Starting phenix.real_space_refine on Sat Aug 23 12:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.map" model { file = "/net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv3_42604/08_2025/8uv3_42604.cif" } resolution = 2.72 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= 0.006 sd= 0.484 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 Mg 3 5.21 5 S 48 5.16 5 C 7599 2.51 5 N 1941 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12069 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3949 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "B" Number of atoms: 3967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3967 Classifications: {'peptide': 517} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 470} Chain: "C" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3874 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 458} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 2.57, per 1000 atoms: 0.21 Number of scatterers: 12069 At special positions: 0 Unit cell: (119.9, 117.7, 122.1, 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 48 16.00 Mg 3 11.99 O 2478 8.00 N 1941 7.00 C 7599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 358.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 21 sheets defined 8.5% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.128A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.993A pdb=" N THR A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.772A pdb=" N ALA B 45 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.054A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.588A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.567A pdb=" N PHE B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.669A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 58 removed outlier: 4.025A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.571A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 137 through 142 removed outlier: 4.060A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.544A pdb=" N TRP C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 286' Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.636A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.604A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG A 204 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 113 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 206 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 111 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LYS A 208 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN A 109 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 210 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 107 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 212 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.604A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG A 204 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 113 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 206 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 111 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LYS A 208 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN A 109 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 210 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 107 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 212 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.836A pdb=" N CYS A 183 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 81 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 181 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA A 119 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.408A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 477 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 488 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 475 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 490 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 473 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 478 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 5.408A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 477 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 488 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 475 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 490 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 473 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 472 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296 removed outlier: 4.716A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A 379 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N THR A 354 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN A 340 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 392 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69 removed outlier: 6.530A pdb=" N LEU B 205 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N LEU B 64 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLY B 203 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLU B 66 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N VAL B 201 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.763A pdb=" N ILE B 78 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 185 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 80 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.263A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 448 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 268 through 269 removed outlier: 4.368A pdb=" N ARG B 268 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 297 removed outlier: 4.629A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 13.222A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 427 through 429 removed outlier: 5.371A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 485 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 479 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69 removed outlier: 6.133A pdb=" N LEU C 205 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU C 64 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY C 203 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLU C 66 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N VAL C 201 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 69 removed outlier: 6.133A pdb=" N LEU C 205 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU C 64 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY C 203 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLU C 66 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N VAL C 201 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.550A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 119 " --> pdb=" O PRO C 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AB9, first strand: chain 'C' and resid 268 through 269 removed outlier: 4.426A pdb=" N ARG C 268 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 297 removed outlier: 4.333A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 377 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 332 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 400 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN C 334 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE C 398 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU C 336 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 394 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN C 340 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG C 392 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU C 342 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ARG C 390 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 289 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 492 removed outlier: 6.939A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU C 488 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 475 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 490 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU C 473 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 783 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: 1.30 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2148 1.32 - 1.44: 3071 1.44 - 1.57: 6823 1.57 - 1.69: 2 1.69 - 1.81: 72 Bond restraints: 12116 Sorted by residual: bond pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.35e+01 bond pdb=" C ASN B 192 " pdb=" N SER B 193 " ideal model delta sigma weight residual 1.335 1.246 0.088 3.04e-02 1.08e+03 8.47e+00 bond pdb=" CB VAL C 103 " pdb=" CG1 VAL C 103 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.53e+00 bond pdb=" C TYR A 130 " pdb=" N PHE A 131 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.63e-02 3.76e+03 6.60e+00 bond pdb=" CB THR C 219 " pdb=" CG2 THR C 219 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 ... (remaining 12111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 16280 3.13 - 6.26: 292 6.26 - 9.38: 38 9.38 - 12.51: 3 12.51 - 15.64: 1 Bond angle restraints: 16614 Sorted by residual: angle pdb=" N ALA B 25 " pdb=" CA ALA B 25 " pdb=" C ALA B 25 " ideal model delta sigma weight residual 112.97 105.19 7.78 1.06e+00 8.90e-01 5.39e+01 angle pdb=" N VAL B 22 " pdb=" CA VAL B 22 " pdb=" C VAL B 22 " ideal model delta sigma weight residual 108.63 113.50 -4.87 8.60e-01 1.35e+00 3.20e+01 angle pdb=" N LEU B 21 " pdb=" CA LEU B 21 " pdb=" C LEU B 21 " ideal model delta sigma weight residual 108.24 115.32 -7.08 1.32e+00 5.74e-01 2.88e+01 angle pdb=" CA VAL A 216 " pdb=" C VAL A 216 " pdb=" N TYR A 217 " ideal model delta sigma weight residual 117.37 121.32 -3.95 7.40e-01 1.83e+00 2.85e+01 angle pdb=" C PHE A 215 " pdb=" N VAL A 216 " pdb=" CA VAL A 216 " ideal model delta sigma weight residual 122.97 117.77 5.20 9.80e-01 1.04e+00 2.82e+01 ... (remaining 16609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6426 17.73 - 35.47: 627 35.47 - 53.20: 104 53.20 - 70.93: 14 70.93 - 88.67: 16 Dihedral angle restraints: 7187 sinusoidal: 2759 harmonic: 4428 Sorted by residual: dihedral pdb=" CA VAL B 26 " pdb=" C VAL B 26 " pdb=" N GLU B 27 " pdb=" CA GLU B 27 " ideal model delta harmonic sigma weight residual 180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" CA GLU B 27 " pdb=" C GLU B 27 " pdb=" N GLN B 28 " pdb=" CA GLN B 28 " ideal model delta harmonic sigma weight residual 180.00 136.50 43.50 0 5.00e+00 4.00e-02 7.57e+01 dihedral pdb=" CA PRO A 194 " pdb=" C PRO A 194 " pdb=" N GLY A 195 " pdb=" CA GLY A 195 " ideal model delta harmonic sigma weight residual 180.00 140.73 39.27 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 7184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1408 0.068 - 0.136: 417 0.136 - 0.204: 53 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CB VAL C 151 " pdb=" CA VAL C 151 " pdb=" CG1 VAL C 151 " pdb=" CG2 VAL C 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE C 199 " pdb=" N PHE C 199 " pdb=" C PHE C 199 " pdb=" CB PHE C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1888 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 199 " 0.039 2.00e-02 2.50e+03 2.71e-02 1.29e+01 pdb=" CG PHE C 199 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 199 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 199 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 199 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 199 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 199 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO C 129 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 89 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 90 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.039 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 122 2.46 - 3.07: 7043 3.07 - 3.68: 17009 3.68 - 4.29: 26650 4.29 - 4.90: 44152 Nonbonded interactions: 94976 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O HOH A 755 " model vdw 1.851 2.170 nonbonded pdb="MG MG C 601 " pdb=" O HOH C 742 " model vdw 1.877 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH B 706 " model vdw 1.904 2.170 nonbonded pdb=" OE1 GLN C 438 " pdb="MG MG C 601 " model vdw 1.941 2.170 nonbonded pdb=" OE1 GLN A 469 " pdb=" O HOH A 701 " model vdw 1.990 3.040 ... (remaining 94971 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 530 or resid 601)) selection = (chain 'B' and (resid 28 through 530 or resid 601)) selection = chain 'C' } 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: 9.750 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.250 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.010 0.092 12116 Z= 0.408 Angle : 1.059 15.640 16614 Z= 0.571 Chirality : 0.064 0.340 1891 Planarity : 0.009 0.085 2176 Dihedral : 14.694 88.666 4347 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.98 % Favored : 91.82 % Rotamer: Outliers : 0.39 % Allowed : 6.06 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.17), residues: 1528 helix: -4.59 (0.31), residues: 55 sheet: -1.23 (0.24), residues: 398 loop : -3.03 (0.14), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 166 TYR 0.040 0.003 TYR C 217 PHE 0.056 0.004 PHE C 199 TRP 0.019 0.004 TRP B 102 HIS 0.008 0.002 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00996 (12116) covalent geometry : angle 1.05864 (16614) hydrogen bonds : bond 0.26480 ( 278) hydrogen bonds : angle 9.96770 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.5430 (pm20) cc_final: 0.5030 (mp0) REVERT: A 255 ASP cc_start: 0.7645 (t0) cc_final: 0.7427 (t0) REVERT: A 281 ILE cc_start: 0.8422 (mt) cc_final: 0.8202 (mm) REVERT: A 407 GLU cc_start: 0.5554 (mm-30) cc_final: 0.4629 (tt0) REVERT: A 486 LEU cc_start: 0.8095 (mt) cc_final: 0.7839 (mt) REVERT: B 21 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7750 (pp) REVERT: B 455 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7207 (mm-40) REVERT: C 148 MET cc_start: 0.8376 (ttm) cc_final: 0.8091 (ttm) REVERT: C 235 ILE cc_start: 0.7968 (mt) cc_final: 0.7668 (mm) REVERT: C 238 ARG cc_start: 0.7401 (ptp-170) cc_final: 0.7117 (ptp90) REVERT: C 356 GLU cc_start: 0.5364 (mm-30) cc_final: 0.5114 (mm-30) REVERT: C 392 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7365 (ttp-170) REVERT: C 478 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6938 (ttm170) REVERT: C 488 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6879 (pt0) outliers start: 5 outliers final: 5 residues processed: 156 average time/residue: 0.7188 time to fit residues: 120.2295 Evaluate side-chains 142 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 50 GLN A 261 ASN A 526 GLN B 73 ASN B 105 ASN B 140 GLN B 170 HIS B 261 ASN B 266 ASN B 270 HIS B 340 GLN B 455 GLN B 493 ASN C 49 ASN C 61 GLN C 105 ASN C 270 HIS C 334 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.208930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.198552 restraints weight = 11085.296| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 0.49 r_work: 0.3881 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 0.94 restraints_weight: 0.2500 r_work: 0.3783 rms_B_bonded: 2.06 restraints_weight: 0.1250 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12116 Z= 0.139 Angle : 0.699 9.780 16614 Z= 0.368 Chirality : 0.047 0.178 1891 Planarity : 0.007 0.068 2176 Dihedral : 6.712 45.194 1665 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 1.49 % Allowed : 9.68 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.18), residues: 1528 helix: -3.38 (0.47), residues: 61 sheet: -0.82 (0.24), residues: 422 loop : -2.35 (0.16), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.015 0.001 TYR B 227 PHE 0.027 0.002 PHE C 199 TRP 0.012 0.001 TRP B 520 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00317 (12116) covalent geometry : angle 0.69935 (16614) hydrogen bonds : bond 0.04607 ( 278) hydrogen bonds : angle 6.75410 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8618 (p0) cc_final: 0.8274 (p0) REVERT: A 274 THR cc_start: 0.8865 (t) cc_final: 0.8555 (t) REVERT: A 488 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 516 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: B 21 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7598 (pp) REVERT: B 22 VAL cc_start: 0.7582 (m) cc_final: 0.7269 (m) REVERT: C 148 MET cc_start: 0.8695 (ttm) cc_final: 0.8426 (ttm) REVERT: C 343 THR cc_start: 0.4873 (OUTLIER) cc_final: 0.4671 (m) REVERT: C 356 GLU cc_start: 0.5361 (mm-30) cc_final: 0.5150 (mm-30) REVERT: C 512 ASP cc_start: 0.8251 (p0) cc_final: 0.7967 (p0) outliers start: 19 outliers final: 8 residues processed: 148 average time/residue: 0.6790 time to fit residues: 108.2309 Evaluate side-chains 138 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 123 optimal weight: 30.0000 chunk 27 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 175 GLN C 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.208168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.193091 restraints weight = 11160.440| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 0.65 r_work: 0.3852 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12116 Z= 0.166 Angle : 0.724 11.646 16614 Z= 0.376 Chirality : 0.049 0.178 1891 Planarity : 0.007 0.068 2176 Dihedral : 6.534 46.015 1662 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 2.12 % Allowed : 11.64 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.19), residues: 1528 helix: -2.60 (0.56), residues: 57 sheet: -0.58 (0.24), residues: 425 loop : -2.07 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 478 TYR 0.020 0.002 TYR A 217 PHE 0.032 0.002 PHE C 199 TRP 0.011 0.002 TRP B 520 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00394 (12116) covalent geometry : angle 0.72423 (16614) hydrogen bonds : bond 0.04205 ( 278) hydrogen bonds : angle 6.32269 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8731 (p0) cc_final: 0.8215 (p0) REVERT: A 175 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: A 176 GLU cc_start: 0.8265 (pm20) cc_final: 0.7350 (pt0) REVERT: A 274 THR cc_start: 0.8823 (t) cc_final: 0.8500 (t) REVERT: B 21 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7691 (pp) REVERT: B 322 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: C 148 MET cc_start: 0.8725 (ttm) cc_final: 0.8463 (ttm) REVERT: C 235 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8042 (mm) REVERT: C 392 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5643 (ttt-90) REVERT: C 433 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7597 (ttm170) REVERT: C 512 ASP cc_start: 0.8072 (p0) cc_final: 0.7838 (p0) REVERT: C 516 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7605 (mt-10) outliers start: 27 outliers final: 12 residues processed: 143 average time/residue: 0.7185 time to fit residues: 110.2579 Evaluate side-chains 139 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 147 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN B 140 GLN B 175 GLN C 266 ASN C 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.209164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.193881 restraints weight = 11213.158| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 0.64 r_work: 0.3860 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12116 Z= 0.132 Angle : 0.654 8.786 16614 Z= 0.340 Chirality : 0.047 0.146 1891 Planarity : 0.006 0.066 2176 Dihedral : 6.166 44.831 1662 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.83 % Allowed : 11.88 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.19), residues: 1528 helix: -2.10 (0.60), residues: 57 sheet: -0.47 (0.24), residues: 429 loop : -1.81 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.017 0.001 TYR A 217 PHE 0.024 0.002 PHE C 199 TRP 0.010 0.001 TRP B 520 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00308 (12116) covalent geometry : angle 0.65378 (16614) hydrogen bonds : bond 0.03583 ( 278) hydrogen bonds : angle 6.02962 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8525 (p0) cc_final: 0.8172 (p0) REVERT: A 176 GLU cc_start: 0.8173 (pm20) cc_final: 0.7467 (pm20) REVERT: A 238 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7182 (ptt180) REVERT: A 478 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7856 (ttm-80) REVERT: A 488 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 21 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7572 (pp) REVERT: B 315 SER cc_start: 0.7450 (t) cc_final: 0.7187 (m) REVERT: B 322 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: C 148 MET cc_start: 0.8715 (ttm) cc_final: 0.8453 (ttm) REVERT: C 253 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7320 (pt) REVERT: C 392 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.5624 (ttt-90) REVERT: C 433 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7712 (ttm170) REVERT: C 512 ASP cc_start: 0.7996 (p0) cc_final: 0.7787 (p0) outliers start: 36 outliers final: 14 residues processed: 150 average time/residue: 0.6762 time to fit residues: 109.3694 Evaluate side-chains 140 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 140 GLN B 175 GLN C 266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.209107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.193614 restraints weight = 11191.841| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 0.64 r_work: 0.3866 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12116 Z= 0.141 Angle : 0.667 9.349 16614 Z= 0.345 Chirality : 0.047 0.151 1891 Planarity : 0.006 0.065 2176 Dihedral : 6.090 45.009 1661 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.52 % Allowed : 12.90 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.19), residues: 1528 helix: -1.87 (0.62), residues: 57 sheet: -0.38 (0.25), residues: 399 loop : -1.70 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.020 0.001 TYR A 217 PHE 0.026 0.002 PHE C 199 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00334 (12116) covalent geometry : angle 0.66701 (16614) hydrogen bonds : bond 0.03612 ( 278) hydrogen bonds : angle 5.94802 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8565 (p0) cc_final: 0.8173 (p0) REVERT: A 176 GLU cc_start: 0.8223 (pm20) cc_final: 0.7532 (pm20) REVERT: A 238 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7061 (ptt180) REVERT: A 412 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6246 (mt) REVERT: A 478 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7828 (ttm-80) REVERT: A 488 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6948 (mt-10) REVERT: B 21 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7653 (pp) REVERT: B 253 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7947 (pt) REVERT: B 322 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: B 432 PHE cc_start: 0.8545 (m-80) cc_final: 0.8325 (m-80) REVERT: C 148 MET cc_start: 0.8704 (ttm) cc_final: 0.8438 (ttm) REVERT: C 392 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.5684 (ttt-90) REVERT: C 433 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7634 (ttm170) outliers start: 32 outliers final: 19 residues processed: 146 average time/residue: 0.6857 time to fit residues: 108.3335 Evaluate side-chains 148 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 122 optimal weight: 0.0040 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 140 GLN B 175 GLN C 526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.211494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.196195 restraints weight = 11066.881| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 0.66 r_work: 0.3889 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12116 Z= 0.099 Angle : 0.589 7.451 16614 Z= 0.305 Chirality : 0.045 0.138 1891 Planarity : 0.006 0.057 2176 Dihedral : 5.614 42.143 1661 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.20 % Allowed : 13.14 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.20), residues: 1528 helix: -1.47 (0.64), residues: 57 sheet: -0.23 (0.24), residues: 418 loop : -1.57 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.012 0.001 TYR A 217 PHE 0.013 0.001 PHE B 355 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00223 (12116) covalent geometry : angle 0.58948 (16614) hydrogen bonds : bond 0.03053 ( 278) hydrogen bonds : angle 5.72928 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8313 (p0) cc_final: 0.8106 (p0) REVERT: A 176 GLU cc_start: 0.8102 (pm20) cc_final: 0.7535 (pm20) REVERT: A 238 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7055 (ptt180) REVERT: A 478 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7837 (ttm-80) REVERT: A 488 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6823 (mt-10) REVERT: B 253 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7873 (pt) REVERT: B 315 SER cc_start: 0.7566 (t) cc_final: 0.7312 (m) REVERT: B 322 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: B 432 PHE cc_start: 0.8508 (m-80) cc_final: 0.8266 (m-80) REVERT: C 148 MET cc_start: 0.8664 (ttm) cc_final: 0.8405 (ttm) outliers start: 28 outliers final: 14 residues processed: 147 average time/residue: 0.7262 time to fit residues: 114.6297 Evaluate side-chains 139 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.208161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.192479 restraints weight = 11079.757| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.63 r_work: 0.3853 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12116 Z= 0.185 Angle : 0.728 11.412 16614 Z= 0.375 Chirality : 0.050 0.247 1891 Planarity : 0.007 0.063 2176 Dihedral : 6.053 46.577 1659 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.36 % Allowed : 13.85 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.19), residues: 1528 helix: -1.75 (0.63), residues: 56 sheet: -0.30 (0.25), residues: 393 loop : -1.61 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 433 TYR 0.023 0.002 TYR A 217 PHE 0.035 0.002 PHE C 199 TRP 0.012 0.002 TRP A 520 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00450 (12116) covalent geometry : angle 0.72805 (16614) hydrogen bonds : bond 0.03915 ( 278) hydrogen bonds : angle 5.93743 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8256 (pm20) cc_final: 0.7585 (pm20) REVERT: A 238 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7069 (ptt180) REVERT: A 478 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7868 (ttm-80) REVERT: A 488 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 21 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 322 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: B 432 PHE cc_start: 0.8605 (m-80) cc_final: 0.8390 (m-80) REVERT: C 148 MET cc_start: 0.8809 (ttm) cc_final: 0.8548 (ttm) REVERT: C 392 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.5700 (ttt-90) REVERT: C 464 ASN cc_start: 0.9025 (m110) cc_final: 0.8779 (m110) outliers start: 30 outliers final: 21 residues processed: 145 average time/residue: 0.7142 time to fit residues: 111.7229 Evaluate side-chains 148 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 40.0000 chunk 13 optimal weight: 0.0060 chunk 116 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN C 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.209109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.193774 restraints weight = 11163.323| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 0.67 r_work: 0.3864 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12116 Z= 0.131 Angle : 0.646 7.851 16614 Z= 0.333 Chirality : 0.047 0.150 1891 Planarity : 0.006 0.062 2176 Dihedral : 5.815 44.786 1659 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.05 % Allowed : 14.24 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.20), residues: 1528 helix: -1.58 (0.64), residues: 56 sheet: -0.25 (0.24), residues: 413 loop : -1.53 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.018 0.001 TYR A 217 PHE 0.025 0.002 PHE C 199 TRP 0.010 0.001 TRP B 520 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00308 (12116) covalent geometry : angle 0.64602 (16614) hydrogen bonds : bond 0.03455 ( 278) hydrogen bonds : angle 5.82044 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8531 (p0) cc_final: 0.8199 (p0) REVERT: A 176 GLU cc_start: 0.8220 (pm20) cc_final: 0.7553 (pm20) REVERT: A 238 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7043 (ptt180) REVERT: A 478 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7843 (ttm-80) REVERT: A 488 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 21 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7566 (pp) REVERT: B 322 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7657 (mtm-85) REVERT: C 148 MET cc_start: 0.8688 (ttm) cc_final: 0.8424 (ttm) REVERT: C 392 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5668 (ttt-90) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.6689 time to fit residues: 101.2233 Evaluate side-chains 135 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 106 optimal weight: 0.0370 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.208273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.193713 restraints weight = 11020.866| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 0.55 r_work: 0.3867 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12116 Z= 0.171 Angle : 0.710 10.599 16614 Z= 0.365 Chirality : 0.049 0.215 1891 Planarity : 0.007 0.065 2176 Dihedral : 6.022 46.217 1659 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.12 % Allowed : 14.63 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.20), residues: 1528 helix: -1.70 (0.63), residues: 56 sheet: -0.24 (0.24), residues: 405 loop : -1.58 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 238 TYR 0.021 0.002 TYR A 217 PHE 0.032 0.002 PHE C 199 TRP 0.023 0.002 TRP A 520 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00412 (12116) covalent geometry : angle 0.71038 (16614) hydrogen bonds : bond 0.03829 ( 278) hydrogen bonds : angle 5.89619 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8242 (pm20) cc_final: 0.7568 (pm20) REVERT: A 238 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7045 (ptt180) REVERT: A 274 THR cc_start: 0.8764 (t) cc_final: 0.8427 (t) REVERT: A 478 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7855 (ttm-80) REVERT: A 488 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7050 (mt-10) REVERT: B 21 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7509 (pp) REVERT: B 322 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: C 392 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.5711 (ttt-90) REVERT: C 464 ASN cc_start: 0.9036 (m110) cc_final: 0.8789 (m110) outliers start: 27 outliers final: 19 residues processed: 139 average time/residue: 0.7195 time to fit residues: 107.7694 Evaluate side-chains 138 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.211072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.196576 restraints weight = 11151.464| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 0.56 r_work: 0.3896 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12116 Z= 0.101 Angle : 0.594 8.000 16614 Z= 0.305 Chirality : 0.045 0.136 1891 Planarity : 0.006 0.061 2176 Dihedral : 5.515 42.506 1659 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.97 % Allowed : 15.03 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.20), residues: 1528 helix: -1.33 (0.64), residues: 56 sheet: -0.11 (0.25), residues: 407 loop : -1.42 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 238 TYR 0.013 0.001 TYR A 250 PHE 0.015 0.001 PHE C 199 TRP 0.011 0.001 TRP A 520 HIS 0.003 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00230 (12116) covalent geometry : angle 0.59441 (16614) hydrogen bonds : bond 0.03092 ( 278) hydrogen bonds : angle 5.67381 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8319 (p0) cc_final: 0.8113 (p0) REVERT: A 176 GLU cc_start: 0.8159 (pm20) cc_final: 0.7621 (pm20) REVERT: A 238 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7055 (ptt180) REVERT: A 274 THR cc_start: 0.8659 (t) cc_final: 0.8302 (t) REVERT: A 478 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7850 (ttm-80) REVERT: B 322 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: C 235 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 433 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7722 (ttm170) outliers start: 25 outliers final: 20 residues processed: 138 average time/residue: 0.7336 time to fit residues: 108.9921 Evaluate side-chains 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN B 140 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.208254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.192628 restraints weight = 11024.935| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 0.66 r_work: 0.3848 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12116 Z= 0.180 Angle : 0.722 10.685 16614 Z= 0.371 Chirality : 0.049 0.186 1891 Planarity : 0.007 0.063 2176 Dihedral : 5.957 46.598 1659 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.12 % Allowed : 14.95 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.20), residues: 1528 helix: -1.67 (0.63), residues: 56 sheet: -0.22 (0.25), residues: 393 loop : -1.50 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 166 TYR 0.022 0.002 TYR A 217 PHE 0.033 0.002 PHE C 199 TRP 0.041 0.002 TRP A 520 HIS 0.004 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00437 (12116) covalent geometry : angle 0.72227 (16614) hydrogen bonds : bond 0.03852 ( 278) hydrogen bonds : angle 5.85718 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.34 seconds wall clock time: 74 minutes 49.83 seconds (4489.83 seconds total)