SS BOND : bond 0.00018 ( 1) SS BOND : angle 1.63999 ( 2) hydrogen bonds : bond 0.02960 ( 579) hydrogen bonds : angle 4.54568 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6949.57 seconds wall clock time: 118 minutes 14.62 seconds (7094.62 seconds total)