Starting phenix.real_space_refine on Sun Aug 24 13:40:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf4_41219/08_2025/8tf4_41219.map" } resolution = 2.86 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= 0.003 sd= 0.047 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 S 136 5.16 5 Cl 12 4.86 5 C 13008 2.51 5 N 3268 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-1': 1, 'CPL:plan-2': 1, 'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.07, per 1000 atoms: 0.20 Number of scatterers: 19888 At special positions: 0 Unit cell: (136.95, 136.95, 121.18, 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) Cl 12 17.00 S 136 16.00 P 4 15.00 O 3460 8.00 N 3268 7.00 C 13008 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: 1.54 Conformation dependent library (CDL) restraints added in 728.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 71.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.660A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.741A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.622A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.974A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.655A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.613A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.626A 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 566 removed outlier: 3.778A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 608 removed outlier: 3.929A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.660A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.741A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.622A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.974A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.654A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.613A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 488 through 513 removed outlier: 3.625A 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 566 removed outlier: 3.779A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 608 removed outlier: 3.929A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.661A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 224 removed outlier: 3.740A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.622A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.974A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.655A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.613A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 513 removed outlier: 3.626A 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 566 removed outlier: 3.779A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 608 removed outlier: 3.929A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 Processing helix chain 'D' and resid 29 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.660A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.741A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.621A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.974A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.654A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.613A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 488 through 513 removed outlier: 3.626A 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 566 removed outlier: 3.777A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 608 removed outlier: 3.929A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.380A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (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: 6.381A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (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: 6.380A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (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: 6.381A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1193 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3423 1.31 - 1.44: 5105 1.44 - 1.57: 11572 1.57 - 1.70: 16 1.70 - 1.82: 236 Bond restraints: 20352 Sorted by residual: bond pdb=" C PRO C 544 " pdb=" O PRO C 544 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C PRO A 544 " pdb=" O PRO A 544 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C PRO D 544 " pdb=" O PRO D 544 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.13e-02 7.83e+03 1.62e+01 bond pdb=" C PRO B 544 " pdb=" O PRO B 544 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.13e-02 7.83e+03 1.59e+01 bond pdb=" CA SER D 291 " pdb=" CB SER D 291 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.55e-02 4.16e+03 1.24e+01 ... (remaining 20347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 23157 2.47 - 4.95: 4239 4.95 - 7.42: 196 7.42 - 9.90: 16 9.90 - 12.37: 4 Bond angle restraints: 27612 Sorted by residual: angle pdb=" N GLN C 73 " pdb=" CA GLN C 73 " pdb=" C GLN C 73 " ideal model delta sigma weight residual 112.93 106.25 6.68 1.12e+00 7.97e-01 3.56e+01 angle pdb=" N GLN A 73 " pdb=" CA GLN A 73 " pdb=" C GLN A 73 " ideal model delta sigma weight residual 112.93 106.26 6.67 1.12e+00 7.97e-01 3.54e+01 angle pdb=" N GLN D 73 " pdb=" CA GLN D 73 " pdb=" C GLN D 73 " ideal model delta sigma weight residual 112.93 106.27 6.66 1.12e+00 7.97e-01 3.53e+01 angle pdb=" N GLN B 73 " pdb=" CA GLN B 73 " pdb=" C GLN B 73 " ideal model delta sigma weight residual 112.93 106.29 6.64 1.12e+00 7.97e-01 3.51e+01 angle pdb=" N PHE B 72 " pdb=" CA PHE B 72 " pdb=" C PHE B 72 " ideal model delta sigma weight residual 112.54 105.58 6.96 1.22e+00 6.72e-01 3.26e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 12222 32.85 - 65.70: 250 65.70 - 98.55: 48 98.55 - 131.39: 4 131.39 - 164.24: 12 Dihedral angle restraints: 12536 sinusoidal: 5508 harmonic: 7028 Sorted by residual: dihedral pdb=" C3 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C2 CPL B 801 " pdb=" O3P CPL B 801 " ideal model delta sinusoidal sigma weight residual 72.09 -123.67 -164.24 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 CPL A 805 " pdb=" C1 CPL A 805 " pdb=" C2 CPL A 805 " pdb=" O3P CPL A 805 " ideal model delta sinusoidal sigma weight residual 72.09 -123.68 -164.23 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 CPL C 801 " pdb=" C1 CPL C 801 " pdb=" C2 CPL C 801 " pdb=" O3P CPL C 801 " ideal model delta sinusoidal sigma weight residual 72.09 -123.68 -164.23 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 12533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1624 0.058 - 0.116: 977 0.116 - 0.174: 368 0.174 - 0.232: 111 0.232 - 0.290: 48 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3125 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 802 " -0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG B 802 " 0.106 2.00e-02 2.50e+03 pdb=" C23 ERG B 802 " 0.141 2.00e-02 2.50e+03 pdb=" C24 ERG B 802 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG D 802 " 0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG D 802 " -0.106 2.00e-02 2.50e+03 pdb=" C23 ERG D 802 " -0.141 2.00e-02 2.50e+03 pdb=" C24 ERG D 802 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 801 " -0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG A 801 " 0.106 2.00e-02 2.50e+03 pdb=" C23 ERG A 801 " 0.141 2.00e-02 2.50e+03 pdb=" C24 ERG A 801 " -0.127 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4252 2.82 - 3.34: 19762 3.34 - 3.86: 34016 3.86 - 4.38: 41765 4.38 - 4.90: 70044 Nonbonded interactions: 169839 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.302 3.040 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.302 3.040 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.302 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.302 3.040 nonbonded pdb=" NH2 ARG C 146 " pdb=" OE1 GLU C 164 " model vdw 2.482 3.120 ... (remaining 169834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802)) selection = (chain 'B' and (resid 28 through 637 or resid 802)) selection = (chain 'C' and (resid 28 through 637 or resid 802)) selection = (chain 'D' and (resid 28 through 637 or resid 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.840 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.012 0.056 20352 Z= 0.725 Angle : 1.774 12.371 27612 Z= 1.198 Chirality : 0.086 0.290 3128 Planarity : 0.013 0.124 3424 Dihedral : 15.620 164.242 7992 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.58 % Allowed : 0.96 % Favored : 98.46 % 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 aren not related in a simple way. whole: -0.60 (0.16), residues: 2384 helix: -0.65 (0.12), residues: 1476 sheet: -0.04 (0.53), residues: 76 loop : 0.47 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 43 TYR 0.108 0.022 TYR A 336 PHE 0.056 0.013 PHE C 256 TRP 0.153 0.018 TRP C 593 HIS 0.009 0.003 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.01183 (20352) covalent geometry : angle 1.77365 (27612) hydrogen bonds : bond 0.17617 ( 1193) hydrogen bonds : angle 6.38834 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 378 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6990 (ttt90) cc_final: 0.6437 (ttt90) REVERT: A 43 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6827 (mmm-85) REVERT: A 80 GLU cc_start: 0.7819 (pt0) cc_final: 0.7483 (pm20) REVERT: A 139 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7251 (mtt-85) REVERT: A 153 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7636 (mpt-90) REVERT: A 176 GLU cc_start: 0.6891 (mp0) cc_final: 0.6611 (tt0) REVERT: A 257 GLN cc_start: 0.7426 (pt0) cc_final: 0.6402 (tp40) REVERT: A 260 MET cc_start: 0.8349 (mmp) cc_final: 0.8143 (mmm) REVERT: A 261 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8110 (mm110) REVERT: A 262 LYS cc_start: 0.8282 (mttt) cc_final: 0.7664 (ptpt) REVERT: A 300 LYS cc_start: 0.8001 (pttm) cc_final: 0.7700 (ptpt) REVERT: A 302 ARG cc_start: 0.7795 (ptp90) cc_final: 0.7376 (ppp-140) REVERT: A 451 VAL cc_start: 0.8419 (t) cc_final: 0.8192 (p) REVERT: A 473 GLN cc_start: 0.8500 (tt0) cc_final: 0.8145 (tp40) REVERT: A 483 GLN cc_start: 0.8054 (tt0) cc_final: 0.7825 (tm-30) REVERT: A 491 MET cc_start: 0.8144 (mmm) cc_final: 0.7649 (tpp) REVERT: B 33 ARG cc_start: 0.6987 (ttt90) cc_final: 0.6439 (ttt90) REVERT: B 43 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6819 (mmm-85) REVERT: B 100 GLU cc_start: 0.7830 (tt0) cc_final: 0.7625 (mt-10) REVERT: B 139 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7232 (mtt-85) REVERT: B 176 GLU cc_start: 0.6910 (mp0) cc_final: 0.6610 (tt0) REVERT: B 184 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 260 MET cc_start: 0.8329 (mmp) cc_final: 0.8126 (mmm) REVERT: B 262 LYS cc_start: 0.8258 (mttt) cc_final: 0.7698 (ptpt) REVERT: B 300 LYS cc_start: 0.7991 (pttm) cc_final: 0.7703 (ptpt) REVERT: B 302 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7376 (ppp-140) REVERT: B 451 VAL cc_start: 0.8390 (t) cc_final: 0.8160 (p) REVERT: B 473 GLN cc_start: 0.8512 (tt0) cc_final: 0.8130 (tp40) REVERT: B 483 GLN cc_start: 0.8048 (tt0) cc_final: 0.7826 (tm-30) REVERT: B 491 MET cc_start: 0.8124 (mmm) cc_final: 0.7634 (tpp) REVERT: C 33 ARG cc_start: 0.7002 (ttt90) cc_final: 0.6464 (ttt90) REVERT: C 43 ARG cc_start: 0.7137 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: C 139 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7244 (mtt-85) REVERT: C 176 GLU cc_start: 0.6909 (mp0) cc_final: 0.6608 (tt0) REVERT: C 260 MET cc_start: 0.8331 (mmp) cc_final: 0.8129 (mmm) REVERT: C 261 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8101 (mm110) REVERT: C 262 LYS cc_start: 0.8260 (mttt) cc_final: 0.7697 (ptpt) REVERT: C 300 LYS cc_start: 0.7995 (pttm) cc_final: 0.7705 (ptpt) REVERT: C 302 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7377 (ppp-140) REVERT: C 451 VAL cc_start: 0.8398 (t) cc_final: 0.8168 (p) REVERT: C 473 GLN cc_start: 0.8513 (tt0) cc_final: 0.8129 (tp40) REVERT: C 483 GLN cc_start: 0.8047 (tt0) cc_final: 0.7826 (tm-30) REVERT: C 491 MET cc_start: 0.8127 (mmm) cc_final: 0.7636 (tpp) REVERT: D 33 ARG cc_start: 0.7032 (ttt90) cc_final: 0.6502 (ttt90) REVERT: D 43 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6831 (mmm-85) REVERT: D 139 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7235 (mtt-85) REVERT: D 176 GLU cc_start: 0.6889 (mp0) cc_final: 0.6598 (tt0) REVERT: D 260 MET cc_start: 0.8332 (mmp) cc_final: 0.8129 (mmm) REVERT: D 261 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8099 (mm110) REVERT: D 262 LYS cc_start: 0.8257 (mttt) cc_final: 0.7691 (ptpt) REVERT: D 300 LYS cc_start: 0.7981 (pttm) cc_final: 0.7702 (ptpt) REVERT: D 302 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7375 (ppp-140) REVERT: D 451 VAL cc_start: 0.8395 (t) cc_final: 0.8165 (p) REVERT: D 473 GLN cc_start: 0.8505 (tt0) cc_final: 0.8117 (tp40) REVERT: D 483 GLN cc_start: 0.8049 (tt0) cc_final: 0.7831 (tm-30) REVERT: D 491 MET cc_start: 0.8126 (mmm) cc_final: 0.7634 (tpp) outliers start: 12 outliers final: 4 residues processed: 386 average time/residue: 0.6584 time to fit residues: 282.3920 Evaluate side-chains 278 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain D residue 315 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 473 GLN A 596 GLN B 74 GLN B 261 GLN B 473 GLN B 596 GLN C 74 GLN C 473 GLN C 596 GLN D 74 GLN D 473 GLN D 596 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110802 restraints weight = 22631.485| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.56 r_work: 0.2923 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20352 Z= 0.135 Angle : 0.566 6.407 27612 Z= 0.294 Chirality : 0.039 0.138 3128 Planarity : 0.004 0.035 3424 Dihedral : 12.870 163.791 3440 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.92 % Allowed : 6.11 % Favored : 91.97 % 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 aren not related in a simple way. whole: 1.56 (0.17), residues: 2384 helix: 1.40 (0.13), residues: 1520 sheet: -1.12 (0.40), residues: 128 loop : 0.93 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.014 0.002 TYR D 555 PHE 0.020 0.002 PHE A 611 TRP 0.023 0.002 TRP C 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00286 (20352) covalent geometry : angle 0.56617 (27612) hydrogen bonds : bond 0.05269 ( 1193) hydrogen bonds : angle 4.01392 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7290 (mmm-85) REVERT: A 90 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: A 176 GLU cc_start: 0.7304 (mp0) cc_final: 0.6960 (tt0) REVERT: A 193 ASP cc_start: 0.7418 (t0) cc_final: 0.7119 (t70) REVERT: A 257 GLN cc_start: 0.7720 (pt0) cc_final: 0.7054 (tp40) REVERT: A 262 LYS cc_start: 0.8560 (mttt) cc_final: 0.8025 (ptpt) REVERT: A 300 LYS cc_start: 0.8225 (pttm) cc_final: 0.7960 (ptpt) REVERT: A 302 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7699 (ptm160) REVERT: A 354 LEU cc_start: 0.8689 (mt) cc_final: 0.8479 (mm) REVERT: A 491 MET cc_start: 0.8185 (mmm) cc_final: 0.7854 (tpp) REVERT: B 43 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: B 90 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: B 97 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6893 (mm) REVERT: B 139 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7791 (mtt-85) REVERT: B 176 GLU cc_start: 0.7304 (mp0) cc_final: 0.6953 (tt0) REVERT: B 193 ASP cc_start: 0.7499 (t0) cc_final: 0.7174 (t70) REVERT: B 257 GLN cc_start: 0.7655 (pt0) cc_final: 0.6958 (tp40) REVERT: B 262 LYS cc_start: 0.8577 (mttt) cc_final: 0.8044 (ptpt) REVERT: B 300 LYS cc_start: 0.8208 (pttm) cc_final: 0.7941 (ptpt) REVERT: B 302 ARG cc_start: 0.8313 (ptp90) cc_final: 0.7701 (ptm160) REVERT: B 491 MET cc_start: 0.8185 (mmm) cc_final: 0.7848 (tpp) REVERT: C 43 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7321 (mmm-85) REVERT: C 80 GLU cc_start: 0.8388 (pt0) cc_final: 0.8099 (pm20) REVERT: C 90 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: C 97 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6890 (mm) REVERT: C 139 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7669 (mtt-85) REVERT: C 176 GLU cc_start: 0.7303 (mp0) cc_final: 0.6958 (tt0) REVERT: C 193 ASP cc_start: 0.7457 (t0) cc_final: 0.7135 (t70) REVERT: C 257 GLN cc_start: 0.7708 (pt0) cc_final: 0.6992 (tp40) REVERT: C 262 LYS cc_start: 0.8542 (mttt) cc_final: 0.8020 (ptpt) REVERT: C 300 LYS cc_start: 0.8200 (pttm) cc_final: 0.7934 (ptpt) REVERT: C 302 ARG cc_start: 0.8311 (ptp90) cc_final: 0.7696 (ptm160) REVERT: C 354 LEU cc_start: 0.8677 (mt) cc_final: 0.8454 (mm) REVERT: C 364 ASP cc_start: 0.8000 (t0) cc_final: 0.7793 (t0) REVERT: C 491 MET cc_start: 0.8189 (mmm) cc_final: 0.7854 (tpp) REVERT: D 43 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: D 80 GLU cc_start: 0.8383 (pt0) cc_final: 0.8115 (pm20) REVERT: D 90 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: D 139 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7795 (mtt-85) REVERT: D 176 GLU cc_start: 0.7319 (mp0) cc_final: 0.6959 (tt0) REVERT: D 193 ASP cc_start: 0.7473 (t0) cc_final: 0.7149 (t70) REVERT: D 257 GLN cc_start: 0.7685 (pt0) cc_final: 0.6980 (tp40) REVERT: D 262 LYS cc_start: 0.8551 (mttt) cc_final: 0.8022 (ptpt) REVERT: D 300 LYS cc_start: 0.8210 (pttm) cc_final: 0.7945 (ptpt) REVERT: D 302 ARG cc_start: 0.8313 (ptp90) cc_final: 0.7709 (ptm-80) REVERT: D 491 MET cc_start: 0.8190 (mmm) cc_final: 0.7851 (tpp) outliers start: 40 outliers final: 8 residues processed: 316 average time/residue: 0.7758 time to fit residues: 271.0066 Evaluate side-chains 263 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 218 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 0.0050 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111034 restraints weight = 22765.129| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.57 r_work: 0.2918 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.128 Angle : 0.539 8.970 27612 Z= 0.273 Chirality : 0.038 0.138 3128 Planarity : 0.004 0.034 3424 Dihedral : 11.929 162.469 3428 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.88 % Allowed : 8.17 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1528 sheet: -1.43 (0.40), residues: 128 loop : 1.02 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 409 TYR 0.013 0.001 TYR D 89 PHE 0.013 0.002 PHE D 534 TRP 0.019 0.002 TRP C 593 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00280 (20352) covalent geometry : angle 0.53896 (27612) hydrogen bonds : bond 0.04606 ( 1193) hydrogen bonds : angle 3.77478 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7346 (tpt-90) cc_final: 0.6985 (mtm180) REVERT: A 35 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7558 (ttt90) REVERT: A 43 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7299 (mmm-85) REVERT: A 80 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 97 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6849 (mm) REVERT: A 176 GLU cc_start: 0.7339 (mp0) cc_final: 0.6937 (tt0) REVERT: A 257 GLN cc_start: 0.7622 (pt0) cc_final: 0.6998 (tp40) REVERT: A 261 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8308 (mm110) REVERT: A 262 LYS cc_start: 0.8541 (mttt) cc_final: 0.8109 (mttp) REVERT: A 300 LYS cc_start: 0.8240 (pttm) cc_final: 0.7971 (ptpt) REVERT: A 302 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7587 (ptm-80) REVERT: A 491 MET cc_start: 0.8174 (mmm) cc_final: 0.7849 (tpp) REVERT: B 33 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.6868 (mtm180) REVERT: B 43 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7278 (mmm-85) REVERT: B 97 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6843 (mm) REVERT: B 139 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7800 (mtt-85) REVERT: B 176 GLU cc_start: 0.7357 (mp0) cc_final: 0.6975 (tt0) REVERT: B 257 GLN cc_start: 0.7592 (pt0) cc_final: 0.7046 (tp40) REVERT: B 262 LYS cc_start: 0.8545 (mttt) cc_final: 0.8122 (mttp) REVERT: B 300 LYS cc_start: 0.8225 (pttm) cc_final: 0.7966 (ptpt) REVERT: B 302 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7623 (ptm-80) REVERT: B 491 MET cc_start: 0.8163 (mmm) cc_final: 0.7834 (tpp) REVERT: C 33 ARG cc_start: 0.7432 (tpt-90) cc_final: 0.6864 (mtm180) REVERT: C 43 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: C 80 GLU cc_start: 0.8391 (pt0) cc_final: 0.8118 (pm20) REVERT: C 97 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6869 (mm) REVERT: C 139 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7778 (mtt-85) REVERT: C 176 GLU cc_start: 0.7356 (mp0) cc_final: 0.6972 (tt0) REVERT: C 257 GLN cc_start: 0.7623 (pt0) cc_final: 0.6970 (tp40) REVERT: C 262 LYS cc_start: 0.8535 (mttt) cc_final: 0.8102 (mttp) REVERT: C 300 LYS cc_start: 0.8219 (pttm) cc_final: 0.7961 (ptpt) REVERT: C 302 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7620 (ptm-80) REVERT: C 323 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8131 (tppt) REVERT: C 364 ASP cc_start: 0.8042 (t0) cc_final: 0.7841 (t0) REVERT: C 491 MET cc_start: 0.8171 (mmm) cc_final: 0.7842 (tpp) REVERT: D 33 ARG cc_start: 0.7446 (tpt-90) cc_final: 0.6878 (mtm180) REVERT: D 43 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7307 (mmm-85) REVERT: D 80 GLU cc_start: 0.8419 (pt0) cc_final: 0.8149 (pm20) REVERT: D 97 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6839 (mm) REVERT: D 139 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7785 (mtt-85) REVERT: D 176 GLU cc_start: 0.7375 (mp0) cc_final: 0.6972 (tt0) REVERT: D 257 GLN cc_start: 0.7615 (pt0) cc_final: 0.7001 (tp40) REVERT: D 262 LYS cc_start: 0.8533 (mttt) cc_final: 0.8103 (mttp) REVERT: D 300 LYS cc_start: 0.8225 (pttm) cc_final: 0.7967 (ptpt) REVERT: D 302 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7622 (ptm-80) REVERT: D 323 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8133 (tppt) REVERT: D 491 MET cc_start: 0.8185 (mmm) cc_final: 0.7855 (tpp) outliers start: 39 outliers final: 8 residues processed: 298 average time/residue: 0.7335 time to fit residues: 243.1118 Evaluate side-chains 259 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 234 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112348 restraints weight = 22718.985| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.46 r_work: 0.3026 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.120 Angle : 0.502 6.877 27612 Z= 0.255 Chirality : 0.038 0.180 3128 Planarity : 0.004 0.036 3424 Dihedral : 11.527 162.417 3428 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.39 % Allowed : 8.46 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.17), residues: 2384 helix: 1.96 (0.13), residues: 1520 sheet: -1.53 (0.42), residues: 128 loop : 1.06 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 409 TYR 0.012 0.001 TYR B 555 PHE 0.023 0.001 PHE D 611 TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00269 (20352) covalent geometry : angle 0.50170 (27612) hydrogen bonds : bond 0.04302 ( 1193) hydrogen bonds : angle 3.70707 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7356 (tpt-90) cc_final: 0.7053 (mtm180) REVERT: A 74 GLN cc_start: 0.7408 (mt0) cc_final: 0.7177 (mt0) REVERT: A 97 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7016 (mm) REVERT: A 176 GLU cc_start: 0.7404 (mp0) cc_final: 0.7082 (tt0) REVERT: A 257 GLN cc_start: 0.7603 (pt0) cc_final: 0.7105 (tp40) REVERT: A 262 LYS cc_start: 0.8493 (mttt) cc_final: 0.8121 (mttp) REVERT: A 300 LYS cc_start: 0.8284 (pttm) cc_final: 0.8042 (ptpt) REVERT: A 302 ARG cc_start: 0.8188 (ptp90) cc_final: 0.7616 (ptm-80) REVERT: A 382 ASP cc_start: 0.8134 (m-30) cc_final: 0.7733 (m-30) REVERT: A 491 MET cc_start: 0.8224 (mmm) cc_final: 0.7904 (tpp) REVERT: B 33 ARG cc_start: 0.7421 (tpt-90) cc_final: 0.6930 (mtm180) REVERT: B 35 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7543 (ttt90) REVERT: B 97 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7029 (mm) REVERT: B 139 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7846 (mtt-85) REVERT: B 176 GLU cc_start: 0.7418 (mp0) cc_final: 0.7093 (tt0) REVERT: B 257 GLN cc_start: 0.7558 (pt0) cc_final: 0.7104 (tp40) REVERT: B 262 LYS cc_start: 0.8519 (mttt) cc_final: 0.8157 (mttp) REVERT: B 300 LYS cc_start: 0.8265 (pttm) cc_final: 0.8035 (ptpt) REVERT: B 302 ARG cc_start: 0.8165 (ptp90) cc_final: 0.7593 (ptm-80) REVERT: B 374 GLN cc_start: 0.7893 (mp-120) cc_final: 0.7629 (pm20) REVERT: B 382 ASP cc_start: 0.8129 (m-30) cc_final: 0.7701 (m-30) REVERT: B 491 MET cc_start: 0.8201 (mmm) cc_final: 0.7876 (tpp) REVERT: C 33 ARG cc_start: 0.7392 (tpt-90) cc_final: 0.6896 (mtm180) REVERT: C 35 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7523 (ttt90) REVERT: C 97 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7002 (mm) REVERT: C 139 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7866 (mtt-85) REVERT: C 176 GLU cc_start: 0.7435 (mp0) cc_final: 0.7100 (tt0) REVERT: C 257 GLN cc_start: 0.7545 (pt0) cc_final: 0.7094 (tp40) REVERT: C 262 LYS cc_start: 0.8516 (mttt) cc_final: 0.8153 (mttp) REVERT: C 300 LYS cc_start: 0.8265 (pttm) cc_final: 0.8035 (ptpt) REVERT: C 302 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7603 (ptm-80) REVERT: C 364 ASP cc_start: 0.8052 (t0) cc_final: 0.7828 (t0) REVERT: C 491 MET cc_start: 0.8220 (mmm) cc_final: 0.7897 (tpp) REVERT: D 33 ARG cc_start: 0.7413 (tpt-90) cc_final: 0.6922 (mtm180) REVERT: D 35 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7528 (ttt90) REVERT: D 97 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6981 (mm) REVERT: D 139 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7836 (mtt-85) REVERT: D 176 GLU cc_start: 0.7442 (mp0) cc_final: 0.7095 (tt0) REVERT: D 257 GLN cc_start: 0.7559 (pt0) cc_final: 0.7027 (tp40) REVERT: D 262 LYS cc_start: 0.8479 (mttt) cc_final: 0.8109 (mttp) REVERT: D 300 LYS cc_start: 0.8274 (pttm) cc_final: 0.8039 (ptpt) REVERT: D 302 ARG cc_start: 0.8197 (ptp90) cc_final: 0.7651 (ptm-80) REVERT: D 382 ASP cc_start: 0.8125 (m-30) cc_final: 0.7705 (m-30) REVERT: D 491 MET cc_start: 0.8230 (mmm) cc_final: 0.7903 (tpp) outliers start: 29 outliers final: 6 residues processed: 274 average time/residue: 0.7735 time to fit residues: 234.5110 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 155 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 206 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100384 restraints weight = 22937.788| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.72 r_work: 0.2913 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20352 Z= 0.111 Angle : 0.478 5.575 27612 Z= 0.244 Chirality : 0.037 0.135 3128 Planarity : 0.004 0.034 3424 Dihedral : 11.196 159.901 3428 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.44 % Allowed : 9.42 % Favored : 89.13 % 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 aren not related in a simple way. whole: 2.23 (0.17), residues: 2384 helix: 2.04 (0.13), residues: 1524 sheet: -1.57 (0.43), residues: 128 loop : 1.05 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 409 TYR 0.012 0.001 TYR B 555 PHE 0.011 0.001 PHE A 534 TRP 0.015 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00245 (20352) covalent geometry : angle 0.47820 (27612) hydrogen bonds : bond 0.04078 ( 1193) hydrogen bonds : angle 3.64664 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7333 (tpt-90) cc_final: 0.7041 (mtm180) REVERT: A 35 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7533 (ttt90) REVERT: A 74 GLN cc_start: 0.7379 (mt0) cc_final: 0.7163 (mt0) REVERT: A 97 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6811 (mm) REVERT: A 176 GLU cc_start: 0.7342 (mp0) cc_final: 0.6912 (tt0) REVERT: A 257 GLN cc_start: 0.7485 (pt0) cc_final: 0.6997 (tp40) REVERT: A 261 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8276 (mm110) REVERT: A 262 LYS cc_start: 0.8534 (mttt) cc_final: 0.8080 (mttp) REVERT: A 300 LYS cc_start: 0.8248 (pttm) cc_final: 0.7942 (ptpt) REVERT: A 302 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7474 (ptm160) REVERT: A 309 GLU cc_start: 0.8257 (mp0) cc_final: 0.7200 (mp0) REVERT: A 382 ASP cc_start: 0.8088 (m-30) cc_final: 0.7591 (m-30) REVERT: A 491 MET cc_start: 0.8229 (mmm) cc_final: 0.7908 (tpp) REVERT: B 33 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.6905 (mtm180) REVERT: B 35 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7545 (ttt90) REVERT: B 97 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6851 (mm) REVERT: B 139 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7732 (mtt-85) REVERT: B 176 GLU cc_start: 0.7374 (mp0) cc_final: 0.6959 (tt0) REVERT: B 257 GLN cc_start: 0.7483 (pt0) cc_final: 0.7124 (tp40) REVERT: B 262 LYS cc_start: 0.8551 (mttt) cc_final: 0.8128 (mttp) REVERT: B 300 LYS cc_start: 0.8238 (pttm) cc_final: 0.7931 (ptpt) REVERT: B 302 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7455 (ptm160) REVERT: B 309 GLU cc_start: 0.8247 (mp0) cc_final: 0.7183 (mp0) REVERT: B 374 GLN cc_start: 0.7931 (mp-120) cc_final: 0.7695 (pm20) REVERT: B 382 ASP cc_start: 0.8095 (m-30) cc_final: 0.7667 (m-30) REVERT: B 491 MET cc_start: 0.8225 (mmm) cc_final: 0.7895 (tpp) REVERT: C 33 ARG cc_start: 0.7325 (tpt-90) cc_final: 0.6880 (mtm180) REVERT: C 35 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7532 (ttt90) REVERT: C 97 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6895 (mm) REVERT: C 139 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7729 (mtt-85) REVERT: C 176 GLU cc_start: 0.7366 (mp0) cc_final: 0.6944 (tt0) REVERT: C 257 GLN cc_start: 0.7479 (pt0) cc_final: 0.7072 (tp40) REVERT: C 262 LYS cc_start: 0.8561 (mttt) cc_final: 0.8104 (mttp) REVERT: C 300 LYS cc_start: 0.8243 (pttm) cc_final: 0.7936 (ptpt) REVERT: C 302 ARG cc_start: 0.8127 (ptp90) cc_final: 0.7461 (ptm160) REVERT: C 309 GLU cc_start: 0.8237 (mp0) cc_final: 0.7174 (mp0) REVERT: C 374 GLN cc_start: 0.7888 (mp-120) cc_final: 0.7593 (pm20) REVERT: C 491 MET cc_start: 0.8233 (mmm) cc_final: 0.7902 (tpp) REVERT: D 33 ARG cc_start: 0.7335 (tpt-90) cc_final: 0.6891 (mtm180) REVERT: D 35 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7536 (ttt90) REVERT: D 97 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6870 (mm) REVERT: D 139 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7725 (mtt-85) REVERT: D 176 GLU cc_start: 0.7384 (mp0) cc_final: 0.6936 (tt0) REVERT: D 257 GLN cc_start: 0.7468 (pt0) cc_final: 0.7061 (tp40) REVERT: D 262 LYS cc_start: 0.8545 (mttt) cc_final: 0.8091 (mttp) REVERT: D 300 LYS cc_start: 0.8249 (pttm) cc_final: 0.7944 (ptpt) REVERT: D 302 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7511 (ptm160) REVERT: D 309 GLU cc_start: 0.8247 (mp0) cc_final: 0.7187 (mp0) REVERT: D 374 GLN cc_start: 0.7890 (mp-120) cc_final: 0.7592 (pm20) REVERT: D 382 ASP cc_start: 0.8066 (m-30) cc_final: 0.7603 (m-30) REVERT: D 491 MET cc_start: 0.8236 (mmm) cc_final: 0.7908 (tpp) outliers start: 30 outliers final: 13 residues processed: 265 average time/residue: 0.6805 time to fit residues: 200.4125 Evaluate side-chains 255 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN C 261 GLN D 261 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.093986 restraints weight = 23026.728| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.72 r_work: 0.2831 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20352 Z= 0.201 Angle : 0.550 5.849 27612 Z= 0.280 Chirality : 0.041 0.139 3128 Planarity : 0.004 0.035 3424 Dihedral : 11.527 161.593 3428 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.97 % Allowed : 9.57 % Favored : 88.46 % 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 aren not related in a simple way. whole: 1.81 (0.17), residues: 2384 helix: 1.77 (0.13), residues: 1528 sheet: -1.94 (0.40), residues: 128 loop : 0.77 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 409 TYR 0.014 0.002 TYR D 89 PHE 0.026 0.002 PHE B 611 TRP 0.011 0.002 TRP A 593 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00504 (20352) covalent geometry : angle 0.55017 (27612) hydrogen bonds : bond 0.05073 ( 1193) hydrogen bonds : angle 3.87660 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7317 (tpt-90) cc_final: 0.6917 (mtm180) REVERT: A 35 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7571 (ttt90) REVERT: A 97 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6796 (mm) REVERT: A 176 GLU cc_start: 0.7440 (mp0) cc_final: 0.6917 (tt0) REVERT: A 193 ASP cc_start: 0.7740 (t0) cc_final: 0.7536 (t0) REVERT: A 257 GLN cc_start: 0.7644 (pt0) cc_final: 0.7044 (tp40) REVERT: A 262 LYS cc_start: 0.8634 (mttt) cc_final: 0.8128 (mttp) REVERT: A 300 LYS cc_start: 0.8216 (pttm) cc_final: 0.7926 (ptpt) REVERT: A 302 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7605 (ptm160) REVERT: A 374 GLN cc_start: 0.7827 (mp-120) cc_final: 0.7559 (pm20) REVERT: A 382 ASP cc_start: 0.8118 (m-30) cc_final: 0.7629 (m-30) REVERT: A 491 MET cc_start: 0.8245 (mmm) cc_final: 0.7865 (tpp) REVERT: B 33 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.6971 (ttp80) REVERT: B 35 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7571 (ttt90) REVERT: B 97 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6763 (mm) REVERT: B 139 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7627 (mtt-85) REVERT: B 176 GLU cc_start: 0.7472 (mp0) cc_final: 0.6908 (tt0) REVERT: B 193 ASP cc_start: 0.7781 (t0) cc_final: 0.7577 (t0) REVERT: B 262 LYS cc_start: 0.8606 (mttt) cc_final: 0.8107 (mttp) REVERT: B 300 LYS cc_start: 0.8213 (pttm) cc_final: 0.7921 (ptpt) REVERT: B 302 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7586 (ptm160) REVERT: B 382 ASP cc_start: 0.8114 (m-30) cc_final: 0.7663 (m-30) REVERT: B 491 MET cc_start: 0.8232 (mmm) cc_final: 0.7850 (tpp) REVERT: B 522 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: C 33 ARG cc_start: 0.7344 (tpt-90) cc_final: 0.6956 (ttp80) REVERT: C 35 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7574 (ttt90) REVERT: C 97 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6785 (mm) REVERT: C 139 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7580 (mtt-85) REVERT: C 176 GLU cc_start: 0.7478 (mp0) cc_final: 0.6919 (tt0) REVERT: C 193 ASP cc_start: 0.7776 (t0) cc_final: 0.7566 (t0) REVERT: C 262 LYS cc_start: 0.8611 (mttt) cc_final: 0.8113 (mttp) REVERT: C 300 LYS cc_start: 0.8214 (pttm) cc_final: 0.7916 (ptpt) REVERT: C 302 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7599 (ptm160) REVERT: C 491 MET cc_start: 0.8240 (mmm) cc_final: 0.7857 (tpp) REVERT: D 33 ARG cc_start: 0.7380 (tpt-90) cc_final: 0.6977 (ttp80) REVERT: D 35 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7576 (ttt90) REVERT: D 97 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6763 (mm) REVERT: D 139 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7583 (mtt-85) REVERT: D 176 GLU cc_start: 0.7477 (mp0) cc_final: 0.6918 (tt0) REVERT: D 193 ASP cc_start: 0.7763 (t0) cc_final: 0.7553 (t0) REVERT: D 257 GLN cc_start: 0.7563 (pt0) cc_final: 0.7003 (tp40) REVERT: D 262 LYS cc_start: 0.8661 (mttt) cc_final: 0.8139 (mttp) REVERT: D 300 LYS cc_start: 0.8204 (pttm) cc_final: 0.7909 (ptpt) REVERT: D 302 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7591 (ptm160) REVERT: D 382 ASP cc_start: 0.8106 (m-30) cc_final: 0.7762 (m-30) REVERT: D 491 MET cc_start: 0.8242 (mmm) cc_final: 0.7862 (tpp) outliers start: 41 outliers final: 16 residues processed: 262 average time/residue: 0.6888 time to fit residues: 200.3361 Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 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 51 GLN A 261 GLN B 51 GLN B 261 GLN B 310 GLN C 51 GLN C 261 GLN C 310 GLN D 51 GLN D 261 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112279 restraints weight = 22481.353| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.45 r_work: 0.2940 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.118 Angle : 0.488 5.877 27612 Z= 0.249 Chirality : 0.037 0.192 3128 Planarity : 0.004 0.036 3424 Dihedral : 11.230 158.873 3428 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.30 % Allowed : 10.77 % Favored : 87.93 % 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 aren not related in a simple way. whole: 2.13 (0.17), residues: 2384 helix: 2.09 (0.13), residues: 1496 sheet: -1.38 (0.44), residues: 108 loop : 0.63 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 409 TYR 0.012 0.001 TYR B 555 PHE 0.010 0.001 PHE C 534 TRP 0.016 0.001 TRP C 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00264 (20352) covalent geometry : angle 0.48777 (27612) hydrogen bonds : bond 0.04198 ( 1193) hydrogen bonds : angle 3.71133 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7273 (tpt-90) cc_final: 0.6947 (mtm180) REVERT: A 35 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7505 (ttt90) REVERT: A 97 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6885 (mm) REVERT: A 173 VAL cc_start: 0.8216 (t) cc_final: 0.7924 (m) REVERT: A 176 GLU cc_start: 0.7403 (mp0) cc_final: 0.6916 (tt0) REVERT: A 257 GLN cc_start: 0.7417 (pt0) cc_final: 0.7070 (tp40) REVERT: A 262 LYS cc_start: 0.8602 (mttt) cc_final: 0.8126 (mttp) REVERT: A 300 LYS cc_start: 0.8216 (pttm) cc_final: 0.7959 (ptpt) REVERT: A 302 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7563 (ptm160) REVERT: A 374 GLN cc_start: 0.7865 (mp-120) cc_final: 0.7647 (pm20) REVERT: A 382 ASP cc_start: 0.8079 (m-30) cc_final: 0.7595 (m-30) REVERT: A 491 MET cc_start: 0.8183 (mmm) cc_final: 0.7864 (tpp) REVERT: B 33 ARG cc_start: 0.7315 (tpt-90) cc_final: 0.6888 (mtm180) REVERT: B 35 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7525 (ttt90) REVERT: B 97 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6909 (mm) REVERT: B 139 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7751 (mtt-85) REVERT: B 176 GLU cc_start: 0.7423 (mp0) cc_final: 0.6905 (tt0) REVERT: B 257 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: B 262 LYS cc_start: 0.8575 (mttt) cc_final: 0.8095 (mttp) REVERT: B 300 LYS cc_start: 0.8215 (pttm) cc_final: 0.7960 (ptpt) REVERT: B 302 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7555 (ptm160) REVERT: B 309 GLU cc_start: 0.8307 (mp0) cc_final: 0.7237 (mp0) REVERT: B 374 GLN cc_start: 0.7956 (mp-120) cc_final: 0.7667 (pm20) REVERT: B 382 ASP cc_start: 0.8078 (m-30) cc_final: 0.7629 (m-30) REVERT: B 491 MET cc_start: 0.8174 (mmm) cc_final: 0.7854 (tpp) REVERT: C 33 ARG cc_start: 0.7294 (tpt-90) cc_final: 0.6866 (mtm180) REVERT: C 35 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7507 (ttt90) REVERT: C 97 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6885 (mm) REVERT: C 139 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7745 (mtt-85) REVERT: C 176 GLU cc_start: 0.7445 (mp0) cc_final: 0.6918 (tt0) REVERT: C 257 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: C 262 LYS cc_start: 0.8565 (mttt) cc_final: 0.8098 (mttp) REVERT: C 300 LYS cc_start: 0.8221 (pttm) cc_final: 0.7963 (ptpt) REVERT: C 302 ARG cc_start: 0.8124 (ptp90) cc_final: 0.7564 (ptm160) REVERT: C 309 GLU cc_start: 0.8296 (mp0) cc_final: 0.7228 (mp0) REVERT: C 374 GLN cc_start: 0.7984 (mp-120) cc_final: 0.7604 (pm20) REVERT: C 491 MET cc_start: 0.8181 (mmm) cc_final: 0.7859 (tpp) REVERT: D 33 ARG cc_start: 0.7289 (tpt-90) cc_final: 0.6869 (mtm180) REVERT: D 35 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7513 (ttt90) REVERT: D 97 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6912 (mm) REVERT: D 139 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7767 (mtt-85) REVERT: D 176 GLU cc_start: 0.7431 (mp0) cc_final: 0.6909 (tt0) REVERT: D 257 GLN cc_start: 0.7404 (pt0) cc_final: 0.7025 (tp40) REVERT: D 262 LYS cc_start: 0.8607 (mttt) cc_final: 0.8116 (mttp) REVERT: D 300 LYS cc_start: 0.8218 (pttm) cc_final: 0.7964 (ptpt) REVERT: D 302 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7557 (ptm160) REVERT: D 374 GLN cc_start: 0.7949 (mp-120) cc_final: 0.7577 (pm20) REVERT: D 382 ASP cc_start: 0.8080 (m-30) cc_final: 0.7571 (m-30) REVERT: D 491 MET cc_start: 0.8197 (mmm) cc_final: 0.7876 (tpp) outliers start: 27 outliers final: 12 residues processed: 260 average time/residue: 0.6468 time to fit residues: 187.4176 Evaluate side-chains 248 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 223 optimal weight: 0.3980 chunk 184 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN B 51 GLN B 261 GLN C 51 GLN C 261 GLN D 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114860 restraints weight = 22324.375| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.44 r_work: 0.2954 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20352 Z= 0.104 Angle : 0.478 6.821 27612 Z= 0.242 Chirality : 0.037 0.234 3128 Planarity : 0.004 0.042 3424 Dihedral : 10.894 155.888 3428 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.11 % Allowed : 11.06 % Favored : 87.84 % 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 aren not related in a simple way. whole: 2.34 (0.17), residues: 2384 helix: 2.24 (0.13), residues: 1500 sheet: -1.33 (0.45), residues: 108 loop : 0.76 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 409 TYR 0.011 0.001 TYR B 555 PHE 0.032 0.001 PHE A 611 TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00227 (20352) covalent geometry : angle 0.47825 (27612) hydrogen bonds : bond 0.03855 ( 1193) hydrogen bonds : angle 3.62137 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7258 (tpt-90) cc_final: 0.6960 (mtm180) REVERT: A 35 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7468 (ttt90) REVERT: A 97 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6898 (mm) REVERT: A 176 GLU cc_start: 0.7402 (mp0) cc_final: 0.6933 (tt0) REVERT: A 257 GLN cc_start: 0.7325 (pt0) cc_final: 0.7094 (tp40) REVERT: A 262 LYS cc_start: 0.8627 (mttt) cc_final: 0.8136 (mttp) REVERT: A 300 LYS cc_start: 0.8224 (pttm) cc_final: 0.7952 (ptpt) REVERT: A 302 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7470 (ptm160) REVERT: A 309 GLU cc_start: 0.8215 (mp0) cc_final: 0.7233 (mp0) REVERT: A 374 GLN cc_start: 0.7898 (mp-120) cc_final: 0.7658 (pm20) REVERT: A 382 ASP cc_start: 0.8037 (m-30) cc_final: 0.7594 (m-30) REVERT: A 491 MET cc_start: 0.8154 (mmm) cc_final: 0.7819 (tpp) REVERT: B 33 ARG cc_start: 0.7311 (tpt-90) cc_final: 0.6911 (mtm180) REVERT: B 35 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7479 (ttt90) REVERT: B 97 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6908 (mm) REVERT: B 139 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7769 (mtt-85) REVERT: B 176 GLU cc_start: 0.7421 (mp0) cc_final: 0.6965 (tt0) REVERT: B 262 LYS cc_start: 0.8532 (mttt) cc_final: 0.8053 (mttp) REVERT: B 300 LYS cc_start: 0.8224 (pttm) cc_final: 0.7955 (ptpt) REVERT: B 302 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7462 (ptm160) REVERT: B 374 GLN cc_start: 0.7882 (mp-120) cc_final: 0.7605 (pm20) REVERT: B 382 ASP cc_start: 0.8057 (m-30) cc_final: 0.7606 (m-30) REVERT: B 491 MET cc_start: 0.8147 (mmm) cc_final: 0.7806 (tpp) REVERT: B 522 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: C 33 ARG cc_start: 0.7252 (tpt-90) cc_final: 0.6849 (mtm180) REVERT: C 35 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7461 (ttt90) REVERT: C 97 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6863 (mm) REVERT: C 139 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7725 (mtt-85) REVERT: C 176 GLU cc_start: 0.7436 (mp0) cc_final: 0.6974 (tt0) REVERT: C 262 LYS cc_start: 0.8526 (mttt) cc_final: 0.8038 (mttp) REVERT: C 300 LYS cc_start: 0.8229 (pttm) cc_final: 0.7958 (ptpt) REVERT: C 302 ARG cc_start: 0.8037 (ptp90) cc_final: 0.7459 (ptm160) REVERT: C 374 GLN cc_start: 0.7904 (mp-120) cc_final: 0.7545 (pm20) REVERT: C 491 MET cc_start: 0.8149 (mmm) cc_final: 0.7809 (tpp) REVERT: D 33 ARG cc_start: 0.7250 (tpt-90) cc_final: 0.6859 (mtm180) REVERT: D 35 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7462 (ttt90) REVERT: D 97 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (mm) REVERT: D 139 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7750 (mtt-85) REVERT: D 176 GLU cc_start: 0.7433 (mp0) cc_final: 0.6960 (tt0) REVERT: D 257 GLN cc_start: 0.7279 (pt0) cc_final: 0.7061 (tp40) REVERT: D 262 LYS cc_start: 0.8614 (mttt) cc_final: 0.8096 (mppt) REVERT: D 300 LYS cc_start: 0.8221 (pttm) cc_final: 0.7951 (ptpt) REVERT: D 302 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7455 (ptm160) REVERT: D 309 GLU cc_start: 0.8202 (mp0) cc_final: 0.7218 (mp0) REVERT: D 374 GLN cc_start: 0.7909 (mp-120) cc_final: 0.7557 (pm20) REVERT: D 382 ASP cc_start: 0.8016 (m-30) cc_final: 0.7540 (m-30) REVERT: D 491 MET cc_start: 0.8154 (mmm) cc_final: 0.7821 (tpp) outliers start: 23 outliers final: 8 residues processed: 243 average time/residue: 0.6443 time to fit residues: 173.6002 Evaluate side-chains 230 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN B 51 GLN C 51 GLN D 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111600 restraints weight = 22233.274| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.44 r_work: 0.2960 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20352 Z= 0.120 Angle : 0.495 7.128 27612 Z= 0.251 Chirality : 0.037 0.225 3128 Planarity : 0.004 0.054 3424 Dihedral : 10.842 154.044 3428 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.87 % Allowed : 11.83 % Favored : 87.31 % 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 aren not related in a simple way. whole: 2.28 (0.17), residues: 2384 helix: 2.14 (0.13), residues: 1524 sheet: -1.33 (0.45), residues: 108 loop : 0.81 (0.25), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 409 TYR 0.011 0.001 TYR B 555 PHE 0.011 0.001 PHE C 534 TRP 0.013 0.001 TRP D 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00278 (20352) covalent geometry : angle 0.49467 (27612) hydrogen bonds : bond 0.04057 ( 1193) hydrogen bonds : angle 3.64396 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7353 (tpt-90) cc_final: 0.7053 (mtm180) REVERT: A 35 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7561 (ttt90) REVERT: A 97 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6965 (mm) REVERT: A 176 GLU cc_start: 0.7465 (mp0) cc_final: 0.6965 (tt0) REVERT: A 262 LYS cc_start: 0.8659 (mttt) cc_final: 0.8207 (mttp) REVERT: A 300 LYS cc_start: 0.8264 (pttm) cc_final: 0.8006 (ptpt) REVERT: A 302 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7559 (ptm160) REVERT: A 309 GLU cc_start: 0.8303 (mp0) cc_final: 0.7336 (mp0) REVERT: A 374 GLN cc_start: 0.7925 (mp-120) cc_final: 0.7668 (pm20) REVERT: A 382 ASP cc_start: 0.8114 (m-30) cc_final: 0.7690 (m-30) REVERT: A 491 MET cc_start: 0.8227 (mmm) cc_final: 0.7902 (tpp) REVERT: B 33 ARG cc_start: 0.7412 (tpt-90) cc_final: 0.7003 (mtm180) REVERT: B 35 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7554 (ttt90) REVERT: B 97 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6939 (mm) REVERT: B 139 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7804 (mtt-85) REVERT: B 176 GLU cc_start: 0.7440 (mp0) cc_final: 0.6929 (tt0) REVERT: B 262 LYS cc_start: 0.8567 (mttt) cc_final: 0.8080 (mttm) REVERT: B 300 LYS cc_start: 0.8260 (pttm) cc_final: 0.8007 (ptpt) REVERT: B 302 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7559 (ptm160) REVERT: B 309 GLU cc_start: 0.8320 (mp0) cc_final: 0.7287 (mp0) REVERT: B 374 GLN cc_start: 0.7976 (mp-120) cc_final: 0.7664 (pm20) REVERT: B 382 ASP cc_start: 0.8122 (m-30) cc_final: 0.7623 (m-30) REVERT: B 491 MET cc_start: 0.8217 (mmm) cc_final: 0.7891 (tpp) REVERT: C 33 ARG cc_start: 0.7400 (tpt-90) cc_final: 0.7019 (ttp-170) REVERT: C 35 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7553 (ttt90) REVERT: C 97 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6916 (mm) REVERT: C 139 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7793 (mtt-85) REVERT: C 176 GLU cc_start: 0.7481 (mp0) cc_final: 0.6970 (tt0) REVERT: C 262 LYS cc_start: 0.8567 (mttt) cc_final: 0.8119 (mttp) REVERT: C 300 LYS cc_start: 0.8264 (pttm) cc_final: 0.8015 (ptpt) REVERT: C 302 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7561 (ptm160) REVERT: C 309 GLU cc_start: 0.8302 (mp0) cc_final: 0.7262 (mp0) REVERT: C 374 GLN cc_start: 0.7917 (mp-120) cc_final: 0.7546 (pm20) REVERT: C 491 MET cc_start: 0.8226 (mmm) cc_final: 0.7898 (tpp) REVERT: D 33 ARG cc_start: 0.7391 (tpt-90) cc_final: 0.6993 (mtm180) REVERT: D 35 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7552 (ttt90) REVERT: D 97 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6944 (mm) REVERT: D 139 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7787 (mtt-85) REVERT: D 176 GLU cc_start: 0.7462 (mp0) cc_final: 0.6983 (tt0) REVERT: D 262 LYS cc_start: 0.8597 (mttt) cc_final: 0.8136 (mppt) REVERT: D 300 LYS cc_start: 0.8264 (pttm) cc_final: 0.8011 (ptpt) REVERT: D 302 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7568 (ptm160) REVERT: D 309 GLU cc_start: 0.8275 (mp0) cc_final: 0.7303 (mp0) REVERT: D 374 GLN cc_start: 0.7950 (mp-120) cc_final: 0.7576 (pm20) REVERT: D 382 ASP cc_start: 0.8111 (m-30) cc_final: 0.7731 (m-30) REVERT: D 491 MET cc_start: 0.8230 (mmm) cc_final: 0.7905 (tpp) outliers start: 18 outliers final: 10 residues processed: 232 average time/residue: 0.6381 time to fit residues: 164.9854 Evaluate side-chains 228 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN B 261 GLN C 51 GLN C 261 GLN D 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112872 restraints weight = 22429.579| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.44 r_work: 0.2980 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20352 Z= 0.110 Angle : 0.492 7.494 27612 Z= 0.249 Chirality : 0.037 0.216 3128 Planarity : 0.004 0.055 3424 Dihedral : 10.687 151.560 3428 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.91 % Allowed : 12.02 % Favored : 87.07 % 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 aren not related in a simple way. whole: 2.38 (0.17), residues: 2384 helix: 2.28 (0.13), residues: 1500 sheet: -1.28 (0.45), residues: 108 loop : 0.75 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 409 TYR 0.011 0.001 TYR B 555 PHE 0.035 0.001 PHE A 611 TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00246 (20352) covalent geometry : angle 0.49234 (27612) hydrogen bonds : bond 0.03899 ( 1193) hydrogen bonds : angle 3.62501 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7338 (tpt-90) cc_final: 0.7052 (mtm180) REVERT: A 35 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7565 (ttt90) REVERT: A 97 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6990 (mm) REVERT: A 176 GLU cc_start: 0.7514 (mp0) cc_final: 0.7002 (tt0) REVERT: A 193 ASP cc_start: 0.7408 (t0) cc_final: 0.7093 (t0) REVERT: A 262 LYS cc_start: 0.8587 (mttt) cc_final: 0.8130 (mppt) REVERT: A 300 LYS cc_start: 0.8267 (pttm) cc_final: 0.8020 (ptpt) REVERT: A 302 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7546 (ptm160) REVERT: A 309 GLU cc_start: 0.8344 (mp0) cc_final: 0.7423 (mp0) REVERT: A 374 GLN cc_start: 0.7907 (mp-120) cc_final: 0.7649 (pm20) REVERT: A 382 ASP cc_start: 0.8108 (m-30) cc_final: 0.7671 (m-30) REVERT: A 491 MET cc_start: 0.8205 (mmm) cc_final: 0.7882 (tpp) REVERT: B 33 ARG cc_start: 0.7408 (tpt-90) cc_final: 0.7020 (mtm180) REVERT: B 35 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7558 (ttt90) REVERT: B 97 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 139 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7836 (mtt-85) REVERT: B 176 GLU cc_start: 0.7429 (mp0) cc_final: 0.6932 (tt0) REVERT: B 215 MET cc_start: 0.8467 (mmm) cc_final: 0.8191 (tpp) REVERT: B 262 LYS cc_start: 0.8563 (mttt) cc_final: 0.8094 (mttm) REVERT: B 300 LYS cc_start: 0.8276 (pttm) cc_final: 0.8022 (ptpt) REVERT: B 302 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7547 (ptm160) REVERT: B 309 GLU cc_start: 0.8298 (mp0) cc_final: 0.7343 (mp0) REVERT: B 374 GLN cc_start: 0.7947 (mp-120) cc_final: 0.7627 (pm20) REVERT: B 382 ASP cc_start: 0.8121 (m-30) cc_final: 0.7673 (m-30) REVERT: B 491 MET cc_start: 0.8201 (mmm) cc_final: 0.7876 (tpp) REVERT: B 522 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: C 33 ARG cc_start: 0.7395 (tpt-90) cc_final: 0.7029 (ttp-170) REVERT: C 35 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7544 (ttt90) REVERT: C 97 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6901 (mm) REVERT: C 139 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7795 (mtt-85) REVERT: C 176 GLU cc_start: 0.7446 (mp0) cc_final: 0.6913 (tt0) REVERT: C 193 ASP cc_start: 0.7421 (t0) cc_final: 0.7138 (t0) REVERT: C 262 LYS cc_start: 0.8565 (mttt) cc_final: 0.8093 (mttm) REVERT: C 300 LYS cc_start: 0.8284 (pttm) cc_final: 0.8038 (ptpt) REVERT: C 302 ARG cc_start: 0.8085 (ptp90) cc_final: 0.7560 (ptm160) REVERT: C 309 GLU cc_start: 0.8286 (mp0) cc_final: 0.7330 (mp0) REVERT: C 374 GLN cc_start: 0.7936 (mp-120) cc_final: 0.7561 (pm20) REVERT: C 491 MET cc_start: 0.8202 (mmm) cc_final: 0.7876 (tpp) REVERT: D 33 ARG cc_start: 0.7400 (tpt-90) cc_final: 0.7018 (mtm180) REVERT: D 35 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7553 (ttt90) REVERT: D 97 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6938 (mm) REVERT: D 139 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7798 (mtt-85) REVERT: D 176 GLU cc_start: 0.7468 (mp0) cc_final: 0.6914 (tt0) REVERT: D 193 ASP cc_start: 0.7412 (t0) cc_final: 0.7133 (t0) REVERT: D 262 LYS cc_start: 0.8553 (mttt) cc_final: 0.8128 (mppt) REVERT: D 300 LYS cc_start: 0.8278 (pttm) cc_final: 0.8032 (ptpt) REVERT: D 302 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7555 (ptm160) REVERT: D 309 GLU cc_start: 0.8335 (mp0) cc_final: 0.7421 (mp0) REVERT: D 374 GLN cc_start: 0.7946 (mp-120) cc_final: 0.7555 (pm20) REVERT: D 382 ASP cc_start: 0.8089 (m-30) cc_final: 0.7567 (m-30) REVERT: D 491 MET cc_start: 0.8202 (mmm) cc_final: 0.7878 (tpp) outliers start: 19 outliers final: 10 residues processed: 233 average time/residue: 0.6472 time to fit residues: 167.9335 Evaluate side-chains 224 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 178 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 204 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN A 310 GLN B 51 GLN C 51 GLN D 51 GLN D 261 GLN D 310 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110980 restraints weight = 22487.936| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.45 r_work: 0.2949 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20352 Z= 0.113 Angle : 0.491 7.445 27612 Z= 0.250 Chirality : 0.038 0.218 3128 Planarity : 0.004 0.053 3424 Dihedral : 10.586 149.541 3428 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.01 % Allowed : 12.40 % Favored : 86.59 % 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 aren not related in a simple way. whole: 2.33 (0.17), residues: 2384 helix: 2.18 (0.13), residues: 1524 sheet: -1.22 (0.46), residues: 108 loop : 0.80 (0.25), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 409 TYR 0.011 0.001 TYR B 555 PHE 0.010 0.001 PHE C 534 TRP 0.014 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00254 (20352) covalent geometry : angle 0.49150 (27612) hydrogen bonds : bond 0.03918 ( 1193) hydrogen bonds : angle 3.64695 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6293.88 seconds wall clock time: 108 minutes 1.17 seconds (6481.17 seconds total)