Starting phenix.real_space_refine on Sun May 3 06:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8e_36948/05_2026/8k8e_36948.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 40 5.16 5 C 7044 2.51 5 N 1705 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10716 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2394 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 95 Unusual residues: {'BOC': 1} Classifications: {'peptide': 14, 'undetermined': 1} Link IDs: {'BOC_C-N': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'AIB:plan-1': 3} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'JUU': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="JUU G 16 " pdbres="LEU G 17 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'JUU:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.85, per 1000 atoms: 0.27 Number of scatterers: 10716 At special positions: 0 Unit cell: (112.58, 94.1775, 130.982, 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 40 16.00 P 1 15.00 O 1926 8.00 N 1705 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM10322 O2 BOC G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-3 " BMA F 1 " - " BMA F 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " BMA F 1 " - " BMA F 3 " NAG-ASN " NAG A 801 " - " ASN A 45 " " NAG A 802 " - " ASN A 435 " " NAG A 803 " - " ASN A 573 " " NAG A 804 " - " ASN A 530 " " NAG A 805 " - " ASN A 506 " " NAG A 806 " - " ASN A 187 " " NAG E 1 " - " ASN A 55 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 604.9 milliseconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 61.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.964A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.781A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.551A pdb=" N PHE A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.604A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.683A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.061A pdb=" N GLY A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.981A pdb=" N ARG A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.590A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.680A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.504A pdb=" N ILE A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.071A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.678A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.638A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.917A pdb=" N SER A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.550A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 104 removed outlier: 3.640A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.844A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 154 Processing helix chain 'B' and resid 160 through 189 removed outlier: 3.885A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.512A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.599A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.357A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.989A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.761A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 104 removed outlier: 3.513A pdb=" N GLU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 6.002A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.632A pdb=" N GLU C 183 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 204 removed outlier: 3.745A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 209 through 232 removed outlier: 3.520A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.601A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 85 removed outlier: 3.685A pdb=" N ILE D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.707A pdb=" N ASP D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.548A pdb=" N ILE G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.634A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 212 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.705A pdb=" N ARG A 652 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 7.024A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.121A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.564A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 288 591 hydrogen bonds defined for protein. 1704 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: 1.86 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.44: 3135 1.44 - 1.57: 6163 1.57 - 1.70: 3 1.70 - 1.84: 61 Bond restraints: 10994 Sorted by residual: bond pdb=" C VLM G 18 " pdb=" NT VLM G 18 " ideal model delta sigma weight residual 1.338 1.451 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C72 JUU G 16 " pdb=" N16 JUU G 16 " ideal model delta sigma weight residual 1.440 1.526 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta sigma weight residual 1.458 1.488 -0.031 7.40e-03 1.83e+04 1.71e+01 bond pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 9.94e+00 bond pdb=" N ILE A 242 " pdb=" CA ILE A 242 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.13e+00 ... (remaining 10989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 14522 1.61 - 3.22: 361 3.22 - 4.83: 75 4.83 - 6.44: 32 6.44 - 8.05: 13 Bond angle restraints: 15003 Sorted by residual: angle pdb=" CA ASN A 562 " pdb=" CB ASN A 562 " pdb=" CG ASN A 562 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASN A 562 " pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 120.90 117.07 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 114.75 110.35 4.40 1.26e+00 6.30e-01 1.22e+01 angle pdb=" CA GLU D 40 " pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA GLU C 106 " pdb=" CB GLU C 106 " pdb=" CG GLU C 106 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 6204 22.74 - 45.48: 397 45.48 - 68.22: 61 68.22 - 90.95: 32 90.95 - 113.69: 11 Dihedral angle restraints: 6705 sinusoidal: 2856 harmonic: 3849 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.34 84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -162.32 76.32 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 213 " pdb=" CB CYS A 213 " ideal model delta sinusoidal sigma weight residual 93.00 40.91 52.09 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1684 0.093 - 0.185: 72 0.185 - 0.278: 7 0.278 - 0.371: 1 0.371 - 0.463: 2 Chirality restraints: 1766 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.95e+00 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1763 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BOC G 1 " 0.249 2.00e-02 2.50e+03 1.77e-01 3.12e+02 pdb=" CT BOC G 1 " 0.075 2.00e-02 2.50e+03 pdb=" O1 BOC G 1 " -0.116 2.00e-02 2.50e+03 pdb=" O2 BOC G 1 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 211 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 40 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" CD GLU D 40 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU D 40 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU D 40 " -0.010 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1638 2.75 - 3.29: 10552 3.29 - 3.83: 18062 3.83 - 4.36: 21018 4.36 - 4.90: 36426 Nonbonded interactions: 87696 Sorted by model distance: nonbonded pdb=" OG SER C 113 " pdb=" OE1 GLN C 116 " model vdw 2.218 3.040 nonbonded pdb=" O GLN B 464 " pdb=" ND2 ASN C 207 " model vdw 2.222 3.120 nonbonded pdb=" N GLU D 9 " pdb=" OE1 GLU D 9 " model vdw 2.243 3.120 nonbonded pdb=" O SER A 235 " pdb=" OG SER A 238 " model vdw 2.245 3.040 nonbonded pdb=" O ILE C 34 " pdb=" OH TYR C 90 " model vdw 2.257 3.040 ... (remaining 87691 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 0.113 11011 Z= 0.224 Angle : 0.698 9.124 15043 Z= 0.351 Chirality : 0.047 0.463 1766 Planarity : 0.006 0.177 1825 Dihedral : 16.349 113.692 4212 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.33 % Allowed : 15.68 % Favored : 82.99 % 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: 0.45 (0.24), residues: 1299 helix: 1.79 (0.20), residues: 682 sheet: -0.72 (0.49), residues: 108 loop : -1.61 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 108 TYR 0.020 0.001 TYR D 47 PHE 0.024 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00443 (10994) covalent geometry : angle 0.68652 (15003) SS BOND : bond 0.00460 ( 5) SS BOND : angle 1.47570 ( 10) hydrogen bonds : bond 0.17039 ( 591) hydrogen bonds : angle 6.01632 ( 1704) Misc. bond : bond 0.00444 ( 2) link_BETA1-3 : bond 0.00292 ( 1) link_BETA1-3 : angle 1.22827 ( 3) link_BETA1-4 : bond 0.02676 ( 1) link_BETA1-4 : angle 1.90184 ( 3) link_BETA1-6 : bond 0.00660 ( 1) link_BETA1-6 : angle 0.87168 ( 3) link_NAG-ASN : bond 0.00726 ( 7) link_NAG-ASN : angle 3.18872 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8876 (tpp) cc_final: 0.8495 (mmt) REVERT: A 237 GLN cc_start: 0.9025 (tp40) cc_final: 0.8155 (tm-30) REVERT: B 112 GLN cc_start: 0.8641 (mt0) cc_final: 0.8433 (pt0) REVERT: B 159 TYR cc_start: 0.4058 (t80) cc_final: 0.3738 (t80) REVERT: C 96 LYS cc_start: 0.7423 (mttt) cc_final: 0.7003 (tppt) REVERT: C 115 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7160 (ttt180) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 0.6481 time to fit residues: 77.1467 Evaluate side-chains 90 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.055511 restraints weight = 28257.173| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.49 r_work: 0.2738 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11011 Z= 0.218 Angle : 0.649 10.286 15043 Z= 0.332 Chirality : 0.046 0.433 1766 Planarity : 0.005 0.057 1825 Dihedral : 11.840 99.958 1916 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.34 % Allowed : 13.73 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.24), residues: 1299 helix: 1.96 (0.20), residues: 693 sheet: -0.82 (0.47), residues: 124 loop : -1.57 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 108 TYR 0.016 0.002 TYR B 466 PHE 0.030 0.002 PHE A 302 TRP 0.012 0.001 TRP B 203 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00514 (10994) covalent geometry : angle 0.63470 (15003) SS BOND : bond 0.00544 ( 5) SS BOND : angle 1.28523 ( 10) hydrogen bonds : bond 0.05370 ( 591) hydrogen bonds : angle 4.42558 ( 1704) Misc. bond : bond 0.00047 ( 2) link_BETA1-3 : bond 0.01148 ( 1) link_BETA1-3 : angle 1.89381 ( 3) link_BETA1-4 : bond 0.00483 ( 1) link_BETA1-4 : angle 1.75161 ( 3) link_BETA1-6 : bond 0.01116 ( 1) link_BETA1-6 : angle 2.60098 ( 3) link_NAG-ASN : bond 0.00658 ( 7) link_NAG-ASN : angle 3.33244 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.9058 (tp40) cc_final: 0.8115 (tm-30) REVERT: A 414 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8203 (mtm110) REVERT: B 159 TYR cc_start: 0.3924 (t80) cc_final: 0.3579 (t80) REVERT: C 96 LYS cc_start: 0.7510 (mttt) cc_final: 0.6948 (tppt) REVERT: C 192 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8813 (tt) outliers start: 49 outliers final: 19 residues processed: 125 average time/residue: 0.4982 time to fit residues: 67.9897 Evaluate side-chains 95 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 243 ASN A 358 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.055851 restraints weight = 28301.552| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.52 r_work: 0.2746 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11011 Z= 0.170 Angle : 0.618 11.079 15043 Z= 0.313 Chirality : 0.044 0.431 1766 Planarity : 0.004 0.053 1825 Dihedral : 10.275 92.845 1905 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.07 % Allowed : 14.88 % Favored : 81.05 % 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: 0.79 (0.24), residues: 1299 helix: 2.06 (0.20), residues: 695 sheet: -0.86 (0.46), residues: 123 loop : -1.46 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 114 TYR 0.017 0.001 TYR B 466 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.007 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00401 (10994) covalent geometry : angle 0.60288 (15003) SS BOND : bond 0.00618 ( 5) SS BOND : angle 0.88396 ( 10) hydrogen bonds : bond 0.04747 ( 591) hydrogen bonds : angle 4.15785 ( 1704) Misc. bond : bond 0.00019 ( 2) link_BETA1-3 : bond 0.00908 ( 1) link_BETA1-3 : angle 1.49928 ( 3) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 1.81076 ( 3) link_BETA1-6 : bond 0.01351 ( 1) link_BETA1-6 : angle 2.67626 ( 3) link_NAG-ASN : bond 0.00566 ( 7) link_NAG-ASN : angle 3.39121 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8649 (pm20) cc_final: 0.8360 (pm20) REVERT: A 237 GLN cc_start: 0.9038 (tp40) cc_final: 0.7940 (tm-30) REVERT: B 159 TYR cc_start: 0.3927 (t80) cc_final: 0.3575 (t80) REVERT: C 96 LYS cc_start: 0.7464 (mttt) cc_final: 0.6909 (tppt) REVERT: C 218 TYR cc_start: 0.9359 (m-80) cc_final: 0.9134 (m-80) outliers start: 46 outliers final: 19 residues processed: 117 average time/residue: 0.4743 time to fit residues: 61.1865 Evaluate side-chains 94 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 222 HIS A 387 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.055455 restraints weight = 28505.682| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.53 r_work: 0.2735 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11011 Z= 0.184 Angle : 0.623 10.954 15043 Z= 0.316 Chirality : 0.045 0.424 1766 Planarity : 0.004 0.057 1825 Dihedral : 9.731 87.626 1905 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.25 % Allowed : 15.68 % Favored : 80.07 % 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: 0.86 (0.24), residues: 1299 helix: 2.12 (0.20), residues: 696 sheet: -0.91 (0.46), residues: 123 loop : -1.40 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 108 TYR 0.018 0.001 TYR B 466 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00437 (10994) covalent geometry : angle 0.60637 (15003) SS BOND : bond 0.00571 ( 5) SS BOND : angle 1.19339 ( 10) hydrogen bonds : bond 0.04655 ( 591) hydrogen bonds : angle 4.10565 ( 1704) Misc. bond : bond 0.00010 ( 2) link_BETA1-3 : bond 0.00917 ( 1) link_BETA1-3 : angle 2.00531 ( 3) link_BETA1-4 : bond 0.00487 ( 1) link_BETA1-4 : angle 1.85795 ( 3) link_BETA1-6 : bond 0.01283 ( 1) link_BETA1-6 : angle 3.03846 ( 3) link_NAG-ASN : bond 0.00610 ( 7) link_NAG-ASN : angle 3.47721 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8659 (pm20) cc_final: 0.8425 (pm20) REVERT: A 237 GLN cc_start: 0.8941 (tp40) cc_final: 0.7874 (tm-30) REVERT: B 159 TYR cc_start: 0.3910 (t80) cc_final: 0.3574 (t80) REVERT: B 278 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.3281 (mpt180) REVERT: C 96 LYS cc_start: 0.7185 (mttt) cc_final: 0.6669 (tppt) REVERT: C 236 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9217 (tt) outliers start: 48 outliers final: 17 residues processed: 121 average time/residue: 0.4962 time to fit residues: 65.9062 Evaluate side-chains 95 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056076 restraints weight = 28168.179| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.52 r_work: 0.2751 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11011 Z= 0.155 Angle : 0.607 11.033 15043 Z= 0.306 Chirality : 0.044 0.421 1766 Planarity : 0.004 0.054 1825 Dihedral : 9.050 79.100 1905 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.72 % Allowed : 16.47 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1299 helix: 2.27 (0.20), residues: 686 sheet: -0.87 (0.46), residues: 123 loop : -1.33 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 108 TYR 0.016 0.001 TYR B 466 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00364 (10994) covalent geometry : angle 0.59009 (15003) SS BOND : bond 0.00720 ( 5) SS BOND : angle 1.19744 ( 10) hydrogen bonds : bond 0.04370 ( 591) hydrogen bonds : angle 4.05048 ( 1704) Misc. bond : bond 0.00008 ( 2) link_BETA1-3 : bond 0.00922 ( 1) link_BETA1-3 : angle 2.13448 ( 3) link_BETA1-4 : bond 0.00125 ( 1) link_BETA1-4 : angle 1.57281 ( 3) link_BETA1-6 : bond 0.01133 ( 1) link_BETA1-6 : angle 3.39340 ( 3) link_NAG-ASN : bond 0.00589 ( 7) link_NAG-ASN : angle 3.40274 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8658 (pm20) cc_final: 0.8359 (pm20) REVERT: A 237 GLN cc_start: 0.8938 (tp40) cc_final: 0.7847 (tm-30) REVERT: B 112 GLN cc_start: 0.8654 (mt0) cc_final: 0.8318 (pt0) REVERT: B 159 TYR cc_start: 0.3882 (t80) cc_final: 0.3510 (t80) REVERT: C 96 LYS cc_start: 0.7149 (mttt) cc_final: 0.6686 (tppt) REVERT: C 192 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8971 (tt) REVERT: C 236 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9207 (tt) outliers start: 42 outliers final: 22 residues processed: 118 average time/residue: 0.4672 time to fit residues: 60.6715 Evaluate side-chains 104 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055016 restraints weight = 28621.783| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.52 r_work: 0.2721 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11011 Z= 0.204 Angle : 0.642 11.181 15043 Z= 0.325 Chirality : 0.046 0.428 1766 Planarity : 0.004 0.057 1825 Dihedral : 8.714 71.280 1905 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.43 % Allowed : 16.47 % Favored : 79.10 % 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: 0.97 (0.24), residues: 1299 helix: 2.19 (0.20), residues: 692 sheet: -0.89 (0.46), residues: 123 loop : -1.29 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.019 0.001 TYR B 466 PHE 0.027 0.001 PHE A 302 TRP 0.012 0.001 TRP B 203 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00487 (10994) covalent geometry : angle 0.62257 (15003) SS BOND : bond 0.00759 ( 5) SS BOND : angle 1.59629 ( 10) hydrogen bonds : bond 0.04709 ( 591) hydrogen bonds : angle 4.09168 ( 1704) Misc. bond : bond 0.00009 ( 2) link_BETA1-3 : bond 0.00914 ( 1) link_BETA1-3 : angle 2.28910 ( 3) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 1.94775 ( 3) link_BETA1-6 : bond 0.00761 ( 1) link_BETA1-6 : angle 3.72340 ( 3) link_NAG-ASN : bond 0.00644 ( 7) link_NAG-ASN : angle 3.67034 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8655 (pm20) cc_final: 0.8434 (pm20) REVERT: A 237 GLN cc_start: 0.8955 (tp40) cc_final: 0.7858 (tm-30) REVERT: A 454 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: B 159 TYR cc_start: 0.3910 (t80) cc_final: 0.3510 (t80) REVERT: C 96 LYS cc_start: 0.7184 (mttt) cc_final: 0.6670 (tppt) REVERT: C 236 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9233 (tt) outliers start: 50 outliers final: 24 residues processed: 121 average time/residue: 0.5195 time to fit residues: 68.7562 Evaluate side-chains 105 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 chunk 115 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056992 restraints weight = 28053.352| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.52 r_work: 0.2772 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11011 Z= 0.126 Angle : 0.592 10.799 15043 Z= 0.301 Chirality : 0.043 0.407 1766 Planarity : 0.004 0.055 1825 Dihedral : 8.020 69.814 1905 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.37 % Allowed : 17.80 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.09 (0.25), residues: 1299 helix: 2.35 (0.20), residues: 687 sheet: -0.90 (0.46), residues: 123 loop : -1.27 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 108 TYR 0.014 0.001 TYR B 225 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00287 (10994) covalent geometry : angle 0.57710 (15003) SS BOND : bond 0.00486 ( 5) SS BOND : angle 1.08731 ( 10) hydrogen bonds : bond 0.04021 ( 591) hydrogen bonds : angle 3.99289 ( 1704) Misc. bond : bond 0.00015 ( 2) link_BETA1-3 : bond 0.00914 ( 1) link_BETA1-3 : angle 1.83894 ( 3) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.22287 ( 3) link_BETA1-6 : bond 0.01030 ( 1) link_BETA1-6 : angle 3.20027 ( 3) link_NAG-ASN : bond 0.00627 ( 7) link_NAG-ASN : angle 3.24561 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8933 (tp40) cc_final: 0.7869 (tm-30) REVERT: A 454 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: B 112 GLN cc_start: 0.8657 (mt0) cc_final: 0.8237 (pt0) REVERT: C 96 LYS cc_start: 0.7113 (mttt) cc_final: 0.6621 (tppt) REVERT: C 106 GLU cc_start: 0.5533 (tm-30) cc_final: 0.5331 (pp20) REVERT: C 236 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9215 (tt) outliers start: 38 outliers final: 18 residues processed: 116 average time/residue: 0.4862 time to fit residues: 61.7336 Evaluate side-chains 100 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 0.0010 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057441 restraints weight = 28041.926| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.52 r_work: 0.2782 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11011 Z= 0.123 Angle : 0.592 10.483 15043 Z= 0.298 Chirality : 0.042 0.393 1766 Planarity : 0.004 0.058 1825 Dihedral : 7.591 72.154 1905 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.83 % Allowed : 19.40 % Favored : 77.77 % 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: 1.14 (0.25), residues: 1299 helix: 2.37 (0.20), residues: 691 sheet: -0.81 (0.45), residues: 128 loop : -1.28 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 108 TYR 0.014 0.001 TYR B 225 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00280 (10994) covalent geometry : angle 0.57852 (15003) SS BOND : bond 0.00551 ( 5) SS BOND : angle 1.13695 ( 10) hydrogen bonds : bond 0.03896 ( 591) hydrogen bonds : angle 3.96233 ( 1704) Misc. bond : bond 0.00021 ( 2) link_BETA1-3 : bond 0.00693 ( 1) link_BETA1-3 : angle 1.78177 ( 3) link_BETA1-4 : bond 0.00028 ( 1) link_BETA1-4 : angle 1.21648 ( 3) link_BETA1-6 : bond 0.00811 ( 1) link_BETA1-6 : angle 2.66053 ( 3) link_NAG-ASN : bond 0.00635 ( 7) link_NAG-ASN : angle 3.15571 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8938 (tp40) cc_final: 0.7896 (tm-30) REVERT: A 454 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: B 112 GLN cc_start: 0.8654 (mt0) cc_final: 0.8244 (pt0) REVERT: B 385 ASP cc_start: 0.8825 (m-30) cc_final: 0.8619 (m-30) REVERT: C 96 LYS cc_start: 0.7166 (mttt) cc_final: 0.6669 (tppt) outliers start: 32 outliers final: 16 residues processed: 110 average time/residue: 0.4700 time to fit residues: 56.7215 Evaluate side-chains 99 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 11 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.057883 restraints weight = 27840.511| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.53 r_work: 0.2792 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11011 Z= 0.122 Angle : 0.599 10.542 15043 Z= 0.301 Chirality : 0.042 0.402 1766 Planarity : 0.004 0.059 1825 Dihedral : 7.357 72.299 1905 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.13 % Allowed : 20.37 % Favored : 77.50 % 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: 1.15 (0.25), residues: 1299 helix: 2.36 (0.20), residues: 691 sheet: -0.85 (0.45), residues: 126 loop : -1.22 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 108 TYR 0.014 0.001 TYR B 225 PHE 0.026 0.001 PHE A 302 TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00281 (10994) covalent geometry : angle 0.58666 (15003) SS BOND : bond 0.00431 ( 5) SS BOND : angle 1.12875 ( 10) hydrogen bonds : bond 0.03795 ( 591) hydrogen bonds : angle 3.96391 ( 1704) Misc. bond : bond 0.00015 ( 2) link_BETA1-3 : bond 0.00626 ( 1) link_BETA1-3 : angle 1.47193 ( 3) link_BETA1-4 : bond 0.00057 ( 1) link_BETA1-4 : angle 1.18708 ( 3) link_BETA1-6 : bond 0.00454 ( 1) link_BETA1-6 : angle 2.22871 ( 3) link_NAG-ASN : bond 0.00616 ( 7) link_NAG-ASN : angle 3.11795 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8933 (tp40) cc_final: 0.7904 (tm-30) REVERT: B 112 GLN cc_start: 0.8648 (mt0) cc_final: 0.8307 (pt0) REVERT: B 385 ASP cc_start: 0.8837 (m-30) cc_final: 0.8628 (m-30) REVERT: C 96 LYS cc_start: 0.7171 (mttt) cc_final: 0.6670 (tppt) REVERT: C 192 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8910 (tt) outliers start: 24 outliers final: 18 residues processed: 97 average time/residue: 0.4850 time to fit residues: 51.6161 Evaluate side-chains 99 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 49 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 118 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.057812 restraints weight = 27988.869| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.51 r_work: 0.2792 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11011 Z= 0.124 Angle : 0.596 10.275 15043 Z= 0.300 Chirality : 0.042 0.391 1766 Planarity : 0.004 0.060 1825 Dihedral : 7.188 72.374 1905 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.30 % Allowed : 20.19 % Favored : 77.50 % 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: 1.20 (0.25), residues: 1299 helix: 2.40 (0.20), residues: 691 sheet: -0.81 (0.45), residues: 126 loop : -1.19 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 108 TYR 0.014 0.001 TYR B 225 PHE 0.026 0.001 PHE A 302 TRP 0.010 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00286 (10994) covalent geometry : angle 0.58341 (15003) SS BOND : bond 0.00548 ( 5) SS BOND : angle 1.21331 ( 10) hydrogen bonds : bond 0.03787 ( 591) hydrogen bonds : angle 3.95173 ( 1704) Misc. bond : bond 0.00012 ( 2) link_BETA1-3 : bond 0.00618 ( 1) link_BETA1-3 : angle 1.43768 ( 3) link_BETA1-4 : bond 0.00030 ( 1) link_BETA1-4 : angle 1.28760 ( 3) link_BETA1-6 : bond 0.00443 ( 1) link_BETA1-6 : angle 1.92905 ( 3) link_NAG-ASN : bond 0.00626 ( 7) link_NAG-ASN : angle 3.07623 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8939 (tp40) cc_final: 0.7928 (tm-30) REVERT: A 454 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: B 112 GLN cc_start: 0.8643 (mt0) cc_final: 0.8310 (pt0) REVERT: B 385 ASP cc_start: 0.8844 (m-30) cc_final: 0.8633 (m-30) REVERT: C 96 LYS cc_start: 0.7143 (mttt) cc_final: 0.6726 (tppt) REVERT: C 192 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8908 (tt) outliers start: 26 outliers final: 17 residues processed: 101 average time/residue: 0.4845 time to fit residues: 53.7703 Evaluate side-chains 100 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.057812 restraints weight = 28234.214| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.55 r_work: 0.2789 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11011 Z= 0.129 Angle : 0.608 10.432 15043 Z= 0.308 Chirality : 0.042 0.399 1766 Planarity : 0.004 0.060 1825 Dihedral : 7.133 72.364 1905 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.13 % Allowed : 20.37 % Favored : 77.50 % 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: 1.21 (0.25), residues: 1299 helix: 2.41 (0.20), residues: 691 sheet: -0.78 (0.45), residues: 126 loop : -1.22 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 108 TYR 0.015 0.001 TYR B 225 PHE 0.026 0.001 PHE A 302 TRP 0.010 0.001 TRP B 203 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00300 (10994) covalent geometry : angle 0.59593 (15003) SS BOND : bond 0.00577 ( 5) SS BOND : angle 1.24372 ( 10) hydrogen bonds : bond 0.03815 ( 591) hydrogen bonds : angle 3.99353 ( 1704) Misc. bond : bond 0.00009 ( 2) link_BETA1-3 : bond 0.00582 ( 1) link_BETA1-3 : angle 1.39992 ( 3) link_BETA1-4 : bond 0.00021 ( 1) link_BETA1-4 : angle 1.35840 ( 3) link_BETA1-6 : bond 0.00448 ( 1) link_BETA1-6 : angle 1.89942 ( 3) link_NAG-ASN : bond 0.00611 ( 7) link_NAG-ASN : angle 3.10150 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.95 seconds wall clock time: 69 minutes 46.36 seconds (4186.36 seconds total)