Starting phenix.real_space_refine on Wed Mar 4 18:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0i_22598/03_2026/7k0i_22598.cif" } 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= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 88 5.16 5 C 9840 2.51 5 N 2610 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15366 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 Restraints were copied for chains: D, E, F Time building chain proxies: 4.51, per 1000 atoms: 0.29 Number of scatterers: 15366 At special positions: 0 Unit cell: (101.05, 155.077, 114.057, 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 88 16.00 P 2 15.00 O 2826 8.00 N 2610 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 564.3 milliseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 51.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.533A pdb=" N LYS A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.773A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.530A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.615A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.572A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.212A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.733A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.524A pdb=" N ALA B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.586A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.767A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 133 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.931A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.514A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.569A pdb=" N TYR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 455 removed outlier: 4.080A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.173A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 53 through 64 removed outlier: 3.532A pdb=" N LYS D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 Processing helix chain 'D' and resid 142 through 156 removed outlier: 3.773A pdb=" N LEU D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 179 removed outlier: 4.531A pdb=" N ILE D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 213 through 231 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.615A pdb=" N LYS D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 359 removed outlier: 3.571A pdb=" N ASN D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 377 removed outlier: 4.212A pdb=" N ALA D 364 " --> pdb=" O PRO D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 422 removed outlier: 3.732A pdb=" N ASP D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 473 Processing helix chain 'F' and resid 9 through 24 Processing helix chain 'F' and resid 30 through 55 Processing helix chain 'F' and resid 58 through 69 Processing helix chain 'E' and resid 67 through 94 removed outlier: 3.523A pdb=" N ALA E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.585A pdb=" N LYS E 109 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 120 through 126 Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.767A pdb=" N ARG E 131 " --> pdb=" O MET E 128 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP E 132 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 133 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.930A pdb=" N GLU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 250 Proline residue: E 247 - end of helix removed outlier: 3.513A pdb=" N VAL E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 273 Processing helix chain 'E' and resid 284 through 299 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 358 through 364 removed outlier: 3.569A pdb=" N TYR E 362 " --> pdb=" O GLY E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 391 through 402 Processing helix chain 'E' and resid 402 through 408 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 433 through 455 removed outlier: 4.080A pdb=" N VAL E 439 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 440 " --> pdb=" O LYS E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 489 removed outlier: 4.171A pdb=" N GLY E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.210A pdb=" N VAL A 94 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.239A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 243 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.154A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.851A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.677A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.754A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 86 removed outlier: 4.210A pdb=" N VAL D 94 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA D 425 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 101 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 160 through 164 removed outlier: 7.239A pdb=" N ILE D 271 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER D 304 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 273 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 243 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLU D 245 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL D 185 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 209 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL D 187 " --> pdb=" O PHE D 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 383 through 386 removed outlier: 4.154A pdb=" N THR D 427 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 152 removed outlier: 6.850A pdb=" N VAL E 146 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE E 167 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE E 148 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASN E 165 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU E 150 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY E 492 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 171 " --> pdb=" O GLY E 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 231 through 235 removed outlier: 6.675A pdb=" N ILE E 310 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR E 342 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE E 312 " --> pdb=" O TYR E 342 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP E 344 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL E 314 " --> pdb=" O ASP E 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 468 through 472 removed outlier: 3.755A pdb=" N VAL E 494 " --> pdb=" O ARG E 509 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4995 1.34 - 1.46: 2296 1.46 - 1.57: 8243 1.57 - 1.69: 2 1.69 - 1.81: 142 Bond restraints: 15678 Sorted by residual: bond pdb=" N GLU D 275 " pdb=" CA GLU D 275 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N GLU A 275 " pdb=" CA GLU A 275 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.93e+00 bond pdb=" N SER A 276 " pdb=" CA SER A 276 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" N SER D 276 " pdb=" CA SER D 276 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N GLU D 274 " pdb=" CA GLU D 274 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.27e-02 6.20e+03 5.93e+00 ... (remaining 15673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 20164 1.35 - 2.70: 835 2.70 - 4.05: 146 4.05 - 5.40: 27 5.40 - 6.75: 10 Bond angle restraints: 21182 Sorted by residual: angle pdb=" N GLU D 58 " pdb=" CA GLU D 58 " pdb=" CB GLU D 58 " ideal model delta sigma weight residual 110.12 113.68 -3.56 1.47e+00 4.63e-01 5.86e+00 angle pdb=" N GLU A 58 " pdb=" CA GLU A 58 " pdb=" CB GLU A 58 " ideal model delta sigma weight residual 110.12 113.67 -3.55 1.47e+00 4.63e-01 5.83e+00 angle pdb=" C GLU D 58 " pdb=" N GLU D 59 " pdb=" CA GLU D 59 " ideal model delta sigma weight residual 120.72 116.76 3.96 1.67e+00 3.59e-01 5.64e+00 angle pdb=" CA GLU D 274 " pdb=" C GLU D 274 " pdb=" O GLU D 274 " ideal model delta sigma weight residual 120.46 117.94 2.52 1.07e+00 8.73e-01 5.54e+00 angle pdb=" C GLU A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 21177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 8870 21.47 - 42.94: 514 42.94 - 64.42: 38 64.42 - 85.89: 10 85.89 - 107.36: 2 Dihedral angle restraints: 9434 sinusoidal: 3788 harmonic: 5646 Sorted by residual: dihedral pdb=" C5A PLP E 601 " pdb=" O4P PLP E 601 " pdb=" P PLP E 601 " pdb=" O1P PLP E 601 " ideal model delta sinusoidal sigma weight residual 76.43 -176.21 -107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -176.22 -107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1225 0.030 - 0.060: 710 0.060 - 0.090: 240 0.090 - 0.120: 145 0.120 - 0.151: 18 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA ILE D 242 " pdb=" N ILE D 242 " pdb=" C ILE D 242 " pdb=" CB ILE D 242 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL E 469 " pdb=" N VAL E 469 " pdb=" C VAL E 469 " pdb=" CB VAL E 469 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2335 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 412 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO E 413 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 413 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 413 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO B 413 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 502 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " 0.028 5.00e-02 4.00e+02 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2512 2.76 - 3.29: 14293 3.29 - 3.83: 24140 3.83 - 4.36: 29372 4.36 - 4.90: 52617 Nonbonded interactions: 122934 Sorted by model distance: nonbonded pdb=" OG1 THR B 378 " pdb=" O1P PLP B 601 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR E 378 " pdb=" O1P PLP E 601 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR D 178 " pdb=" O VAL D 324 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 436 " pdb=" OH TYR B 407 " model vdw 2.302 3.040 ... (remaining 122929 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 3.600 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.100 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.005 0.046 15680 Z= 0.226 Angle : 0.643 6.753 21182 Z= 0.358 Chirality : 0.045 0.151 2338 Planarity : 0.005 0.073 2720 Dihedral : 12.839 107.361 5826 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.25 % Allowed : 0.37 % Favored : 99.38 % 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 (0.19), residues: 1942 helix: 1.44 (0.17), residues: 862 sheet: -1.10 (0.34), residues: 222 loop : -1.02 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 95 TYR 0.022 0.002 TYR A 166 PHE 0.019 0.002 PHE D 209 TRP 0.012 0.001 TRP C 32 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00530 (15678) covalent geometry : angle 0.64339 (21182) hydrogen bonds : bond 0.13635 ( 774) hydrogen bonds : angle 6.01515 ( 2232) Misc. bond : bond 0.02925 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.617 Fit side-chains REVERT: A 230 LYS cc_start: 0.7455 (tttm) cc_final: 0.6954 (mmtt) REVERT: A 455 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6104 (tm-30) REVERT: B 244 MET cc_start: 0.7974 (mtt) cc_final: 0.7748 (mtt) REVERT: E 244 MET cc_start: 0.7945 (mtt) cc_final: 0.7709 (mtt) outliers start: 4 outliers final: 4 residues processed: 162 average time/residue: 0.1236 time to fit residues: 30.2493 Evaluate side-chains 130 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 229 GLN C 19 GLN D 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160622 restraints weight = 17116.042| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.13 r_work: 0.3806 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15680 Z= 0.104 Angle : 0.500 6.498 21182 Z= 0.268 Chirality : 0.040 0.131 2338 Planarity : 0.005 0.054 2720 Dihedral : 5.938 76.742 2190 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.43 % Allowed : 5.47 % Favored : 94.10 % 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: 0.72 (0.19), residues: 1942 helix: 1.97 (0.18), residues: 870 sheet: -0.36 (0.33), residues: 242 loop : -0.89 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 459 TYR 0.012 0.001 TYR C 20 PHE 0.011 0.001 PHE B 118 TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00222 (15678) covalent geometry : angle 0.49962 (21182) hydrogen bonds : bond 0.03882 ( 774) hydrogen bonds : angle 4.69642 ( 2232) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.593 Fit side-chains REVERT: B 244 MET cc_start: 0.8120 (mtt) cc_final: 0.7913 (mtt) REVERT: E 355 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7854 (t) outliers start: 7 outliers final: 4 residues processed: 152 average time/residue: 0.1198 time to fit residues: 27.4675 Evaluate side-chains 133 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157981 restraints weight = 17365.185| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.12 r_work: 0.3738 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15680 Z= 0.136 Angle : 0.512 6.624 21182 Z= 0.271 Chirality : 0.042 0.144 2338 Planarity : 0.005 0.050 2720 Dihedral : 5.222 57.293 2189 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.18 % Allowed : 6.83 % Favored : 91.99 % 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: 0.73 (0.19), residues: 1942 helix: 2.05 (0.17), residues: 882 sheet: -0.41 (0.33), residues: 242 loop : -1.01 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 136 TYR 0.012 0.001 TYR C 20 PHE 0.014 0.001 PHE D 209 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00328 (15678) covalent geometry : angle 0.51168 (21182) hydrogen bonds : bond 0.04004 ( 774) hydrogen bonds : angle 4.49590 ( 2232) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.561 Fit side-chains REVERT: A 58 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 326 ASP cc_start: 0.8159 (m-30) cc_final: 0.7957 (m-30) REVERT: B 244 MET cc_start: 0.8160 (mtt) cc_final: 0.7955 (mtt) REVERT: D 58 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7410 (mp0) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.1195 time to fit residues: 27.0132 Evaluate side-chains 134 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS D 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.159226 restraints weight = 17253.497| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.12 r_work: 0.3751 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15680 Z= 0.119 Angle : 0.486 6.585 21182 Z= 0.259 Chirality : 0.041 0.143 2338 Planarity : 0.004 0.048 2720 Dihedral : 4.843 54.698 2189 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.93 % Allowed : 8.20 % Favored : 90.87 % 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: 0.81 (0.19), residues: 1942 helix: 2.16 (0.17), residues: 882 sheet: -0.40 (0.33), residues: 242 loop : -1.00 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 541 TYR 0.010 0.001 TYR C 20 PHE 0.012 0.001 PHE D 209 TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00284 (15678) covalent geometry : angle 0.48561 (21182) hydrogen bonds : bond 0.03617 ( 774) hydrogen bonds : angle 4.32320 ( 2232) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.534 Fit side-chains REVERT: A 58 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 326 ASP cc_start: 0.8162 (m-30) cc_final: 0.7958 (m-30) REVERT: D 58 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: D 274 GLU cc_start: 0.6700 (tt0) cc_final: 0.6463 (tt0) outliers start: 15 outliers final: 12 residues processed: 139 average time/residue: 0.1309 time to fit residues: 27.0211 Evaluate side-chains 134 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 160 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 150 optimal weight: 0.0770 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160051 restraints weight = 17154.224| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.11 r_work: 0.3815 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15680 Z= 0.110 Angle : 0.466 6.590 21182 Z= 0.248 Chirality : 0.041 0.142 2338 Planarity : 0.004 0.047 2720 Dihedral : 4.581 51.984 2189 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 8.82 % Favored : 89.81 % 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: 0.90 (0.19), residues: 1942 helix: 2.27 (0.17), residues: 884 sheet: -0.38 (0.34), residues: 242 loop : -1.00 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.011 0.001 TYR C 20 PHE 0.013 0.001 PHE A 168 TRP 0.010 0.001 TRP C 32 HIS 0.002 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00262 (15678) covalent geometry : angle 0.46607 (21182) hydrogen bonds : bond 0.03401 ( 774) hydrogen bonds : angle 4.21875 ( 2232) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.578 Fit side-chains REVERT: A 58 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 58 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: D 274 GLU cc_start: 0.6794 (tt0) cc_final: 0.6555 (tt0) outliers start: 22 outliers final: 10 residues processed: 150 average time/residue: 0.1169 time to fit residues: 26.7020 Evaluate side-chains 132 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 155 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157978 restraints weight = 17250.226| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.12 r_work: 0.3816 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.003 0.032 15680 Z= 0.140 Angle : 0.497 6.642 21182 Z= 0.264 Chirality : 0.042 0.148 2338 Planarity : 0.004 0.047 2720 Dihedral : 4.588 49.567 2189 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.12 % Allowed : 10.06 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1942 helix: 2.23 (0.17), residues: 884 sheet: -0.46 (0.34), residues: 242 loop : -1.06 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.011 0.001 TYR C 20 PHE 0.014 0.001 PHE D 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00343 (15678) covalent geometry : angle 0.49746 (21182) hydrogen bonds : bond 0.03730 ( 774) hydrogen bonds : angle 4.24915 ( 2232) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.577 Fit side-chains REVERT: A 58 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 303 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7778 (p) REVERT: D 58 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: D 274 GLU cc_start: 0.6813 (tt0) cc_final: 0.6544 (tt0) outliers start: 18 outliers final: 9 residues processed: 142 average time/residue: 0.1237 time to fit residues: 26.5069 Evaluate side-chains 132 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157363 restraints weight = 17093.284| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.12 r_work: 0.3761 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15680 Z= 0.142 Angle : 0.502 6.637 21182 Z= 0.267 Chirality : 0.042 0.149 2338 Planarity : 0.004 0.047 2720 Dihedral : 4.562 46.455 2189 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.24 % Allowed : 10.81 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1942 helix: 2.21 (0.17), residues: 886 sheet: -0.47 (0.34), residues: 242 loop : -1.07 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.010 0.001 TYR C 20 PHE 0.014 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00349 (15678) covalent geometry : angle 0.50153 (21182) hydrogen bonds : bond 0.03720 ( 774) hydrogen bonds : angle 4.23769 ( 2232) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.584 Fit side-chains REVERT: A 58 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 410 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7903 (mtm-85) REVERT: B 303 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7775 (p) REVERT: D 58 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 274 GLU cc_start: 0.6929 (tt0) cc_final: 0.6649 (tt0) outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 0.1198 time to fit residues: 25.0733 Evaluate side-chains 137 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 355 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158459 restraints weight = 17217.869| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.10 r_work: 0.3802 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15680 Z= 0.126 Angle : 0.488 6.598 21182 Z= 0.260 Chirality : 0.041 0.144 2338 Planarity : 0.004 0.047 2720 Dihedral : 4.443 41.691 2189 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.37 % Allowed : 10.75 % Favored : 87.89 % 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: 0.85 (0.19), residues: 1942 helix: 2.25 (0.17), residues: 886 sheet: -0.46 (0.34), residues: 242 loop : -1.05 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.009 0.001 TYR C 20 PHE 0.014 0.001 PHE D 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS E 403 Details of bonding type rmsd covalent geometry : bond 0.00306 (15678) covalent geometry : angle 0.48849 (21182) hydrogen bonds : bond 0.03542 ( 774) hydrogen bonds : angle 4.21096 ( 2232) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.525 Fit side-chains REVERT: A 58 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 59 GLU cc_start: 0.7574 (pp20) cc_final: 0.7340 (pp20) REVERT: A 410 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7882 (mtm-85) REVERT: D 58 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7363 (mp0) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.1220 time to fit residues: 27.4229 Evaluate side-chains 142 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 166 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 96 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.158800 restraints weight = 17126.653| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.10 r_work: 0.3829 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15680 Z= 0.122 Angle : 0.483 6.598 21182 Z= 0.257 Chirality : 0.041 0.144 2338 Planarity : 0.004 0.046 2720 Dihedral : 4.340 36.242 2189 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.24 % Allowed : 10.75 % Favored : 88.01 % 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: 0.89 (0.19), residues: 1942 helix: 2.29 (0.17), residues: 886 sheet: -0.45 (0.34), residues: 242 loop : -1.03 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.011 0.001 TYR F 20 PHE 0.013 0.001 PHE D 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.001 HIS E 403 Details of bonding type rmsd covalent geometry : bond 0.00293 (15678) covalent geometry : angle 0.48273 (21182) hydrogen bonds : bond 0.03476 ( 774) hydrogen bonds : angle 4.18894 ( 2232) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.557 Fit side-chains REVERT: A 58 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 410 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7821 (mtm-85) REVERT: B 303 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (p) REVERT: D 58 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7381 (mp0) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 0.1226 time to fit residues: 26.8034 Evaluate side-chains 142 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 191 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156252 restraints weight = 17191.179| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.12 r_work: 0.3799 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15680 Z= 0.158 Angle : 0.522 6.655 21182 Z= 0.277 Chirality : 0.043 0.150 2338 Planarity : 0.005 0.048 2720 Dihedral : 4.386 38.162 2187 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.12 % Allowed : 10.75 % Favored : 88.14 % 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: 0.69 (0.19), residues: 1942 helix: 2.22 (0.17), residues: 882 sheet: -0.91 (0.36), residues: 216 loop : -1.12 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 151 TYR 0.015 0.001 TYR C 20 PHE 0.016 0.001 PHE D 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00390 (15678) covalent geometry : angle 0.52246 (21182) hydrogen bonds : bond 0.03912 ( 774) hydrogen bonds : angle 4.27667 ( 2232) Misc. bond : bond 0.00030 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.544 Fit side-chains REVERT: A 58 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: A 410 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7914 (mtm-85) REVERT: B 303 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7838 (p) REVERT: D 58 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7356 (mp0) outliers start: 18 outliers final: 14 residues processed: 137 average time/residue: 0.1158 time to fit residues: 24.1311 Evaluate side-chains 138 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 165 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 187 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 123 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160280 restraints weight = 17038.952| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.09 r_work: 0.3767 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15680 Z= 0.108 Angle : 0.469 6.583 21182 Z= 0.251 Chirality : 0.040 0.140 2338 Planarity : 0.004 0.046 2720 Dihedral : 4.170 37.152 2187 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.18 % Allowed : 10.93 % Favored : 87.89 % 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: 0.93 (0.19), residues: 1942 helix: 2.34 (0.18), residues: 880 sheet: -0.51 (0.34), residues: 242 loop : -0.98 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.010 0.001 TYR C 20 PHE 0.012 0.001 PHE D 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.000 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00258 (15678) covalent geometry : angle 0.46914 (21182) hydrogen bonds : bond 0.03293 ( 774) hydrogen bonds : angle 4.15306 ( 2232) Misc. bond : bond 0.00019 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.46 seconds wall clock time: 55 minutes 47.50 seconds (3347.50 seconds total)