Starting phenix.real_space_refine on Thu Feb 5 18:27:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.map" model { file = "/net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nq9_49646/02_2026/9nq9_49646.cif" } resolution = 2.97 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= 0.004 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 4 5.49 5 Mg 5 5.21 5 S 152 5.16 5 C 12604 2.51 5 N 3148 2.21 5 O 3372 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19285 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4653 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain breaks: 2 Chain: "B" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4653 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain breaks: 2 Chain: "C" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4653 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4653 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain breaks: 2 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 175 Unusual residues: {' MG': 2, 'POV': 5, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 4, 'POV:plan-3': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 197 Unusual residues: {' MG': 1, 'POV': 3, 'Y01': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 133 Unusual residues: {' MG': 1, 'POV': 4, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Unusual residues: {' MG': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 4.35, per 1000 atoms: 0.23 Number of scatterers: 19285 At special positions: 0 Unit cell: (123.521, 123.521, 118.547, 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 152 16.00 P 4 15.00 Mg 5 11.99 O 3372 8.00 N 3148 7.00 C 12604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 867.4 milliseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 64.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 27 through 47 removed outlier: 3.758A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.558A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.559A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.517A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.727A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.643A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.968A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.649A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.582A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.662A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.636A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.856A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 584 removed outlier: 3.802A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.758A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.558A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.558A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.518A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.727A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.643A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.969A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.648A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.582A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.662A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.636A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.856A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 584 removed outlier: 3.803A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.757A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.558A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.559A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.518A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.727A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.643A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.969A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.648A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.582A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 402 Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.663A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.635A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.856A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 584 removed outlier: 3.803A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.757A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.557A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.559A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.517A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.727A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.644A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.968A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.649A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.582A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 402 Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.662A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.636A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.856A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 584 removed outlier: 3.803A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.760A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.759A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.758A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.759A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1053 hydrogen bonds defined for protein. 3051 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: 3.32 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 3052 1.31 - 1.46: 7533 1.46 - 1.62: 8803 1.62 - 1.77: 72 1.77 - 1.93: 268 Bond restraints: 19728 Sorted by residual: bond pdb=" CAV Y01 D 702 " pdb=" CAZ Y01 D 702 " ideal model delta sigma weight residual 1.507 1.930 -0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" CAV Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.507 1.930 -0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" CAV Y01 B 702 " pdb=" CAZ Y01 B 702 " ideal model delta sigma weight residual 1.507 1.928 -0.421 2.00e-02 2.50e+03 4.42e+02 bond pdb=" CAV Y01 C 801 " pdb=" CAZ Y01 C 801 " ideal model delta sigma weight residual 1.507 1.927 -0.420 2.00e-02 2.50e+03 4.42e+02 bond pdb=" CAV Y01 A 802 " pdb=" CAZ Y01 A 802 " ideal model delta sigma weight residual 1.507 1.909 -0.402 2.00e-02 2.50e+03 4.04e+02 ... (remaining 19723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 25766 2.99 - 5.98: 679 5.98 - 8.97: 226 8.97 - 11.96: 82 11.96 - 14.94: 23 Bond angle restraints: 26776 Sorted by residual: angle pdb=" CAR Y01 B 703 " pdb=" CBC Y01 B 703 " pdb=" OAW Y01 B 703 " ideal model delta sigma weight residual 107.47 122.41 -14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CAD Y01 B 704 " pdb=" CBH Y01 B 704 " pdb=" CBF Y01 B 704 " ideal model delta sigma weight residual 111.82 97.06 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CAD Y01 B 701 " pdb=" CBH Y01 B 701 " pdb=" CBF Y01 B 701 " ideal model delta sigma weight residual 111.82 97.30 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CAD Y01 A 809 " pdb=" CBH Y01 A 809 " pdb=" CBF Y01 A 809 " ideal model delta sigma weight residual 111.82 97.38 14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CAD Y01 D 701 " pdb=" CBH Y01 D 701 " pdb=" CBF Y01 D 701 " ideal model delta sigma weight residual 111.82 97.46 14.36 3.00e+00 1.11e-01 2.29e+01 ... (remaining 26771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.38: 11578 27.38 - 54.75: 619 54.75 - 82.13: 143 82.13 - 109.50: 59 109.50 - 136.88: 29 Dihedral angle restraints: 12428 sinusoidal: 5640 harmonic: 6788 Sorted by residual: dihedral pdb=" CA ARG B 621 " pdb=" C ARG B 621 " pdb=" N GLU B 622 " pdb=" CA GLU B 622 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ARG A 621 " pdb=" C ARG A 621 " pdb=" N GLU A 622 " pdb=" CA GLU A 622 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ARG D 621 " pdb=" C ARG D 621 " pdb=" N GLU D 622 " pdb=" CA GLU D 622 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 12425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.926: 2992 0.926 - 1.852: 0 1.852 - 2.778: 0 2.778 - 3.704: 0 3.704 - 4.630: 48 Chirality restraints: 3040 Sorted by residual: chirality pdb=" CBC Y01 C 802 " pdb=" CAR Y01 C 802 " pdb=" CAV Y01 C 802 " pdb=" OAW Y01 C 802 " both_signs ideal model delta sigma weight residual False -2.54 2.09 -4.63 2.00e-01 2.50e+01 5.36e+02 chirality pdb=" CBC Y01 D 703 " pdb=" CAR Y01 D 703 " pdb=" CAV Y01 D 703 " pdb=" OAW Y01 D 703 " both_signs ideal model delta sigma weight residual False -2.54 2.07 -4.62 2.00e-01 2.50e+01 5.33e+02 chirality pdb=" CBC Y01 A 802 " pdb=" CAR Y01 A 802 " pdb=" CAV Y01 A 802 " pdb=" OAW Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.54 2.07 -4.62 2.00e-01 2.50e+01 5.33e+02 ... (remaining 3037 not shown) Planarity restraints: 3296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 102 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO A 103 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 102 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 103 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 103 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 103 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 102 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO D 103 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.038 5.00e-02 4.00e+02 ... (remaining 3293 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 106 2.59 - 3.16: 15343 3.16 - 3.74: 30863 3.74 - 4.32: 44186 4.32 - 4.90: 71224 Nonbonded interactions: 161722 Sorted by model distance: nonbonded pdb=" OD2 ASP C 542 " pdb="MG MG A 810 " model vdw 2.007 2.170 nonbonded pdb=" OD2 ASP A 542 " pdb="MG MG A 810 " model vdw 2.009 2.170 nonbonded pdb=" OD2 ASP B 542 " pdb="MG MG A 810 " model vdw 2.013 2.170 nonbonded pdb=" OD2 ASP D 542 " pdb="MG MG A 810 " model vdw 2.018 2.170 nonbonded pdb=" OH TYR C 377 " pdb=" OE1 GLU C 389 " model vdw 2.280 3.040 ... (remaining 161717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 802) selection = (chain 'B' and resid 27 through 702) selection = (chain 'C' and resid 27 through 802) selection = (chain 'D' and resid 27 through 702) } 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=0.45 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.024 0.423 19728 Z= 1.174 Angle : 1.408 14.944 26776 Z= 0.626 Chirality : 0.529 4.630 3040 Planarity : 0.008 0.069 3296 Dihedral : 19.789 136.877 8036 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.80 % Allowed : 4.37 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.14), residues: 2296 helix: -1.93 (0.09), residues: 1412 sheet: 0.39 (0.58), residues: 84 loop : -0.79 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 350 TYR 0.035 0.004 TYR C 547 PHE 0.028 0.004 PHE A 169 TRP 0.019 0.003 TRP C 321 HIS 0.016 0.003 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.02401 (19728) covalent geometry : angle 1.40845 (26776) hydrogen bonds : bond 0.25852 ( 1053) hydrogen bonds : angle 7.78446 ( 3051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 700 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7054 (tp40) cc_final: 0.6393 (tp-100) REVERT: A 35 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 139 ARG cc_start: 0.7020 (mpt180) cc_final: 0.6730 (tmm160) REVERT: A 150 THR cc_start: 0.8455 (p) cc_final: 0.8156 (t) REVERT: A 255 MET cc_start: 0.8059 (mmm) cc_final: 0.7730 (mmp) REVERT: A 437 LEU cc_start: 0.8046 (mt) cc_final: 0.7829 (mt) REVERT: A 577 MET cc_start: 0.7330 (mtt) cc_final: 0.7055 (mtm) REVERT: A 623 TYR cc_start: 0.7344 (m-80) cc_final: 0.6921 (m-80) REVERT: B 152 PHE cc_start: 0.7834 (m-80) cc_final: 0.7520 (m-80) REVERT: B 155 SER cc_start: 0.6448 (p) cc_final: 0.6197 (p) REVERT: B 158 ASN cc_start: 0.7308 (m-40) cc_final: 0.7010 (m110) REVERT: B 295 LEU cc_start: 0.8049 (mm) cc_final: 0.7756 (mp) REVERT: B 317 VAL cc_start: 0.8344 (t) cc_final: 0.7940 (m) REVERT: B 373 LEU cc_start: 0.7483 (tp) cc_final: 0.7228 (tp) REVERT: B 434 PHE cc_start: 0.6850 (t80) cc_final: 0.6519 (t80) REVERT: B 602 VAL cc_start: 0.8336 (t) cc_final: 0.8110 (m) REVERT: C 31 GLN cc_start: 0.6798 (tp40) cc_final: 0.6539 (tp-100) REVERT: C 35 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6303 (mt-10) REVERT: C 81 THR cc_start: 0.7179 (p) cc_final: 0.6335 (p) REVERT: C 181 LEU cc_start: 0.7810 (tp) cc_final: 0.7136 (mp) REVERT: C 373 LEU cc_start: 0.7684 (tp) cc_final: 0.7450 (tp) REVERT: C 437 LEU cc_start: 0.8085 (mt) cc_final: 0.7792 (mt) REVERT: C 577 MET cc_start: 0.7404 (mtt) cc_final: 0.7159 (mtm) REVERT: C 623 TYR cc_start: 0.7073 (m-80) cc_final: 0.6824 (m-80) REVERT: D 31 GLN cc_start: 0.6998 (tp40) cc_final: 0.6551 (tp-100) REVERT: D 35 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6609 (mt-10) REVERT: D 150 THR cc_start: 0.8510 (p) cc_final: 0.8036 (t) REVERT: D 181 LEU cc_start: 0.7927 (tp) cc_final: 0.7297 (mt) REVERT: D 185 HIS cc_start: 0.7129 (m90) cc_final: 0.6637 (m90) REVERT: D 209 LYS cc_start: 0.7308 (mttp) cc_final: 0.7091 (mtpp) REVERT: D 255 MET cc_start: 0.8243 (mmm) cc_final: 0.7989 (mmp) REVERT: D 372 LEU cc_start: 0.7568 (mt) cc_final: 0.7309 (mm) REVERT: D 437 LEU cc_start: 0.8185 (mt) cc_final: 0.7806 (mt) REVERT: D 623 TYR cc_start: 0.7627 (m-80) cc_final: 0.7376 (m-80) outliers start: 16 outliers final: 5 residues processed: 711 average time/residue: 0.6432 time to fit residues: 507.7481 Evaluate side-chains 435 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 430 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain D residue 603 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 HIS A 165 HIS A 201 HIS A 228 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 122 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 201 HIS B 228 HIS B 230 GLN B 267 GLN B 290 GLN B 370 GLN C 31 GLN C 41 GLN C 122 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 228 HIS C 230 GLN C 267 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS D 165 HIS D 201 HIS D 228 HIS D 230 GLN D 267 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125389 restraints weight = 25503.753| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.62 r_work: 0.3340 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19728 Z= 0.142 Angle : 0.639 11.631 26776 Z= 0.320 Chirality : 0.041 0.189 3040 Planarity : 0.006 0.057 3296 Dihedral : 11.306 112.060 3582 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.98 % Allowed : 17.84 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2296 helix: 0.63 (0.13), residues: 1408 sheet: 0.01 (0.59), residues: 84 loop : -0.32 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 606 TYR 0.014 0.002 TYR B 324 PHE 0.031 0.002 PHE C 107 TRP 0.014 0.001 TRP A 462 HIS 0.007 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00309 (19728) covalent geometry : angle 0.63880 (26776) hydrogen bonds : bond 0.04996 ( 1053) hydrogen bonds : angle 4.21659 ( 3051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 485 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6980 (tp40) cc_final: 0.6493 (tp-100) REVERT: A 35 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 139 ARG cc_start: 0.7825 (mpt180) cc_final: 0.6852 (tmm160) REVERT: A 159 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 229 LEU cc_start: 0.4423 (OUTLIER) cc_final: 0.4198 (tm) REVERT: A 311 THR cc_start: 0.6225 (OUTLIER) cc_final: 0.5307 (t) REVERT: A 315 GLU cc_start: 0.8098 (mp0) cc_final: 0.7765 (mp0) REVERT: A 359 ARG cc_start: 0.7343 (mtp85) cc_final: 0.7049 (mtp85) REVERT: A 372 LEU cc_start: 0.8037 (mm) cc_final: 0.7821 (mm) REVERT: A 435 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (mmp) REVERT: A 482 ILE cc_start: 0.7954 (mp) cc_final: 0.7533 (mt) REVERT: A 589 ARG cc_start: 0.5603 (ptm160) cc_final: 0.5295 (ptm-80) REVERT: A 603 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7271 (ptt) REVERT: B 131 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7557 (m-40) REVERT: B 134 ARG cc_start: 0.7484 (tpp80) cc_final: 0.7068 (mtt-85) REVERT: B 152 PHE cc_start: 0.8095 (m-80) cc_final: 0.7851 (m-80) REVERT: B 283 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 315 GLU cc_start: 0.8218 (mp0) cc_final: 0.7827 (mp0) REVERT: B 317 VAL cc_start: 0.8583 (t) cc_final: 0.8166 (m) REVERT: B 324 TYR cc_start: 0.7199 (m-80) cc_final: 0.6643 (m-80) REVERT: B 373 LEU cc_start: 0.7721 (tp) cc_final: 0.7426 (tp) REVERT: B 434 PHE cc_start: 0.7433 (t80) cc_final: 0.7214 (t80) REVERT: B 589 ARG cc_start: 0.6997 (ttp80) cc_final: 0.6776 (ttp80) REVERT: B 625 LEU cc_start: 0.7401 (mt) cc_final: 0.7194 (mt) REVERT: C 35 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6663 (mt-10) REVERT: C 146 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7116 (mtt180) REVERT: C 218 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7253 (tt) REVERT: C 359 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6940 (mtp85) REVERT: C 373 LEU cc_start: 0.7843 (tp) cc_final: 0.7625 (tp) REVERT: C 394 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 482 ILE cc_start: 0.7972 (mp) cc_final: 0.7588 (mt) REVERT: C 577 MET cc_start: 0.7457 (mtt) cc_final: 0.6980 (mtm) REVERT: D 31 GLN cc_start: 0.6906 (tp40) cc_final: 0.6457 (tp-100) REVERT: D 35 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6889 (mt-10) REVERT: D 233 ASP cc_start: 0.6544 (p0) cc_final: 0.6165 (p0) REVERT: D 235 VAL cc_start: 0.8420 (t) cc_final: 0.8187 (m) REVERT: D 373 LEU cc_start: 0.7867 (tp) cc_final: 0.7600 (tp) REVERT: D 394 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 482 ILE cc_start: 0.7964 (mp) cc_final: 0.7548 (mt) outliers start: 80 outliers final: 33 residues processed: 535 average time/residue: 0.6395 time to fit residues: 380.5314 Evaluate side-chains 462 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 418 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 21 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 128 GLN B 129 ASN B 261 GLN B 483 GLN C 31 GLN C 73 HIS C 91 ASN C 267 GLN D 128 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123076 restraints weight = 25566.975| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.61 r_work: 0.3317 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19728 Z= 0.135 Angle : 0.608 7.561 26776 Z= 0.304 Chirality : 0.039 0.214 3040 Planarity : 0.005 0.060 3296 Dihedral : 10.255 88.850 3571 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.07 % Allowed : 19.58 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2296 helix: 1.26 (0.13), residues: 1416 sheet: -0.38 (0.59), residues: 84 loop : -0.06 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 606 TYR 0.014 0.001 TYR C 524 PHE 0.034 0.002 PHE C 107 TRP 0.026 0.002 TRP B 593 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00309 (19728) covalent geometry : angle 0.60807 (26776) hydrogen bonds : bond 0.04330 ( 1053) hydrogen bonds : angle 3.94886 ( 3051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 451 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6455 (tp-100) REVERT: A 35 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 113 GLU cc_start: 0.7948 (tp30) cc_final: 0.7720 (tp30) REVERT: A 139 ARG cc_start: 0.7673 (mpt180) cc_final: 0.6732 (tmm160) REVERT: A 218 LEU cc_start: 0.7580 (mp) cc_final: 0.7155 (tt) REVERT: A 311 THR cc_start: 0.6107 (OUTLIER) cc_final: 0.4849 (t) REVERT: A 315 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 324 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: A 372 LEU cc_start: 0.7951 (mm) cc_final: 0.7647 (mm) REVERT: A 373 LEU cc_start: 0.7744 (tt) cc_final: 0.7513 (tp) REVERT: A 482 ILE cc_start: 0.7988 (mp) cc_final: 0.7566 (mt) REVERT: A 497 MET cc_start: 0.8087 (ttm) cc_final: 0.7689 (mtt) REVERT: A 589 ARG cc_start: 0.5640 (ptm160) cc_final: 0.5322 (ptm-80) REVERT: B 134 ARG cc_start: 0.7442 (tpp80) cc_final: 0.7051 (mtt-85) REVERT: B 192 GLN cc_start: 0.8206 (mt0) cc_final: 0.7956 (mt0) REVERT: B 230 GLN cc_start: 0.7278 (mm-40) cc_final: 0.7059 (mm-40) REVERT: B 283 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8106 (mp) REVERT: B 290 GLN cc_start: 0.5487 (mp10) cc_final: 0.5210 (mm110) REVERT: B 317 VAL cc_start: 0.8605 (t) cc_final: 0.8151 (m) REVERT: B 324 TYR cc_start: 0.7294 (m-80) cc_final: 0.6724 (m-80) REVERT: B 332 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8030 (tp) REVERT: B 373 LEU cc_start: 0.7883 (tp) cc_final: 0.7668 (tp) REVERT: B 434 PHE cc_start: 0.7540 (t80) cc_final: 0.7333 (t80) REVERT: B 589 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6710 (ttp80) REVERT: C 146 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7159 (mtt180) REVERT: C 174 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (m110) REVERT: C 230 GLN cc_start: 0.6656 (mt0) cc_final: 0.6423 (mt0) REVERT: C 315 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 324 TYR cc_start: 0.7256 (m-80) cc_final: 0.6476 (m-80) REVERT: C 359 ARG cc_start: 0.7314 (mtp85) cc_final: 0.7010 (mtp85) REVERT: C 373 LEU cc_start: 0.7926 (tp) cc_final: 0.7710 (tp) REVERT: C 482 ILE cc_start: 0.8027 (mp) cc_final: 0.7607 (mt) REVERT: C 490 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7118 (tm) REVERT: D 31 GLN cc_start: 0.6848 (tp40) cc_final: 0.6540 (tp-100) REVERT: D 35 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6915 (mt-10) REVERT: D 146 ARG cc_start: 0.6971 (mtp180) cc_final: 0.6641 (mtt180) REVERT: D 233 ASP cc_start: 0.6447 (p0) cc_final: 0.6243 (p0) REVERT: D 315 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: D 324 TYR cc_start: 0.7189 (m-80) cc_final: 0.6480 (m-80) REVERT: D 359 ARG cc_start: 0.7417 (mtp85) cc_final: 0.6964 (mtp85) REVERT: D 373 LEU cc_start: 0.7895 (tp) cc_final: 0.7653 (tp) REVERT: D 482 ILE cc_start: 0.8033 (mp) cc_final: 0.7621 (mt) REVERT: D 589 ARG cc_start: 0.5743 (ptm160) cc_final: 0.5464 (ptm-80) REVERT: D 622 GLU cc_start: 0.6386 (tm-30) cc_final: 0.6173 (tm-30) outliers start: 102 outliers final: 44 residues processed: 511 average time/residue: 0.6616 time to fit residues: 374.3517 Evaluate side-chains 460 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 406 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 128 GLN A 546 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 483 GLN C 31 GLN C 546 ASN D 91 ASN D 128 GLN D 129 ASN D 546 ASN ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120067 restraints weight = 25483.631| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.64 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19728 Z= 0.149 Angle : 0.630 9.489 26776 Z= 0.313 Chirality : 0.041 0.212 3040 Planarity : 0.005 0.061 3296 Dihedral : 10.063 82.113 3568 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.92 % Allowed : 20.73 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2296 helix: 1.43 (0.13), residues: 1408 sheet: -0.74 (0.57), residues: 84 loop : -0.09 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 323 TYR 0.014 0.001 TYR B 524 PHE 0.013 0.002 PHE B 244 TRP 0.026 0.002 TRP B 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00344 (19728) covalent geometry : angle 0.63025 (26776) hydrogen bonds : bond 0.04331 ( 1053) hydrogen bonds : angle 3.98163 ( 3051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 436 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6630 (tp-100) REVERT: A 35 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7083 (mt-10) REVERT: A 113 GLU cc_start: 0.7992 (tp30) cc_final: 0.7740 (tp30) REVERT: A 158 ASN cc_start: 0.7813 (m-40) cc_final: 0.7559 (m-40) REVERT: A 233 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 234 LEU cc_start: 0.8214 (mp) cc_final: 0.7881 (mt) REVERT: A 300 LYS cc_start: 0.7853 (mptt) cc_final: 0.7649 (mptt) REVERT: A 311 THR cc_start: 0.6021 (OUTLIER) cc_final: 0.4819 (t) REVERT: A 315 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: A 324 TYR cc_start: 0.7355 (m-80) cc_final: 0.6604 (m-80) REVERT: A 482 ILE cc_start: 0.8099 (mp) cc_final: 0.7658 (mt) REVERT: A 497 MET cc_start: 0.8107 (ttm) cc_final: 0.7735 (mtt) REVERT: A 553 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7096 (p90) REVERT: A 589 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.5537 (ptm-80) REVERT: B 131 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (m-40) REVERT: B 192 GLN cc_start: 0.8226 (mt0) cc_final: 0.7863 (mt0) REVERT: B 283 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 290 GLN cc_start: 0.5619 (mp10) cc_final: 0.5381 (mp10) REVERT: B 315 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: B 317 VAL cc_start: 0.8728 (t) cc_final: 0.8296 (m) REVERT: B 323 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7600 (mmm-85) REVERT: B 324 TYR cc_start: 0.7439 (m-80) cc_final: 0.6890 (m-80) REVERT: B 332 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8033 (tp) REVERT: B 434 PHE cc_start: 0.7627 (t80) cc_final: 0.7416 (t80) REVERT: B 497 MET cc_start: 0.7991 (ttm) cc_final: 0.7632 (mtt) REVERT: B 553 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7061 (p90) REVERT: B 589 ARG cc_start: 0.6939 (ttp80) cc_final: 0.6686 (ttp80) REVERT: C 146 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7067 (mtp85) REVERT: C 219 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7405 (mm) REVERT: C 234 LEU cc_start: 0.8135 (mp) cc_final: 0.7655 (mp) REVERT: C 306 GLN cc_start: 0.8413 (mp10) cc_final: 0.8195 (mm110) REVERT: C 315 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: C 324 TYR cc_start: 0.7349 (m-80) cc_final: 0.6653 (m-80) REVERT: C 359 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6958 (mtp85) REVERT: C 482 ILE cc_start: 0.8118 (mp) cc_final: 0.7668 (mt) REVERT: C 490 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7190 (tm) REVERT: C 497 MET cc_start: 0.8167 (ttm) cc_final: 0.7813 (mtt) REVERT: C 578 MET cc_start: 0.7317 (ppp) cc_final: 0.7015 (ppp) REVERT: D 31 GLN cc_start: 0.6987 (tp40) cc_final: 0.6670 (tp-100) REVERT: D 35 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7108 (mt-10) REVERT: D 157 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7426 (m) REVERT: D 219 LEU cc_start: 0.7905 (mm) cc_final: 0.7670 (mm) REVERT: D 234 LEU cc_start: 0.8439 (mp) cc_final: 0.8169 (mp) REVERT: D 315 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: D 324 TYR cc_start: 0.7224 (m-80) cc_final: 0.6529 (m-80) REVERT: D 375 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: D 482 ILE cc_start: 0.8131 (mp) cc_final: 0.7697 (mt) REVERT: D 497 MET cc_start: 0.8039 (ttm) cc_final: 0.7671 (mtt) REVERT: D 553 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7732 (t80) REVERT: D 589 ARG cc_start: 0.5802 (ptm160) cc_final: 0.5545 (ptm-80) outliers start: 99 outliers final: 48 residues processed: 488 average time/residue: 0.6266 time to fit residues: 339.1916 Evaluate side-chains 470 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 404 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 627 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 261 GLN B 306 GLN B 483 GLN B 546 ASN C 174 ASN ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114225 restraints weight = 25262.579| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.69 r_work: 0.3180 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19728 Z= 0.220 Angle : 0.698 10.796 26776 Z= 0.349 Chirality : 0.044 0.215 3040 Planarity : 0.006 0.060 3296 Dihedral : 10.605 91.833 3568 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.82 % Allowed : 20.83 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2296 helix: 1.20 (0.13), residues: 1404 sheet: -1.06 (0.56), residues: 84 loop : -0.23 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 134 TYR 0.015 0.002 TYR B 524 PHE 0.018 0.002 PHE D 512 TRP 0.026 0.002 TRP B 593 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00527 (19728) covalent geometry : angle 0.69848 (26776) hydrogen bonds : bond 0.04797 ( 1053) hydrogen bonds : angle 4.16601 ( 3051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 420 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7043 (tp40) cc_final: 0.6706 (tp-100) REVERT: A 35 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 92 LEU cc_start: 0.7336 (tp) cc_final: 0.6945 (tp) REVERT: A 157 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7310 (m) REVERT: A 158 ASN cc_start: 0.7959 (m-40) cc_final: 0.7673 (m-40) REVERT: A 219 LEU cc_start: 0.7956 (mm) cc_final: 0.7712 (mm) REVERT: A 233 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7086 (p0) REVERT: A 234 LEU cc_start: 0.8189 (mp) cc_final: 0.7854 (mt) REVERT: A 300 LYS cc_start: 0.7891 (mptt) cc_final: 0.7658 (mptt) REVERT: A 311 THR cc_start: 0.6108 (OUTLIER) cc_final: 0.4802 (t) REVERT: A 315 GLU cc_start: 0.8356 (mp0) cc_final: 0.8004 (mp0) REVERT: A 324 TYR cc_start: 0.7514 (m-80) cc_final: 0.6797 (m-80) REVERT: A 482 ILE cc_start: 0.8067 (mp) cc_final: 0.7604 (mt) REVERT: A 497 MET cc_start: 0.8297 (ttm) cc_final: 0.7890 (mtt) REVERT: A 553 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7195 (p90) REVERT: A 589 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5690 (ptm-80) REVERT: B 131 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7723 (m-40) REVERT: B 134 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6818 (mtt-85) REVERT: B 192 GLN cc_start: 0.8243 (mt0) cc_final: 0.7884 (mt0) REVERT: B 283 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8252 (mp) REVERT: B 315 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: B 434 PHE cc_start: 0.7722 (t80) cc_final: 0.7462 (t80) REVERT: B 497 MET cc_start: 0.8160 (ttm) cc_final: 0.7781 (mtt) REVERT: B 553 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7234 (p90) REVERT: B 589 ARG cc_start: 0.6906 (ttp80) cc_final: 0.6607 (ttp80) REVERT: C 219 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7569 (mm) REVERT: C 233 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7156 (p0) REVERT: C 234 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 306 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8297 (mm110) REVERT: C 315 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: C 319 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7945 (tm) REVERT: C 373 LEU cc_start: 0.7922 (tp) cc_final: 0.7681 (tp) REVERT: C 375 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: C 428 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8039 (mp) REVERT: C 482 ILE cc_start: 0.8127 (mp) cc_final: 0.7711 (mt) REVERT: C 490 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7163 (tm) REVERT: C 497 MET cc_start: 0.8301 (ttm) cc_final: 0.7919 (mtt) REVERT: C 553 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7874 (t80) REVERT: C 612 LEU cc_start: 0.7483 (mt) cc_final: 0.7256 (mm) REVERT: D 31 GLN cc_start: 0.7073 (tp40) cc_final: 0.6830 (tp-100) REVERT: D 35 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7196 (mt-10) REVERT: D 92 LEU cc_start: 0.7332 (tp) cc_final: 0.6802 (tp) REVERT: D 159 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8659 (mp) REVERT: D 219 LEU cc_start: 0.8049 (mm) cc_final: 0.7779 (mm) REVERT: D 315 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: D 324 TYR cc_start: 0.7434 (m-80) cc_final: 0.6842 (m-80) REVERT: D 359 ARG cc_start: 0.7302 (mtp85) cc_final: 0.6912 (mtp85) REVERT: D 373 LEU cc_start: 0.7878 (tp) cc_final: 0.7650 (tp) REVERT: D 375 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: D 378 MET cc_start: 0.7191 (ptp) cc_final: 0.6954 (ptp) REVERT: D 482 ILE cc_start: 0.8073 (mp) cc_final: 0.7650 (mt) REVERT: D 497 MET cc_start: 0.8221 (ttm) cc_final: 0.7842 (mtt) REVERT: D 553 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7841 (t80) outliers start: 117 outliers final: 47 residues processed: 486 average time/residue: 0.7179 time to fit residues: 385.8880 Evaluate side-chains 463 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 393 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 103 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 129 ASN A 217 ASN A 258 HIS D 73 HIS D 217 ASN D 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118095 restraints weight = 25199.884| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3231 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19728 Z= 0.125 Angle : 0.645 16.872 26776 Z= 0.317 Chirality : 0.040 0.206 3040 Planarity : 0.005 0.060 3296 Dihedral : 9.655 74.711 3568 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.27 % Allowed : 23.06 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2296 helix: 1.52 (0.14), residues: 1404 sheet: -1.05 (0.56), residues: 84 loop : -0.10 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 180 TYR 0.014 0.001 TYR C 324 PHE 0.013 0.001 PHE D 211 TRP 0.032 0.002 TRP B 593 HIS 0.010 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00281 (19728) covalent geometry : angle 0.64457 (26776) hydrogen bonds : bond 0.04007 ( 1053) hydrogen bonds : angle 4.01699 ( 3051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 437 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6980 (tp40) cc_final: 0.6712 (tp-100) REVERT: A 35 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 146 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7149 (mmt180) REVERT: A 157 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7175 (m) REVERT: A 158 ASN cc_start: 0.7855 (m-40) cc_final: 0.7558 (m-40) REVERT: A 219 LEU cc_start: 0.7856 (mm) cc_final: 0.7590 (mm) REVERT: A 233 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6934 (p0) REVERT: A 234 LEU cc_start: 0.8255 (mp) cc_final: 0.7873 (mt) REVERT: A 300 LYS cc_start: 0.7942 (mptt) cc_final: 0.7733 (mptt) REVERT: A 311 THR cc_start: 0.5860 (OUTLIER) cc_final: 0.4446 (t) REVERT: A 315 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: A 324 TYR cc_start: 0.7383 (m-80) cc_final: 0.6691 (m-80) REVERT: A 428 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 482 ILE cc_start: 0.8009 (mp) cc_final: 0.7594 (mt) REVERT: A 497 MET cc_start: 0.8174 (ttm) cc_final: 0.7809 (mtt) REVERT: A 553 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7157 (p90) REVERT: A 589 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5712 (ptm-80) REVERT: B 35 GLU cc_start: 0.7226 (pt0) cc_final: 0.6961 (mt-10) REVERT: B 44 ILE cc_start: 0.8345 (mt) cc_final: 0.7889 (mp) REVERT: B 93 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7574 (pm20) REVERT: B 131 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: B 134 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6726 (mtt-85) REVERT: B 283 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 315 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 434 PHE cc_start: 0.7717 (t80) cc_final: 0.7462 (t80) REVERT: B 497 MET cc_start: 0.8051 (ttm) cc_final: 0.7725 (mtt) REVERT: B 553 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7179 (p90) REVERT: B 589 ARG cc_start: 0.6897 (ttp80) cc_final: 0.6683 (ttp80) REVERT: C 96 MET cc_start: 0.6631 (mmm) cc_final: 0.6412 (mmm) REVERT: C 219 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7352 (mm) REVERT: C 232 LEU cc_start: 0.8176 (tp) cc_final: 0.7898 (tp) REVERT: C 315 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: C 323 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7656 (mmm160) REVERT: C 324 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: C 428 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7956 (mp) REVERT: C 482 ILE cc_start: 0.8039 (mp) cc_final: 0.7572 (mt) REVERT: C 490 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7237 (tm) REVERT: C 497 MET cc_start: 0.8214 (ttm) cc_final: 0.7851 (mtt) REVERT: C 553 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7814 (t80) REVERT: D 31 GLN cc_start: 0.6963 (tp40) cc_final: 0.6718 (tp-100) REVERT: D 35 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7221 (mt-10) REVERT: D 219 LEU cc_start: 0.7996 (mm) cc_final: 0.7748 (mm) REVERT: D 315 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: D 324 TYR cc_start: 0.7330 (m-80) cc_final: 0.6665 (m-80) REVERT: D 359 ARG cc_start: 0.7297 (mtp85) cc_final: 0.7013 (mtp85) REVERT: D 482 ILE cc_start: 0.8033 (mp) cc_final: 0.7620 (mt) REVERT: D 497 MET cc_start: 0.8128 (ttm) cc_final: 0.7765 (mtt) REVERT: D 553 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7765 (t80) REVERT: D 622 GLU cc_start: 0.6379 (tm-30) cc_final: 0.6060 (tm-30) outliers start: 86 outliers final: 32 residues processed: 475 average time/residue: 0.7182 time to fit residues: 378.0462 Evaluate side-chains 449 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 398 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 627 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 217 ASN B 261 GLN B 290 GLN B 306 GLN D 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117459 restraints weight = 25250.349| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3218 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19728 Z= 0.132 Angle : 0.651 14.564 26776 Z= 0.321 Chirality : 0.040 0.204 3040 Planarity : 0.005 0.059 3296 Dihedral : 9.436 75.853 3568 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.27 % Allowed : 23.56 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2296 helix: 1.56 (0.13), residues: 1408 sheet: -1.10 (0.56), residues: 84 loop : -0.02 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 180 TYR 0.025 0.001 TYR B 324 PHE 0.013 0.001 PHE D 107 TRP 0.038 0.002 TRP B 593 HIS 0.021 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00304 (19728) covalent geometry : angle 0.65085 (26776) hydrogen bonds : bond 0.04057 ( 1053) hydrogen bonds : angle 3.99128 ( 3051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 412 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6977 (tp40) cc_final: 0.6682 (tp-100) REVERT: A 35 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 146 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7173 (mmt180) REVERT: A 157 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7210 (m) REVERT: A 158 ASN cc_start: 0.7892 (m-40) cc_final: 0.7559 (m-40) REVERT: A 219 LEU cc_start: 0.7909 (mm) cc_final: 0.7646 (mm) REVERT: A 233 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6945 (p0) REVERT: A 234 LEU cc_start: 0.8123 (mp) cc_final: 0.7847 (mt) REVERT: A 300 LYS cc_start: 0.7928 (mptt) cc_final: 0.7660 (mptt) REVERT: A 315 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 323 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7693 (mmm-85) REVERT: A 324 TYR cc_start: 0.7435 (m-80) cc_final: 0.6726 (m-80) REVERT: A 428 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 482 ILE cc_start: 0.7996 (mp) cc_final: 0.7580 (mt) REVERT: A 497 MET cc_start: 0.8164 (ttm) cc_final: 0.7820 (mtt) REVERT: A 553 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 589 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5683 (ptm-80) REVERT: B 35 GLU cc_start: 0.7249 (pt0) cc_final: 0.6948 (mt-10) REVERT: B 44 ILE cc_start: 0.8313 (mt) cc_final: 0.7856 (mp) REVERT: B 131 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7620 (m-40) REVERT: B 134 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6668 (mtt-85) REVERT: B 192 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7455 (mm-40) REVERT: B 283 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 315 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 324 TYR cc_start: 0.7557 (m-80) cc_final: 0.7004 (m-80) REVERT: B 434 PHE cc_start: 0.7761 (t80) cc_final: 0.7513 (t80) REVERT: B 497 MET cc_start: 0.8075 (ttm) cc_final: 0.7751 (mtt) REVERT: B 553 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7206 (p90) REVERT: B 589 ARG cc_start: 0.6863 (ttp80) cc_final: 0.6621 (ttp80) REVERT: B 607 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7637 (ttmm) REVERT: C 219 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7411 (mm) REVERT: C 232 LEU cc_start: 0.8137 (tp) cc_final: 0.7814 (tp) REVERT: C 234 LEU cc_start: 0.8268 (mt) cc_final: 0.8055 (mt) REVERT: C 315 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: C 319 LEU cc_start: 0.8380 (tt) cc_final: 0.7865 (tm) REVERT: C 324 TYR cc_start: 0.7502 (m-80) cc_final: 0.6728 (m-80) REVERT: C 428 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7999 (mp) REVERT: C 482 ILE cc_start: 0.7985 (mp) cc_final: 0.7607 (mt) REVERT: C 490 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7164 (tm) REVERT: C 497 MET cc_start: 0.8193 (ttm) cc_final: 0.7847 (mtt) REVERT: C 553 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7810 (t80) REVERT: D 31 GLN cc_start: 0.6947 (tp40) cc_final: 0.6694 (tp-100) REVERT: D 35 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7169 (mt-10) REVERT: D 96 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6438 (mpp) REVERT: D 219 LEU cc_start: 0.7987 (mm) cc_final: 0.7740 (mm) REVERT: D 233 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7186 (p0) REVERT: D 300 LYS cc_start: 0.7850 (mptt) cc_final: 0.7629 (mptt) REVERT: D 315 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: D 324 TYR cc_start: 0.7376 (m-80) cc_final: 0.6722 (m-80) REVERT: D 359 ARG cc_start: 0.7331 (mtp85) cc_final: 0.7024 (mtp85) REVERT: D 482 ILE cc_start: 0.8032 (mp) cc_final: 0.7616 (mt) REVERT: D 497 MET cc_start: 0.8132 (ttm) cc_final: 0.7793 (mtt) REVERT: D 553 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7800 (t80) REVERT: D 589 ARG cc_start: 0.6353 (ptm160) cc_final: 0.5972 (ttp80) REVERT: D 603 MET cc_start: 0.8098 (ttp) cc_final: 0.7748 (ttp) REVERT: D 622 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6084 (tm-30) outliers start: 86 outliers final: 36 residues processed: 456 average time/residue: 0.7583 time to fit residues: 381.8995 Evaluate side-chains 451 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 395 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN B 290 GLN B 306 GLN C 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116201 restraints weight = 25131.864| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.86 r_work: 0.3196 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19728 Z= 0.155 Angle : 0.699 13.548 26776 Z= 0.342 Chirality : 0.041 0.231 3040 Planarity : 0.005 0.060 3296 Dihedral : 9.403 78.747 3568 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.93 % Allowed : 24.50 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2296 helix: 1.51 (0.13), residues: 1408 sheet: -0.86 (0.59), residues: 76 loop : -0.09 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 180 TYR 0.018 0.002 TYR B 324 PHE 0.013 0.001 PHE A 553 TRP 0.046 0.002 TRP B 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00365 (19728) covalent geometry : angle 0.69871 (26776) hydrogen bonds : bond 0.04207 ( 1053) hydrogen bonds : angle 4.06567 ( 3051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 406 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7009 (tp40) cc_final: 0.6722 (tp-100) REVERT: A 35 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 44 ILE cc_start: 0.8284 (mt) cc_final: 0.7787 (mp) REVERT: A 146 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7222 (mmt180) REVERT: A 157 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7295 (m) REVERT: A 158 ASN cc_start: 0.7881 (m-40) cc_final: 0.7548 (m-40) REVERT: A 219 LEU cc_start: 0.7984 (mm) cc_final: 0.7707 (mm) REVERT: A 233 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 300 LYS cc_start: 0.7948 (mptt) cc_final: 0.7685 (mptt) REVERT: A 315 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 428 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 482 ILE cc_start: 0.8018 (mp) cc_final: 0.7594 (mt) REVERT: A 497 MET cc_start: 0.8205 (ttm) cc_final: 0.7847 (mtt) REVERT: A 553 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 589 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5709 (ptm-80) REVERT: B 35 GLU cc_start: 0.7268 (pt0) cc_final: 0.6939 (mt-10) REVERT: B 42 LYS cc_start: 0.7887 (tttp) cc_final: 0.7687 (tttp) REVERT: B 44 ILE cc_start: 0.8344 (mt) cc_final: 0.7893 (mp) REVERT: B 131 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (m-40) REVERT: B 283 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 434 PHE cc_start: 0.7781 (t80) cc_final: 0.7512 (t80) REVERT: B 497 MET cc_start: 0.8132 (ttm) cc_final: 0.7758 (mtt) REVERT: B 553 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7802 (t80) REVERT: B 589 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6538 (ttp80) REVERT: C 51 LEU cc_start: 0.7601 (tp) cc_final: 0.7207 (tp) REVERT: C 96 MET cc_start: 0.6503 (mmm) cc_final: 0.6240 (mmm) REVERT: C 219 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7530 (mm) REVERT: C 232 LEU cc_start: 0.8131 (tp) cc_final: 0.7848 (tp) REVERT: C 315 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: C 319 LEU cc_start: 0.8410 (tt) cc_final: 0.7915 (tm) REVERT: C 323 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7612 (mmm160) REVERT: C 324 TYR cc_start: 0.7549 (m-80) cc_final: 0.6847 (m-80) REVERT: C 359 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6940 (mtp85) REVERT: C 428 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 482 ILE cc_start: 0.8004 (mp) cc_final: 0.7607 (mt) REVERT: C 490 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7163 (tm) REVERT: C 497 MET cc_start: 0.8245 (ttm) cc_final: 0.7882 (mtt) REVERT: C 553 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7837 (t80) REVERT: C 603 MET cc_start: 0.8110 (ttp) cc_final: 0.7793 (ttp) REVERT: D 31 GLN cc_start: 0.7019 (tp40) cc_final: 0.6682 (tp-100) REVERT: D 35 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7189 (mt-10) REVERT: D 219 LEU cc_start: 0.7986 (mm) cc_final: 0.7714 (mm) REVERT: D 233 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7141 (p0) REVERT: D 315 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: D 328 TYR cc_start: 0.8077 (m-10) cc_final: 0.7763 (m-80) REVERT: D 482 ILE cc_start: 0.8062 (mp) cc_final: 0.7656 (mt) REVERT: D 497 MET cc_start: 0.8169 (ttm) cc_final: 0.7800 (mtt) REVERT: D 553 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7821 (t80) REVERT: D 589 ARG cc_start: 0.6243 (ptm160) cc_final: 0.5918 (ttp80) REVERT: D 622 GLU cc_start: 0.6409 (tm-30) cc_final: 0.6094 (tm-30) outliers start: 79 outliers final: 40 residues processed: 451 average time/residue: 0.7289 time to fit residues: 363.1286 Evaluate side-chains 452 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 166 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115953 restraints weight = 24998.026| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.89 r_work: 0.3187 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19728 Z= 0.170 Angle : 0.722 13.789 26776 Z= 0.355 Chirality : 0.042 0.206 3040 Planarity : 0.006 0.059 3296 Dihedral : 9.436 80.480 3568 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.17 % Allowed : 24.45 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2296 helix: 1.48 (0.14), residues: 1400 sheet: -0.91 (0.59), residues: 76 loop : -0.16 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 180 TYR 0.025 0.002 TYR B 324 PHE 0.013 0.001 PHE A 553 TRP 0.051 0.002 TRP B 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00405 (19728) covalent geometry : angle 0.72171 (26776) hydrogen bonds : bond 0.04324 ( 1053) hydrogen bonds : angle 4.10494 ( 3051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 405 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7037 (tp40) cc_final: 0.6771 (tp-100) REVERT: A 35 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 44 ILE cc_start: 0.8347 (mt) cc_final: 0.7865 (mp) REVERT: A 157 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7292 (m) REVERT: A 158 ASN cc_start: 0.7909 (m-40) cc_final: 0.7584 (m-40) REVERT: A 219 LEU cc_start: 0.8015 (mm) cc_final: 0.7731 (mm) REVERT: A 232 LEU cc_start: 0.8112 (tp) cc_final: 0.7820 (tp) REVERT: A 233 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 300 LYS cc_start: 0.8000 (mptt) cc_final: 0.7728 (mptt) REVERT: A 315 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: A 324 TYR cc_start: 0.7512 (m-80) cc_final: 0.6819 (m-80) REVERT: A 428 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 482 ILE cc_start: 0.8006 (mp) cc_final: 0.7596 (mt) REVERT: A 497 MET cc_start: 0.8244 (ttm) cc_final: 0.7894 (mtt) REVERT: A 553 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 589 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5727 (ptm-80) REVERT: B 35 GLU cc_start: 0.7278 (pt0) cc_final: 0.6932 (mt-10) REVERT: B 44 ILE cc_start: 0.8355 (mt) cc_final: 0.7909 (mp) REVERT: B 131 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7671 (m-40) REVERT: B 134 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.6862 (mtt-85) REVERT: B 255 MET cc_start: 0.8797 (tpt) cc_final: 0.8415 (tpp) REVERT: B 261 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: B 262 LYS cc_start: 0.8084 (tptp) cc_final: 0.7870 (tptt) REVERT: B 283 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 434 PHE cc_start: 0.7851 (t80) cc_final: 0.7572 (t80) REVERT: B 497 MET cc_start: 0.8198 (ttm) cc_final: 0.7801 (mtt) REVERT: B 553 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 589 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6539 (ttp80) REVERT: C 44 ILE cc_start: 0.8207 (mt) cc_final: 0.7754 (mp) REVERT: C 96 MET cc_start: 0.6757 (mmm) cc_final: 0.6520 (mmm) REVERT: C 134 ARG cc_start: 0.7298 (tpp80) cc_final: 0.7058 (mtt-85) REVERT: C 219 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7476 (mm) REVERT: C 315 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 319 LEU cc_start: 0.8437 (tt) cc_final: 0.7931 (tm) REVERT: C 323 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7696 (mmm160) REVERT: C 324 TYR cc_start: 0.7596 (m-80) cc_final: 0.6912 (m-80) REVERT: C 359 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6930 (mtp85) REVERT: C 428 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7975 (mp) REVERT: C 482 ILE cc_start: 0.7992 (mp) cc_final: 0.7596 (mt) REVERT: C 490 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7153 (tm) REVERT: C 497 MET cc_start: 0.8260 (ttm) cc_final: 0.7872 (mtt) REVERT: C 553 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7815 (t80) REVERT: C 603 MET cc_start: 0.8050 (ttp) cc_final: 0.7800 (ttp) REVERT: D 31 GLN cc_start: 0.7022 (tp40) cc_final: 0.6731 (tp-100) REVERT: D 35 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7292 (mt-10) REVERT: D 176 GLU cc_start: 0.7352 (pm20) cc_final: 0.6998 (pm20) REVERT: D 219 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7748 (mm) REVERT: D 233 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7152 (p0) REVERT: D 315 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: D 323 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: D 324 TYR cc_start: 0.7475 (m-80) cc_final: 0.6824 (m-80) REVERT: D 328 TYR cc_start: 0.8131 (m-10) cc_final: 0.7799 (m-80) REVERT: D 482 ILE cc_start: 0.8089 (mp) cc_final: 0.7666 (mt) REVERT: D 497 MET cc_start: 0.8177 (ttm) cc_final: 0.7789 (mtt) REVERT: D 553 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 589 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5876 (ttp80) REVERT: D 622 GLU cc_start: 0.6456 (tm-30) cc_final: 0.6141 (tm-30) outliers start: 84 outliers final: 44 residues processed: 457 average time/residue: 0.7304 time to fit residues: 369.6985 Evaluate side-chains 459 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 394 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 589 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN B 306 GLN B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117900 restraints weight = 25297.385| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.73 r_work: 0.3228 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19728 Z= 0.135 Angle : 0.727 13.571 26776 Z= 0.353 Chirality : 0.041 0.203 3040 Planarity : 0.006 0.060 3296 Dihedral : 8.928 77.299 3568 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.58 % Allowed : 25.50 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2296 helix: 1.53 (0.14), residues: 1404 sheet: -0.89 (0.59), residues: 76 loop : -0.08 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 180 TYR 0.024 0.001 TYR B 324 PHE 0.013 0.001 PHE A 553 TRP 0.058 0.002 TRP D 593 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00311 (19728) covalent geometry : angle 0.72655 (26776) hydrogen bonds : bond 0.04035 ( 1053) hydrogen bonds : angle 4.09263 ( 3051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 415 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7013 (tp40) cc_final: 0.6767 (tp-100) REVERT: A 35 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 44 ILE cc_start: 0.8368 (mt) cc_final: 0.7885 (mp) REVERT: A 157 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7318 (m) REVERT: A 158 ASN cc_start: 0.7859 (m-40) cc_final: 0.7556 (m-40) REVERT: A 219 LEU cc_start: 0.8040 (mm) cc_final: 0.7754 (mm) REVERT: A 232 LEU cc_start: 0.7997 (tp) cc_final: 0.7716 (tp) REVERT: A 233 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7030 (p0) REVERT: A 300 LYS cc_start: 0.7978 (mptt) cc_final: 0.7706 (mptt) REVERT: A 315 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: A 324 TYR cc_start: 0.7439 (m-80) cc_final: 0.6811 (m-80) REVERT: A 428 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 482 ILE cc_start: 0.7972 (mp) cc_final: 0.7561 (mt) REVERT: A 497 MET cc_start: 0.8151 (ttm) cc_final: 0.7823 (mtt) REVERT: A 553 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 589 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5680 (ptm-80) REVERT: B 35 GLU cc_start: 0.7237 (pt0) cc_final: 0.6922 (mt-10) REVERT: B 44 ILE cc_start: 0.8275 (mt) cc_final: 0.7827 (mp) REVERT: B 134 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.6834 (mtt-85) REVERT: B 192 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7828 (mm-40) REVERT: B 255 MET cc_start: 0.8693 (tpt) cc_final: 0.8383 (tpp) REVERT: B 283 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 315 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: B 434 PHE cc_start: 0.7775 (t80) cc_final: 0.7491 (t80) REVERT: B 497 MET cc_start: 0.8098 (ttm) cc_final: 0.7772 (mtt) REVERT: B 553 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7759 (t80) REVERT: B 589 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6416 (ttp80) REVERT: B 612 LEU cc_start: 0.7593 (mt) cc_final: 0.7207 (mm) REVERT: C 44 ILE cc_start: 0.8200 (mt) cc_final: 0.7754 (mp) REVERT: C 96 MET cc_start: 0.6725 (mmm) cc_final: 0.6519 (mmm) REVERT: C 134 ARG cc_start: 0.7269 (tpp80) cc_final: 0.6997 (mtt-85) REVERT: C 219 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7568 (mm) REVERT: C 232 LEU cc_start: 0.8266 (tp) cc_final: 0.7978 (tp) REVERT: C 315 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: C 324 TYR cc_start: 0.7565 (m-80) cc_final: 0.6939 (m-80) REVERT: C 328 TYR cc_start: 0.8073 (m-10) cc_final: 0.7774 (m-80) REVERT: C 359 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6931 (mtp85) REVERT: C 428 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 482 ILE cc_start: 0.8002 (mp) cc_final: 0.7614 (mt) REVERT: C 490 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7140 (tm) REVERT: C 497 MET cc_start: 0.8152 (ttm) cc_final: 0.7800 (mtt) REVERT: C 553 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7808 (t80) REVERT: D 31 GLN cc_start: 0.6961 (tp40) cc_final: 0.6673 (tp-100) REVERT: D 35 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 44 ILE cc_start: 0.8396 (mt) cc_final: 0.7915 (mp) REVERT: D 219 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (mm) REVERT: D 315 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: D 324 TYR cc_start: 0.7426 (m-80) cc_final: 0.6825 (m-80) REVERT: D 328 TYR cc_start: 0.8082 (m-10) cc_final: 0.7795 (m-80) REVERT: D 359 ARG cc_start: 0.7363 (mtp85) cc_final: 0.7023 (mtp85) REVERT: D 482 ILE cc_start: 0.8016 (mp) cc_final: 0.7593 (mt) REVERT: D 497 MET cc_start: 0.8089 (ttm) cc_final: 0.7746 (mtt) REVERT: D 553 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7799 (t80) REVERT: D 622 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6120 (tm-30) outliers start: 72 outliers final: 33 residues processed: 449 average time/residue: 0.7523 time to fit residues: 373.4376 Evaluate side-chains 451 residues out of total 2012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 400 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 123 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 217 ASN B 91 ASN B 131 ASN B 483 GLN C 473 GLN D 217 ASN D 258 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118259 restraints weight = 25239.694| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.81 r_work: 0.3222 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19728 Z= 0.140 Angle : 0.736 13.660 26776 Z= 0.358 Chirality : 0.041 0.202 3040 Planarity : 0.006 0.060 3296 Dihedral : 8.786 76.809 3568 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.88 % Allowed : 26.34 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2296 helix: 1.52 (0.14), residues: 1404 sheet: -0.89 (0.59), residues: 76 loop : -0.07 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 180 TYR 0.022 0.001 TYR B 324 PHE 0.013 0.001 PHE A 553 TRP 0.066 0.003 TRP B 593 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00325 (19728) covalent geometry : angle 0.73584 (26776) hydrogen bonds : bond 0.04085 ( 1053) hydrogen bonds : angle 4.08808 ( 3051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9290.97 seconds wall clock time: 158 minutes 23.40 seconds (9503.40 seconds total)