Starting phenix.real_space_refine on Sat Jan 18 09:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv3_42604/01_2025/8uv3_42604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv3_42604/01_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_42604/01_2025/8uv3_42604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv3_42604/01_2025/8uv3_42604.map" model { file = "/net/cci-nas-00/data/ceres_data/8uv3_42604/01_2025/8uv3_42604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv3_42604/01_2025/8uv3_42604.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.91, per 1000 atoms: 0.82 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.38 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: 3.62 Time building geometry restraints manager: 3.06 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: 9.000 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.400 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- 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= 0.658 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.004 TRP B 102 HIS 0.008 0.002 HIS B 94 PHE 0.056 0.004 PHE C 199 TYR 0.040 0.003 TYR C 217 ARG 0.010 0.001 ARG C 166 *********************** 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 : 1.333 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: 1.4791 time to fit residues: 248.2531 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 : 1.325 ------------------------------------------------------------------------------- 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 128 optimal weight: 50.0000 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 61 GLN C 105 ASN C 270 HIS C 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.212544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.202086 restraints weight = 11075.399| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 0.50 r_work: 0.3973 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 1.49 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12116 Z= 0.155 Angle : 0.617 7.510 16614 Z= 0.326 Chirality : 0.045 0.147 1891 Planarity : 0.006 0.059 2176 Dihedral : 6.130 42.656 1665 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.42 % Allowed : 9.52 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1528 helix: -3.19 (0.50), residues: 56 sheet: -0.78 (0.24), residues: 417 loop : -2.22 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.003 0.001 HIS A 270 PHE 0.019 0.001 PHE B 355 TYR 0.013 0.001 TYR A 250 ARG 0.003 0.000 ARG A 72 *********************** 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 160 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 274 THR cc_start: 0.8772 (t) cc_final: 0.8420 (t) REVERT: A 488 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 21 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7252 (pp) REVERT: B 22 VAL cc_start: 0.7249 (m) cc_final: 0.7024 (m) REVERT: B 322 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: C 148 MET cc_start: 0.8504 (ttm) cc_final: 0.8281 (ttm) REVERT: C 229 MET cc_start: 0.8518 (tpt) cc_final: 0.7706 (tpt) REVERT: C 512 ASP cc_start: 0.8101 (p0) cc_final: 0.7798 (p0) outliers start: 18 outliers final: 7 residues processed: 155 average time/residue: 1.4449 time to fit residues: 241.9585 Evaluate side-chains 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 514 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 281 ILE 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 22 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 81 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 173 GLN B 140 GLN B 175 GLN C 49 ASN C 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.207597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.192598 restraints weight = 11140.037| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 0.62 r_work: 0.3845 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12116 Z= 0.304 Angle : 0.753 12.685 16614 Z= 0.391 Chirality : 0.050 0.191 1891 Planarity : 0.007 0.067 2176 Dihedral : 6.411 46.392 1660 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 2.12 % Allowed : 12.12 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1528 helix: -2.65 (0.56), residues: 57 sheet: -0.58 (0.24), residues: 421 loop : -2.02 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 520 HIS 0.005 0.001 HIS A 270 PHE 0.037 0.002 PHE C 199 TYR 0.021 0.002 TYR A 217 ARG 0.004 0.001 ARG A 165 *********************** 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 155 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8982 (t) REVERT: A 173 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.6616 (mp-120) REVERT: A 175 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: A 176 GLU cc_start: 0.8357 (pm20) cc_final: 0.7524 (pm20) REVERT: A 238 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7252 (ptt180) REVERT: A 274 THR cc_start: 0.8820 (t) cc_final: 0.8484 (t) REVERT: A 488 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 21 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 322 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7612 (mtm-85) REVERT: C 148 MET cc_start: 0.8803 (ttm) cc_final: 0.8534 (ttm) REVERT: C 235 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8051 (mm) REVERT: C 392 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.5554 (ttt-90) REVERT: C 512 ASP cc_start: 0.8096 (p0) cc_final: 0.7841 (p0) outliers start: 27 outliers final: 10 residues processed: 140 average time/residue: 1.4603 time to fit residues: 220.4308 Evaluate side-chains 142 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 GLN 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 219 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL 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 21 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 64 optimal weight: 0.0670 chunk 99 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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 C 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.207765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.192488 restraints weight = 11074.995| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.63 r_work: 0.3845 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12116 Z= 0.282 Angle : 0.733 12.065 16614 Z= 0.380 Chirality : 0.049 0.176 1891 Planarity : 0.007 0.069 2176 Dihedral : 6.376 46.239 1660 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.75 % Allowed : 12.43 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1528 helix: -2.34 (0.59), residues: 57 sheet: -0.47 (0.24), residues: 421 loop : -1.92 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 520 HIS 0.004 0.001 HIS C 170 PHE 0.035 0.002 PHE C 199 TYR 0.022 0.002 TYR C 217 ARG 0.004 0.000 ARG A 72 *********************** 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 164 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8330 (pm20) cc_final: 0.7588 (pm20) REVERT: A 238 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7190 (ptt180) REVERT: A 274 THR cc_start: 0.8813 (t) cc_final: 0.8472 (t) REVERT: A 478 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7885 (ttm-80) REVERT: A 488 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 21 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7753 (pp) REVERT: B 238 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7503 (ptp-170) REVERT: B 322 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: C 148 MET cc_start: 0.8754 (ttm) cc_final: 0.8479 (ttm) REVERT: C 235 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (mm) REVERT: C 392 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.5562 (ttt-90) REVERT: C 464 ASN cc_start: 0.9051 (m110) cc_final: 0.8766 (m110) REVERT: C 512 ASP cc_start: 0.8047 (p0) cc_final: 0.7828 (p0) REVERT: C 516 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 35 outliers final: 14 residues processed: 149 average time/residue: 1.4368 time to fit residues: 230.7358 Evaluate side-chains 139 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 315 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL 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 Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 40.0000 chunk 70 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 90 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.208486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.192972 restraints weight = 11024.841| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 0.66 r_work: 0.3854 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12116 Z= 0.242 Angle : 0.694 10.699 16614 Z= 0.360 Chirality : 0.048 0.160 1891 Planarity : 0.007 0.067 2176 Dihedral : 6.220 45.622 1660 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.83 % Allowed : 12.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.19), residues: 1528 helix: -2.07 (0.61), residues: 57 sheet: -0.41 (0.24), residues: 421 loop : -1.81 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 520 HIS 0.004 0.001 HIS A 270 PHE 0.030 0.002 PHE C 199 TYR 0.020 0.002 TYR A 217 ARG 0.003 0.000 ARG A 72 *********************** 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 159 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8393 (pm20) cc_final: 0.7756 (pm20) REVERT: A 274 THR cc_start: 0.8807 (t) cc_final: 0.8468 (t) REVERT: A 478 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7889 (ttm-80) REVERT: A 488 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 21 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7699 (pp) REVERT: B 253 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8082 (pt) REVERT: B 322 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7617 (mtm-85) REVERT: C 148 MET cc_start: 0.8789 (ttm) cc_final: 0.8517 (ttm) REVERT: C 392 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.5583 (ttt-90) outliers start: 36 outliers final: 19 residues processed: 147 average time/residue: 1.3561 time to fit residues: 216.1554 Evaluate side-chains 140 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 436 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 21 LEU 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 315 SER 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 468 VAL Chi-restraints excluded: chain C residue 512 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 0.0980 chunk 52 optimal weight: 0.0170 chunk 76 optimal weight: 8.9990 chunk 51 optimal weight: 0.0570 chunk 11 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 34 optimal weight: 0.0050 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.215431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.200808 restraints weight = 11332.468| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 0.62 r_work: 0.3939 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12116 Z= 0.124 Angle : 0.548 7.411 16614 Z= 0.282 Chirality : 0.044 0.141 1891 Planarity : 0.006 0.057 2176 Dihedral : 5.192 39.425 1660 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.42 % Allowed : 14.32 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1528 helix: -1.48 (0.62), residues: 58 sheet: -0.29 (0.24), residues: 422 loop : -1.43 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS B 94 PHE 0.013 0.001 PHE B 355 TYR 0.012 0.001 TYR B 99 ARG 0.002 0.000 ARG A 72 *********************** 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 150 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8211 (pm20) cc_final: 0.6816 (tt0) REVERT: A 238 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6957 (ptt180) REVERT: A 478 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7695 (ttm-80) REVERT: A 488 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 322 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7632 (mtm-85) REVERT: C 148 MET cc_start: 0.8604 (ttm) cc_final: 0.8347 (ttm) outliers start: 18 outliers final: 8 residues processed: 144 average time/residue: 1.4061 time to fit residues: 218.4930 Evaluate side-chains 130 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 238 ARG Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL 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 96 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 chunk 20 optimal weight: 0.0010 chunk 59 optimal weight: 6.9990 overall best weight: 2.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 236 GLN A 270 HIS A 402 GLN B 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.210920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.195769 restraints weight = 11113.127| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 0.67 r_work: 0.3884 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12116 Z= 0.183 Angle : 0.622 7.945 16614 Z= 0.319 Chirality : 0.046 0.157 1891 Planarity : 0.006 0.057 2176 Dihedral : 5.433 43.402 1658 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.65 % Allowed : 15.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1528 helix: -1.26 (0.64), residues: 56 sheet: -0.20 (0.24), residues: 419 loop : -1.45 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS C 170 PHE 0.024 0.002 PHE C 199 TYR 0.017 0.001 TYR C 317 ARG 0.003 0.000 ARG A 392 *********************** 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 145 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8387 (pm20) cc_final: 0.7474 (pt0) REVERT: A 238 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7054 (ptt180) REVERT: A 478 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7800 (ttm-80) REVERT: A 488 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 21 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7526 (pp) REVERT: B 22 VAL cc_start: 0.7452 (m) cc_final: 0.7083 (m) REVERT: B 322 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7645 (mtm-85) REVERT: C 148 MET cc_start: 0.8686 (ttm) cc_final: 0.8429 (ttm) REVERT: C 433 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7991 (ttm170) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 1.4305 time to fit residues: 213.2095 Evaluate side-chains 132 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 C residue 77 GLU Chi-restraints excluded: chain C residue 103 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 407 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 142 optimal weight: 40.0000 chunk 100 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 263 GLN A 270 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.210517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.199707 restraints weight = 11201.158| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 0.50 r_work: 0.3901 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.3782 rms_B_bonded: 2.43 restraints_weight: 0.1250 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12116 Z= 0.187 Angle : 0.627 7.735 16614 Z= 0.321 Chirality : 0.046 0.157 1891 Planarity : 0.006 0.058 2176 Dihedral : 5.494 43.631 1658 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.42 % Allowed : 15.74 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1528 helix: -1.27 (0.64), residues: 56 sheet: -0.22 (0.24), residues: 417 loop : -1.42 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 520 HIS 0.003 0.001 HIS C 170 PHE 0.023 0.001 PHE C 199 TYR 0.017 0.001 TYR A 217 ARG 0.003 0.000 ARG A 392 *********************** 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 137 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8404 (pm20) cc_final: 0.7037 (tt0) REVERT: A 238 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7083 (ptt180) REVERT: A 478 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7823 (ttm-80) REVERT: A 488 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 21 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7537 (pp) REVERT: B 322 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: C 148 MET cc_start: 0.8744 (ttm) cc_final: 0.8490 (ttm) REVERT: C 433 ARG cc_start: 0.8249 (ttm170) cc_final: 0.8046 (ttm170) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 1.4648 time to fit residues: 208.3722 Evaluate side-chains 134 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 173 GLN 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 304 VAL Chi-restraints excluded: chain B residue 353 THR 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 359 LEU Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.210651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.195969 restraints weight = 11122.372| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 0.63 r_work: 0.3888 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2080 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= 0.178 Angle : 0.619 7.851 16614 Z= 0.317 Chirality : 0.046 0.151 1891 Planarity : 0.006 0.058 2176 Dihedral : 5.466 43.526 1658 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.49 % Allowed : 15.89 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1528 helix: -1.25 (0.64), residues: 56 sheet: -0.18 (0.25), residues: 411 loop : -1.38 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.002 0.001 HIS C 170 PHE 0.021 0.001 PHE C 199 TYR 0.016 0.001 TYR A 217 ARG 0.003 0.000 ARG A 392 *********************** 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 138 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8362 (pm20) cc_final: 0.7008 (tt0) REVERT: A 238 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7014 (ptt180) REVERT: A 478 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7779 (ttm-80) REVERT: A 488 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 21 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7488 (pp) REVERT: B 322 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: C 148 MET cc_start: 0.8628 (ttm) cc_final: 0.8368 (ttm) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 1.4420 time to fit residues: 206.8810 Evaluate side-chains 136 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 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 407 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 0.0870 chunk 67 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 50.0000 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 149 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 270 HIS B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.210780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.197027 restraints weight = 11134.846| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 0.55 r_work: 0.3896 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12116 Z= 0.164 Angle : 0.606 7.709 16614 Z= 0.310 Chirality : 0.045 0.141 1891 Planarity : 0.006 0.057 2176 Dihedral : 5.399 42.814 1658 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.34 % Allowed : 16.13 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1528 helix: -1.16 (0.64), residues: 56 sheet: -0.13 (0.25), residues: 413 loop : -1.36 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS C 170 PHE 0.018 0.001 PHE C 199 TYR 0.015 0.001 TYR C 317 ARG 0.003 0.000 ARG A 392 ********************** 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 133 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8337 (pm20) cc_final: 0.6996 (tt0) REVERT: A 238 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6886 (ptt180) REVERT: A 478 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7662 (ttm-80) REVERT: A 488 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 21 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7401 (pp) REVERT: B 322 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: C 148 MET cc_start: 0.8607 (ttm) cc_final: 0.8340 (ttm) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 1.4813 time to fit residues: 205.8298 Evaluate side-chains 129 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 407 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 270 HIS B 140 GLN B 175 GLN C 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.207382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.191955 restraints weight = 11038.159| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.65 r_work: 0.3839 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12116 Z= 0.384 Angle : 0.804 12.581 16614 Z= 0.414 Chirality : 0.053 0.294 1891 Planarity : 0.007 0.061 2176 Dihedral : 6.158 47.649 1658 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 1.73 % Allowed : 15.74 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1528 helix: -1.82 (0.62), residues: 56 sheet: -0.28 (0.25), residues: 400 loop : -1.54 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 520 HIS 0.004 0.002 HIS B 94 PHE 0.042 0.003 PHE C 199 TYR 0.026 0.002 TYR C 217 ARG 0.005 0.001 ARG C 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8291.97 seconds wall clock time: 147 minutes 40.85 seconds (8860.85 seconds total)