Starting phenix.real_space_refine on Sat Jul 4 04:15:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.map" model { file = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dpt_30810/07_2026/7dpt_30810.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 11256 2.51 5 N 3132 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18052 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "B" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "C" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "D" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4384 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {' MG': 4, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' MG': 2, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {' MG': 4, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 104 Unusual residues: {' MG': 2, '5ZL': 1, 'ADP': 1, 'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'DON:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 3.12, per 1000 atoms: 0.17 Number of scatterers: 18052 At special positions: 0 Unit cell: (128.26, 98.58, 128.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 36 15.00 Mg 12 11.99 O 3528 8.00 N 3132 7.00 C 11256 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 580.9 milliseconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 20 sheets defined 50.1% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 46 through 50 removed outlier: 4.400A pdb=" N THR A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.981A pdb=" N HIS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.059A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 112 through 130 removed outlier: 7.339A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 169 removed outlier: 4.281A pdb=" N PHE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 250 through 258 removed outlier: 4.345A pdb=" N LEU A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.630A pdb=" N ARG A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 279 " --> pdb=" O MET A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.648A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.620A pdb=" N ALA A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.840A pdb=" N LEU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 348' Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.729A pdb=" N LYS A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 437 through 440 removed outlier: 3.670A pdb=" N HIS A 440 " --> pdb=" O PRO A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 488 through 494 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.708A pdb=" N TYR A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 530' Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 46 through 50 removed outlier: 4.400A pdb=" N THR B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.981A pdb=" N HIS B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.059A pdb=" N GLY B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 112 through 130 removed outlier: 7.339A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 155 through 169 removed outlier: 4.281A pdb=" N PHE B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 250 through 258 removed outlier: 4.345A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.630A pdb=" N ARG B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.648A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 314 through 328 removed outlier: 3.620A pdb=" N ALA B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.840A pdb=" N LEU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 348' Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.729A pdb=" N LYS B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 437 through 440 removed outlier: 3.670A pdb=" N HIS B 440 " --> pdb=" O PRO B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 437 through 440' Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 526 through 530 removed outlier: 3.708A pdb=" N TYR B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 530 " --> pdb=" O PRO B 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 530' Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 4.400A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.981A pdb=" N HIS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.059A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.339A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 155 through 169 removed outlier: 4.281A pdb=" N PHE C 167 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 250 through 258 removed outlier: 4.345A pdb=" N LEU C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.630A pdb=" N ARG C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 279 " --> pdb=" O MET C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 274 through 279' Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.648A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 314 through 328 removed outlier: 3.620A pdb=" N ALA C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.840A pdb=" N LEU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 343 through 348' Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.729A pdb=" N LYS C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 437 through 440 removed outlier: 3.670A pdb=" N HIS C 440 " --> pdb=" O PRO C 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.708A pdb=" N TYR C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 530 " --> pdb=" O PRO C 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 526 through 530' Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'D' and resid 15 through 30 Processing helix chain 'D' and resid 46 through 50 removed outlier: 4.400A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.981A pdb=" N HIS D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.059A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 112 through 130 removed outlier: 7.339A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 155 through 169 removed outlier: 4.281A pdb=" N PHE D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 250 through 258 removed outlier: 4.345A pdb=" N LEU D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.630A pdb=" N ARG D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 279 " --> pdb=" O MET D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 279' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.648A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 314 through 328 removed outlier: 3.620A pdb=" N ALA D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.840A pdb=" N LEU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 343 through 348' Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 377 through 391 removed outlier: 3.729A pdb=" N LYS D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 437 through 440 removed outlier: 3.670A pdb=" N HIS D 440 " --> pdb=" O PRO D 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 437 through 440' Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 526 through 530 removed outlier: 3.708A pdb=" N TYR D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 530' Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 550 through 556 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.429A pdb=" N GLY A 8 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 3 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA A 177 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 5 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 179 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 7 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU A 181 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N LEU A 212 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 176 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 214 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS A 178 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG A 216 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER A 180 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 217 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 338 removed outlier: 6.917A pdb=" N CYS A 300 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU A 368 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR A 523 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 397 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 522 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET A 509 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR A 502 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 511 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 500 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.897A pdb=" N ASN A 420 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP A 435 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL A 474 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.429A pdb=" N GLY B 8 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 3 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA B 177 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 5 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 179 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 7 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU B 181 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N LEU B 212 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 176 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL B 214 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS B 178 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG B 216 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER B 180 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 217 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 338 removed outlier: 6.917A pdb=" N CYS B 300 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU B 368 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR B 523 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 397 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 522 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET B 509 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 502 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 511 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 500 " --> pdb=" O ILE B 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 421 removed outlier: 6.897A pdb=" N ASN B 420 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP B 435 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL B 474 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 89 removed outlier: 4.429A pdb=" N GLY C 8 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 3 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 177 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 5 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 179 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR C 7 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU C 181 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N LEU C 212 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 176 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 214 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS C 178 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG C 216 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 180 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 217 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 332 through 338 removed outlier: 6.917A pdb=" N CYS C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU C 368 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR C 523 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY C 397 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 522 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET C 509 " --> pdb=" O THR C 502 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 500 " --> pdb=" O ILE C 511 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.897A pdb=" N ASN C 420 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP C 435 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL C 474 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 89 removed outlier: 4.429A pdb=" N GLY D 8 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR D 3 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA D 177 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU D 5 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL D 179 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 7 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU D 181 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N LEU D 212 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 176 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL D 214 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS D 178 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG D 216 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER D 180 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 217 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 338 removed outlier: 6.917A pdb=" N CYS D 300 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 368 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR D 523 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY D 397 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 522 " --> pdb=" O ILE D 512 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET D 509 " --> pdb=" O THR D 502 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR D 502 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 500 " --> pdb=" O ILE D 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 420 through 421 removed outlier: 6.897A pdb=" N ASN D 420 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP D 435 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 449 through 456 removed outlier: 3.675A pdb=" N VAL D 474 " --> pdb=" O THR D 455 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2172 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: 3.24 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5880 1.34 - 1.46: 2644 1.46 - 1.57: 9608 1.57 - 1.69: 60 1.69 - 1.81: 124 Bond restraints: 18316 Sorted by residual: bond pdb=" O12 5ZL D 706 " pdb=" P30 5ZL D 706 " ideal model delta sigma weight residual 1.845 1.633 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O12 5ZL B 706 " pdb=" P30 5ZL B 706 " ideal model delta sigma weight residual 1.845 1.633 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O12 5ZL C 708 " pdb=" P30 5ZL C 708 " ideal model delta sigma weight residual 1.845 1.633 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O12 5ZL A 708 " pdb=" P30 5ZL A 708 " ideal model delta sigma weight residual 1.845 1.633 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C DON A 702 " pdb=" O DON A 702 " ideal model delta sigma weight residual 1.231 1.357 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 18311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 24650 3.78 - 7.55: 120 7.55 - 11.33: 54 11.33 - 15.10: 40 15.10 - 18.88: 12 Bond angle restraints: 24876 Sorted by residual: angle pdb=" O10 5ZL C 708 " pdb=" P01 5ZL C 708 " pdb=" O11 5ZL C 708 " ideal model delta sigma weight residual 120.19 101.31 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O10 5ZL A 708 " pdb=" P01 5ZL A 708 " pdb=" O11 5ZL A 708 " ideal model delta sigma weight residual 120.19 101.31 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O10 5ZL B 706 " pdb=" P01 5ZL B 706 " pdb=" O11 5ZL B 706 " ideal model delta sigma weight residual 120.19 101.31 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O10 5ZL D 706 " pdb=" P01 5ZL D 706 " pdb=" O11 5ZL D 706 " ideal model delta sigma weight residual 120.19 101.31 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O14 5ZL D 706 " pdb=" P02 5ZL D 706 " pdb=" O15 5ZL D 706 " ideal model delta sigma weight residual 118.15 100.61 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 24871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 10448 31.02 - 62.03: 528 62.03 - 93.05: 66 93.05 - 124.06: 4 124.06 - 155.08: 10 Dihedral angle restraints: 11056 sinusoidal: 4664 harmonic: 6392 Sorted by residual: dihedral pdb=" O2A ADP D 703 " pdb=" O3A ADP D 703 " pdb=" PA ADP D 703 " pdb=" PB ADP D 703 " ideal model delta sinusoidal sigma weight residual -60.00 95.08 -155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP C 703 " pdb=" O3A ADP C 703 " pdb=" PA ADP C 703 " pdb=" PB ADP C 703 " ideal model delta sinusoidal sigma weight residual -60.00 95.08 -155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP C 703 " pdb=" O5' ADP C 703 " pdb=" PA ADP C 703 " pdb=" O2A ADP C 703 " ideal model delta sinusoidal sigma weight residual 300.00 162.88 137.12 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 11053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1836 0.041 - 0.082: 668 0.082 - 0.123: 248 0.123 - 0.164: 20 0.164 - 0.206: 8 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C21 5ZL C 708 " pdb=" C22 5ZL C 708 " pdb=" C23 5ZL C 708 " pdb=" O05 5ZL C 708 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C21 5ZL A 708 " pdb=" C22 5ZL A 708 " pdb=" C23 5ZL A 708 " pdb=" O05 5ZL A 708 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C21 5ZL B 706 " pdb=" C22 5ZL B 706 " pdb=" C23 5ZL B 706 " pdb=" O05 5ZL B 706 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2777 not shown) Planarity restraints: 3156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 369 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 370 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 369 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 370 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 369 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 370 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " -0.025 5.00e-02 4.00e+02 ... (remaining 3153 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.14: 24 2.14 - 2.83: 5476 2.83 - 3.52: 24300 3.52 - 4.21: 45520 4.21 - 4.90: 79144 Nonbonded interactions: 154464 Sorted by model distance: nonbonded pdb=" OD2 ASP C 70 " pdb=" O HOH C 801 " model vdw 1.445 3.040 nonbonded pdb=" OD2 ASP A 70 " pdb=" O HOH A 801 " model vdw 1.445 3.040 nonbonded pdb=" OD2 ASP B 70 " pdb=" O HOH B 801 " model vdw 1.445 3.040 nonbonded pdb=" OD2 ASP D 70 " pdb=" O HOH D 801 " model vdw 1.445 3.040 nonbonded pdb=" O3B ADP C 703 " pdb=" O HOH C 801 " model vdw 1.833 3.040 ... (remaining 154459 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.100 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.100 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.009 0.212 18320 Z= 0.413 Angle : 1.055 18.879 24876 Z= 0.439 Chirality : 0.048 0.206 2780 Planarity : 0.004 0.045 3156 Dihedral : 18.580 155.078 6960 Min Nonbonded Distance : 1.445 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.23 % Allowed : 17.49 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.15), residues: 2216 helix: -1.94 (0.14), residues: 908 sheet: -0.60 (0.25), residues: 376 loop : -2.60 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 102 TYR 0.013 0.001 TYR D 106 PHE 0.010 0.001 PHE D 162 TRP 0.007 0.001 TRP D 124 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.41 (18316) covalent geometry : angle 1.05496 / 0.44 (24876) hydrogen bonds : bond 0.13418 / 8.77 ( 744) hydrogen bonds : angle 7.11557 / 5.04 ( 2172) Misc. bond : bond 0.00065 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.677 Fit side-chains REVERT: A 219 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7630 (mttm) REVERT: A 287 ASP cc_start: 0.8015 (m-30) cc_final: 0.7666 (m-30) REVERT: A 550 ARG cc_start: 0.7313 (mmt-90) cc_final: 0.7060 (mmp80) REVERT: B 263 GLU cc_start: 0.7741 (mp0) cc_final: 0.7525 (mm-30) REVERT: B 276 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7361 (m) REVERT: B 550 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.7034 (mmp80) REVERT: C 263 GLU cc_start: 0.7757 (mp0) cc_final: 0.7503 (mm-30) REVERT: C 276 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7343 (m) REVERT: C 287 ASP cc_start: 0.8006 (m-30) cc_final: 0.7671 (m-30) REVERT: C 550 ARG cc_start: 0.7314 (mmt-90) cc_final: 0.7028 (mmp80) REVERT: D 219 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7626 (mttm) REVERT: D 287 ASP cc_start: 0.7993 (m-30) cc_final: 0.7653 (m-30) REVERT: D 550 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.7012 (mmp80) outliers start: 24 outliers final: 0 residues processed: 322 average time/residue: 0.6493 time to fit residues: 229.2640 Evaluate side-chains 247 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain C residue 276 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125834 restraints weight = 18284.920| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.50 r_work: 0.3292 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18320 Z= 0.203 Angle : 0.760 8.659 24876 Z= 0.372 Chirality : 0.050 0.154 2780 Planarity : 0.006 0.048 3156 Dihedral : 13.410 151.894 2618 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 3.65 % Allowed : 19.96 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2216 helix: -0.09 (0.16), residues: 924 sheet: -0.07 (0.24), residues: 376 loop : -1.55 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 481 TYR 0.014 0.002 TYR B 106 PHE 0.021 0.002 PHE A 162 TRP 0.014 0.002 TRP C 124 HIS 0.006 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (18316) covalent geometry : angle 0.76022 / 0.37 (24876) hydrogen bonds : bond 0.04608 / 3.04 ( 744) hydrogen bonds : angle 5.24051 / 3.71 ( 2172) Misc. bond : bond 0.00004 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8045 (mttt) REVERT: A 275 MET cc_start: 0.7143 (mmm) cc_final: 0.6744 (mmt) REVERT: A 287 ASP cc_start: 0.8305 (m-30) cc_final: 0.7967 (m-30) REVERT: A 363 ASP cc_start: 0.7297 (p0) cc_final: 0.7063 (p0) REVERT: A 411 ARG cc_start: 0.6554 (ptp-170) cc_final: 0.6252 (ptp-170) REVERT: A 550 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.7051 (mmp80) REVERT: B 263 GLU cc_start: 0.8301 (mp0) cc_final: 0.8057 (mm-30) REVERT: B 363 ASP cc_start: 0.7254 (p0) cc_final: 0.7021 (p0) REVERT: B 550 ARG cc_start: 0.7276 (mmt-90) cc_final: 0.7017 (mmp80) REVERT: C 287 ASP cc_start: 0.8313 (m-30) cc_final: 0.8018 (m-30) REVERT: C 293 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: C 363 ASP cc_start: 0.7241 (p0) cc_final: 0.7026 (p0) REVERT: C 411 ARG cc_start: 0.6561 (ptp-170) cc_final: 0.6259 (ptp-170) REVERT: D 219 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8058 (mttt) REVERT: D 275 MET cc_start: 0.7003 (mmm) cc_final: 0.6592 (mmt) REVERT: D 287 ASP cc_start: 0.8327 (m-30) cc_final: 0.7982 (m-30) REVERT: D 363 ASP cc_start: 0.7269 (p0) cc_final: 0.7059 (p0) REVERT: D 411 ARG cc_start: 0.6545 (ptp-170) cc_final: 0.6246 (ptp-170) REVERT: D 550 ARG cc_start: 0.7307 (mmt-90) cc_final: 0.7031 (mmp80) outliers start: 71 outliers final: 26 residues processed: 293 average time/residue: 0.5814 time to fit residues: 189.4177 Evaluate side-chains 250 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 473 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 150 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129873 restraints weight = 18523.090| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.51 r_work: 0.3345 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18320 Z= 0.120 Angle : 0.628 7.843 24876 Z= 0.305 Chirality : 0.045 0.125 2780 Planarity : 0.004 0.045 3156 Dihedral : 12.481 163.012 2616 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.34 % Favored : 96.48 % Rotamer: Outliers : 2.73 % Allowed : 19.70 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2216 helix: 0.73 (0.17), residues: 924 sheet: 0.35 (0.24), residues: 372 loop : -1.22 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 481 TYR 0.012 0.001 TYR C 42 PHE 0.009 0.001 PHE A 162 TRP 0.008 0.001 TRP A 124 HIS 0.003 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18316) covalent geometry : angle 0.62833 / 0.31 (24876) hydrogen bonds : bond 0.03445 / 2.28 ( 744) hydrogen bonds : angle 4.73261 / 3.35 ( 2172) Misc. bond : bond 0.00005 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: A 219 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8025 (mttt) REVERT: A 287 ASP cc_start: 0.8261 (m-30) cc_final: 0.7961 (m-30) REVERT: A 363 ASP cc_start: 0.6982 (p0) cc_final: 0.6781 (p0) REVERT: A 505 ASP cc_start: 0.7264 (t70) cc_final: 0.6847 (m-30) REVERT: A 550 ARG cc_start: 0.7227 (mmt-90) cc_final: 0.7007 (mmp80) REVERT: B 57 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: B 263 GLU cc_start: 0.8233 (mp0) cc_final: 0.7946 (mm-30) REVERT: B 363 ASP cc_start: 0.6932 (p0) cc_final: 0.6731 (p0) REVERT: B 448 MET cc_start: 0.7810 (mtm) cc_final: 0.7584 (mtt) REVERT: B 550 ARG cc_start: 0.7244 (mmt-90) cc_final: 0.6988 (mmp80) REVERT: C 57 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: C 287 ASP cc_start: 0.8278 (m-30) cc_final: 0.7991 (m-30) REVERT: C 293 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: D 57 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: D 219 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8016 (mttt) REVERT: D 287 ASP cc_start: 0.8265 (m-30) cc_final: 0.7976 (m-30) REVERT: D 448 MET cc_start: 0.7801 (mtm) cc_final: 0.7575 (mtt) REVERT: D 550 ARG cc_start: 0.7227 (mmt-90) cc_final: 0.6955 (mmp80) outliers start: 53 outliers final: 23 residues processed: 284 average time/residue: 0.6190 time to fit residues: 194.8878 Evaluate side-chains 254 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 193 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 123 optimal weight: 0.0270 chunk 162 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127717 restraints weight = 18565.155| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.50 r_work: 0.3317 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18320 Z= 0.146 Angle : 0.666 7.890 24876 Z= 0.324 Chirality : 0.046 0.135 2780 Planarity : 0.005 0.046 3156 Dihedral : 12.492 169.492 2616 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.15 % Favored : 95.67 % Rotamer: Outliers : 2.98 % Allowed : 19.75 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2216 helix: 1.00 (0.18), residues: 908 sheet: 0.41 (0.24), residues: 376 loop : -0.99 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 508 TYR 0.012 0.001 TYR D 106 PHE 0.016 0.001 PHE B 162 TRP 0.010 0.002 TRP C 358 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (18316) covalent geometry : angle 0.66626 / 0.32 (24876) hydrogen bonds : bond 0.03840 / 2.52 ( 744) hydrogen bonds : angle 4.75170 / 3.36 ( 2172) Misc. bond : bond 0.00002 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 219 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8016 (mttt) REVERT: A 287 ASP cc_start: 0.8287 (m-30) cc_final: 0.7973 (m-30) REVERT: A 363 ASP cc_start: 0.7090 (p0) cc_final: 0.6871 (p0) REVERT: A 379 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: A 550 ARG cc_start: 0.7232 (mmt-90) cc_final: 0.6986 (mmp80) REVERT: B 57 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: B 263 GLU cc_start: 0.8186 (mp0) cc_final: 0.7648 (mm-30) REVERT: B 287 ASP cc_start: 0.8270 (m-30) cc_final: 0.8050 (m-30) REVERT: B 363 ASP cc_start: 0.7084 (p0) cc_final: 0.6877 (p0) REVERT: B 379 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6338 (tt0) REVERT: B 448 MET cc_start: 0.7930 (mtm) cc_final: 0.7720 (mtt) REVERT: B 550 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.6984 (mmp80) REVERT: C 57 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: C 287 ASP cc_start: 0.8299 (m-30) cc_final: 0.8021 (m-30) REVERT: C 379 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6377 (tt0) REVERT: D 57 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: D 219 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8024 (mttt) REVERT: D 287 ASP cc_start: 0.8279 (m-30) cc_final: 0.7981 (m-30) REVERT: D 379 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: D 550 ARG cc_start: 0.7260 (mmt-90) cc_final: 0.6997 (mmp80) outliers start: 58 outliers final: 30 residues processed: 267 average time/residue: 0.6414 time to fit residues: 189.2942 Evaluate side-chains 249 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 96 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131753 restraints weight = 18505.038| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.50 r_work: 0.3370 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18320 Z= 0.108 Angle : 0.609 7.871 24876 Z= 0.294 Chirality : 0.044 0.125 2780 Planarity : 0.004 0.045 3156 Dihedral : 12.156 176.534 2616 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 2.73 % Allowed : 20.37 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2216 helix: 1.38 (0.18), residues: 896 sheet: 0.41 (0.24), residues: 392 loop : -0.92 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 286 TYR 0.012 0.001 TYR C 42 PHE 0.007 0.001 PHE C 23 TRP 0.007 0.001 TRP A 358 HIS 0.002 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (18316) covalent geometry : angle 0.60918 / 0.29 (24876) hydrogen bonds : bond 0.03062 / 2.03 ( 744) hydrogen bonds : angle 4.51480 / 3.19 ( 2172) Misc. bond : bond 0.00004 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 0.712 Fit side-chains REVERT: A 57 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: A 219 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8003 (mttt) REVERT: A 287 ASP cc_start: 0.8239 (m-30) cc_final: 0.7931 (m-30) REVERT: A 379 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6351 (tp30) REVERT: A 550 ARG cc_start: 0.7174 (mmt-90) cc_final: 0.6950 (mmp80) REVERT: B 57 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: B 263 GLU cc_start: 0.8170 (mp0) cc_final: 0.7650 (mm-30) REVERT: B 275 MET cc_start: 0.6923 (mmt) cc_final: 0.6453 (mmt) REVERT: B 287 ASP cc_start: 0.8224 (m-30) cc_final: 0.8013 (m-30) REVERT: B 379 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6239 (tp30) REVERT: B 550 ARG cc_start: 0.7213 (mmt-90) cc_final: 0.6956 (mmp80) REVERT: C 57 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: C 287 ASP cc_start: 0.8278 (m-30) cc_final: 0.7969 (m-30) REVERT: C 379 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6266 (tp30) REVERT: D 57 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: D 219 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8009 (mttt) REVERT: D 287 ASP cc_start: 0.8226 (m-30) cc_final: 0.7935 (m-30) REVERT: D 379 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6231 (tp30) REVERT: D 550 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6889 (mmp80) outliers start: 53 outliers final: 17 residues processed: 275 average time/residue: 0.6564 time to fit residues: 200.6327 Evaluate side-chains 247 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 180 optimal weight: 0.0870 overall best weight: 2.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124694 restraints weight = 18379.374| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.48 r_work: 0.3277 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18320 Z= 0.216 Angle : 0.745 9.266 24876 Z= 0.364 Chirality : 0.049 0.155 2780 Planarity : 0.005 0.048 3156 Dihedral : 12.842 175.483 2616 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.99 % Rotamer: Outliers : 2.98 % Allowed : 20.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2216 helix: 1.11 (0.17), residues: 904 sheet: 0.36 (0.24), residues: 376 loop : -0.93 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 411 TYR 0.014 0.002 TYR A 106 PHE 0.022 0.002 PHE A 162 TRP 0.013 0.002 TRP C 124 HIS 0.009 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (18316) covalent geometry : angle 0.74534 / 0.36 (24876) hydrogen bonds : bond 0.04688 / 3.08 ( 744) hydrogen bonds : angle 4.92537 / 3.47 ( 2172) Misc. bond : bond 0.00019 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.628 Fit side-chains REVERT: A 54 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 57 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: A 219 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7980 (mttt) REVERT: A 287 ASP cc_start: 0.8341 (m-30) cc_final: 0.8010 (m-30) REVERT: A 550 ARG cc_start: 0.7308 (mmt-90) cc_final: 0.7054 (mmp80) REVERT: B 54 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: B 57 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: B 379 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: B 550 ARG cc_start: 0.7294 (mmt-90) cc_final: 0.7025 (mmp80) REVERT: C 54 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 57 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: C 263 GLU cc_start: 0.8220 (mp0) cc_final: 0.7905 (mm-30) REVERT: C 287 ASP cc_start: 0.8344 (m-30) cc_final: 0.8040 (m-30) REVERT: C 379 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: D 54 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: D 57 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: D 219 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7976 (mttt) REVERT: D 287 ASP cc_start: 0.8337 (m-30) cc_final: 0.8029 (m-30) REVERT: D 353 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7670 (mttm) REVERT: D 379 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6440 (tp30) REVERT: D 550 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.7038 (mmp80) outliers start: 58 outliers final: 21 residues processed: 275 average time/residue: 0.6246 time to fit residues: 191.1473 Evaluate side-chains 250 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 193 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129195 restraints weight = 18545.872| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.50 r_work: 0.3341 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18320 Z= 0.120 Angle : 0.632 7.608 24876 Z= 0.308 Chirality : 0.045 0.129 2780 Planarity : 0.004 0.045 3156 Dihedral : 12.333 179.944 2616 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 21.40 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2216 helix: 1.39 (0.18), residues: 892 sheet: 0.25 (0.24), residues: 396 loop : -0.80 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 411 TYR 0.012 0.001 TYR C 42 PHE 0.009 0.001 PHE A 162 TRP 0.008 0.001 TRP C 124 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (18316) covalent geometry : angle 0.63198 / 0.31 (24876) hydrogen bonds : bond 0.03290 / 2.18 ( 744) hydrogen bonds : angle 4.60403 / 3.25 ( 2172) Misc. bond : bond 0.00008 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.731 Fit side-chains REVERT: A 57 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: A 219 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7968 (mttt) REVERT: A 287 ASP cc_start: 0.8292 (m-30) cc_final: 0.7968 (m-30) REVERT: A 379 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6414 (tp30) REVERT: A 464 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7182 (pt) REVERT: A 550 ARG cc_start: 0.7221 (mmt-90) cc_final: 0.6970 (mmp80) REVERT: B 57 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: B 379 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: B 550 ARG cc_start: 0.7192 (mmt-90) cc_final: 0.6924 (mmp80) REVERT: C 57 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: C 263 GLU cc_start: 0.8212 (mp0) cc_final: 0.7925 (mm-30) REVERT: C 287 ASP cc_start: 0.8309 (m-30) cc_final: 0.7993 (m-30) REVERT: C 312 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7933 (t0) REVERT: C 379 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6346 (tp30) REVERT: D 57 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: D 219 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7973 (mttt) REVERT: D 287 ASP cc_start: 0.8311 (m-30) cc_final: 0.8000 (m-30) REVERT: D 379 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6325 (tp30) REVERT: D 550 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.6907 (mmp80) outliers start: 44 outliers final: 19 residues processed: 271 average time/residue: 0.6587 time to fit residues: 198.3590 Evaluate side-chains 253 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126522 restraints weight = 18539.317| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.49 r_work: 0.3305 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18320 Z= 0.166 Angle : 0.686 8.958 24876 Z= 0.334 Chirality : 0.047 0.137 2780 Planarity : 0.005 0.046 3156 Dihedral : 12.516 179.437 2616 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.56 % Favored : 95.26 % Rotamer: Outliers : 2.37 % Allowed : 21.50 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2216 helix: 1.22 (0.18), residues: 908 sheet: 0.19 (0.23), residues: 396 loop : -0.76 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 411 TYR 0.012 0.002 TYR A 106 PHE 0.017 0.002 PHE B 162 TRP 0.011 0.002 TRP A 124 HIS 0.007 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (18316) covalent geometry : angle 0.68620 / 0.33 (24876) hydrogen bonds : bond 0.04006 / 2.64 ( 744) hydrogen bonds : angle 4.73920 / 3.34 ( 2172) Misc. bond : bond 0.00011 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.673 Fit side-chains REVERT: A 57 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: A 219 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7973 (mttt) REVERT: A 287 ASP cc_start: 0.8320 (m-30) cc_final: 0.7991 (m-30) REVERT: A 312 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8012 (t0) REVERT: A 379 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6457 (tp30) REVERT: A 464 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7260 (pt) REVERT: A 550 ARG cc_start: 0.7200 (mmt-90) cc_final: 0.6964 (mmp80) REVERT: B 54 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 57 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: B 312 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7925 (t0) REVERT: B 379 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6445 (tt0) REVERT: B 550 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.6956 (mmp80) REVERT: C 57 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: C 287 ASP cc_start: 0.8331 (m-30) cc_final: 0.8018 (m-30) REVERT: C 312 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7995 (t0) REVERT: C 379 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6477 (tp30) REVERT: D 54 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: D 57 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: D 219 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7957 (mttt) REVERT: D 287 ASP cc_start: 0.8324 (m-30) cc_final: 0.8006 (m-30) REVERT: D 379 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: D 411 ARG cc_start: 0.6539 (ptp-170) cc_final: 0.6330 (ptp-170) REVERT: D 550 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6928 (mmp80) outliers start: 46 outliers final: 19 residues processed: 267 average time/residue: 0.6338 time to fit residues: 188.0942 Evaluate side-chains 254 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 473 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 35 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127784 restraints weight = 18516.086| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.49 r_work: 0.3323 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18320 Z= 0.134 Angle : 0.650 7.920 24876 Z= 0.316 Chirality : 0.046 0.139 2780 Planarity : 0.005 0.045 3156 Dihedral : 12.316 178.818 2616 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 2.62 % Allowed : 21.55 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2216 helix: 1.36 (0.18), residues: 896 sheet: 0.21 (0.24), residues: 396 loop : -0.71 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 411 TYR 0.011 0.001 TYR A 106 PHE 0.012 0.001 PHE C 162 TRP 0.009 0.001 TRP D 358 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (18316) covalent geometry : angle 0.64996 / 0.32 (24876) hydrogen bonds : bond 0.03547 / 2.34 ( 744) hydrogen bonds : angle 4.64759 / 3.27 ( 2172) Misc. bond : bond 0.00001 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.632 Fit side-chains REVERT: A 57 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: A 219 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7958 (mttt) REVERT: A 287 ASP cc_start: 0.8306 (m-30) cc_final: 0.7979 (m-30) REVERT: A 312 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7998 (t0) REVERT: A 379 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6468 (tp30) REVERT: A 464 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (pt) REVERT: A 500 VAL cc_start: 0.8285 (m) cc_final: 0.8074 (p) REVERT: A 550 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6899 (mmp80) REVERT: B 57 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: B 312 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 379 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6407 (tt0) REVERT: B 550 ARG cc_start: 0.7127 (mmt-90) cc_final: 0.6865 (mmp80) REVERT: C 57 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: C 287 ASP cc_start: 0.8335 (m-30) cc_final: 0.8024 (m-30) REVERT: C 312 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7975 (t0) REVERT: C 379 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: D 57 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: D 219 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7940 (mttt) REVERT: D 287 ASP cc_start: 0.8316 (m-30) cc_final: 0.8028 (m-30) REVERT: D 312 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7894 (t0) REVERT: D 379 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6426 (tp30) REVERT: D 411 ARG cc_start: 0.6540 (ptp-170) cc_final: 0.6338 (ptp-170) REVERT: D 550 ARG cc_start: 0.7105 (mmt-90) cc_final: 0.6834 (mmp80) outliers start: 51 outliers final: 25 residues processed: 272 average time/residue: 0.6151 time to fit residues: 186.3939 Evaluate side-chains 255 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124317 restraints weight = 18421.927| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.47 r_work: 0.3274 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18320 Z= 0.229 Angle : 0.763 9.827 24876 Z= 0.373 Chirality : 0.050 0.156 2780 Planarity : 0.005 0.047 3156 Dihedral : 12.869 179.932 2616 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.65 % Favored : 95.17 % Rotamer: Outliers : 2.47 % Allowed : 21.81 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2216 helix: 1.06 (0.17), residues: 904 sheet: 0.19 (0.24), residues: 396 loop : -0.79 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 411 TYR 0.015 0.002 TYR A 106 PHE 0.023 0.002 PHE A 162 TRP 0.014 0.003 TRP D 124 HIS 0.008 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (18316) covalent geometry : angle 0.76260 / 0.37 (24876) hydrogen bonds : bond 0.04749 / 3.12 ( 744) hydrogen bonds : angle 4.94593 / 3.48 ( 2172) Misc. bond : bond 0.00027 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.534 Fit side-chains REVERT: A 54 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: A 57 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: A 219 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8042 (mttt) REVERT: A 287 ASP cc_start: 0.8314 (m-30) cc_final: 0.7983 (m-30) REVERT: A 312 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7961 (t0) REVERT: A 379 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: A 500 VAL cc_start: 0.8334 (m) cc_final: 0.8130 (p) REVERT: A 550 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6997 (mmp80) REVERT: B 57 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: B 312 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 379 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: B 493 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 550 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.6964 (mmp80) REVERT: C 54 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 57 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: C 287 ASP cc_start: 0.8345 (m-30) cc_final: 0.8052 (m-30) REVERT: C 312 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7939 (t0) REVERT: C 379 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: D 57 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: D 219 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8007 (mttt) REVERT: D 287 ASP cc_start: 0.8362 (m-30) cc_final: 0.8025 (m-30) REVERT: D 312 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7874 (t0) REVERT: D 353 LYS cc_start: 0.8108 (mttp) cc_final: 0.7749 (mttm) REVERT: D 379 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6516 (tt0) REVERT: D 550 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6908 (mmp80) outliers start: 48 outliers final: 23 residues processed: 262 average time/residue: 0.6027 time to fit residues: 176.1453 Evaluate side-chains 255 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 463 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 163 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128165 restraints weight = 18527.013| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.41 r_work: 0.3328 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18320 Z= 0.134 Angle : 0.660 8.008 24876 Z= 0.322 Chirality : 0.046 0.142 2780 Planarity : 0.005 0.045 3156 Dihedral : 12.376 178.518 2616 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 22.74 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2216 helix: 1.23 (0.17), residues: 904 sheet: 0.18 (0.23), residues: 396 loop : -0.69 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 411 TYR 0.012 0.001 TYR C 106 PHE 0.011 0.001 PHE C 162 TRP 0.009 0.002 TRP A 124 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (18316) covalent geometry : angle 0.65993 / 0.32 (24876) hydrogen bonds : bond 0.03574 / 2.36 ( 744) hydrogen bonds : angle 4.68681 / 3.30 ( 2172) Misc. bond : bond 0.00002 / 0.00 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6500.40 seconds wall clock time: 111 minutes 20.55 seconds (6680.55 seconds total)