Starting phenix.real_space_refine on Tue Jun 17 19:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf4_41219/06_2025/8tf4_41219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf4_41219/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tf4_41219/06_2025/8tf4_41219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf4_41219/06_2025/8tf4_41219.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf4_41219/06_2025/8tf4_41219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf4_41219/06_2025/8tf4_41219_neut.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 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-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 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-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 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-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 12.01, per 1000 atoms: 0.60 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: 4.47 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.01 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: 7.52 Time building geometry restraints manager: 5.33 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: 0.04 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.890 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.153 0.018 TRP C 593 HIS 0.009 0.003 HIS A 238 PHE 0.056 0.013 PHE C 256 TYR 0.108 0.022 TYR A 336 ARG 0.007 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.17617 ( 1193) hydrogen bonds : angle 6.38834 ( 3363) covalent geometry : bond 0.01183 (20352) covalent geometry : angle 1.77365 (27612) *********************** 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 : 2.204 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: 1.5133 time to fit residues: 650.2787 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 : 2.185 ------------------------------------------------------------------------------- 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 202 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106542 restraints weight = 22668.940| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.44 r_work: 0.2872 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20352 Z= 0.186 Angle : 0.607 7.065 27612 Z= 0.312 Chirality : 0.042 0.145 3128 Planarity : 0.004 0.038 3424 Dihedral : 13.277 166.253 3440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.88 % Allowed : 6.35 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2384 helix: 1.25 (0.13), residues: 1520 sheet: -1.20 (0.41), residues: 128 loop : 0.83 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 593 HIS 0.005 0.001 HIS A 201 PHE 0.019 0.002 PHE B 611 TYR 0.014 0.002 TYR B 89 ARG 0.004 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 1193) hydrogen bonds : angle 4.11143 ( 3363) covalent geometry : bond 0.00450 (20352) covalent geometry : angle 0.60710 (27612) *********************** 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 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7517 (ttt90) REVERT: A 43 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7230 (mmm-85) REVERT: A 90 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: A 153 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8248 (mpt-90) REVERT: A 176 GLU cc_start: 0.7329 (mp0) cc_final: 0.6941 (tt0) REVERT: A 193 ASP cc_start: 0.7555 (t0) cc_final: 0.7245 (t70) REVERT: A 257 GLN cc_start: 0.7726 (pt0) cc_final: 0.6969 (tp40) REVERT: A 262 LYS cc_start: 0.8515 (mttt) cc_final: 0.8031 (mttp) REVERT: A 300 LYS cc_start: 0.8202 (pttm) cc_final: 0.7917 (ptpt) REVERT: A 302 ARG cc_start: 0.8301 (ptp90) cc_final: 0.7676 (ptm160) REVERT: A 491 MET cc_start: 0.8167 (mmm) cc_final: 0.7842 (tpp) REVERT: B 43 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: B 90 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: B 97 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6881 (mm) REVERT: B 139 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7619 (mtt-85) REVERT: B 176 GLU cc_start: 0.7328 (mp0) cc_final: 0.6942 (tt0) REVERT: B 257 GLN cc_start: 0.7697 (pt0) cc_final: 0.6893 (tp40) REVERT: B 262 LYS cc_start: 0.8525 (mttt) cc_final: 0.8045 (mttp) REVERT: B 300 LYS cc_start: 0.8166 (pttm) cc_final: 0.7894 (ptpt) REVERT: B 302 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7716 (ptm160) REVERT: B 491 MET cc_start: 0.8166 (mmm) cc_final: 0.7839 (tpp) REVERT: C 43 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: C 90 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: C 97 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6893 (mm) REVERT: C 139 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7630 (mtt-85) REVERT: C 176 GLU cc_start: 0.7329 (mp0) cc_final: 0.6949 (tt0) REVERT: C 257 GLN cc_start: 0.7735 (pt0) cc_final: 0.6939 (tp40) REVERT: C 262 LYS cc_start: 0.8517 (mttt) cc_final: 0.8024 (mttp) REVERT: C 300 LYS cc_start: 0.8145 (pttm) cc_final: 0.7879 (ptpt) REVERT: C 302 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7713 (ptm160) REVERT: C 491 MET cc_start: 0.8177 (mmm) cc_final: 0.7848 (tpp) REVERT: D 43 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: D 90 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: D 139 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7713 (mtt-85) REVERT: D 176 GLU cc_start: 0.7343 (mp0) cc_final: 0.6943 (tt0) REVERT: D 257 GLN cc_start: 0.7727 (pt0) cc_final: 0.6929 (tp40) REVERT: D 262 LYS cc_start: 0.8516 (mttt) cc_final: 0.8022 (mttp) REVERT: D 300 LYS cc_start: 0.8150 (pttm) cc_final: 0.7886 (ptpt) REVERT: D 302 ARG cc_start: 0.8313 (ptp90) cc_final: 0.7715 (ptm160) REVERT: D 491 MET cc_start: 0.8188 (mmm) cc_final: 0.7855 (tpp) outliers start: 39 outliers final: 8 residues processed: 298 average time/residue: 1.6946 time to fit residues: 557.0241 Evaluate side-chains 252 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG 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 102 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 635 ASN B 40 GLN B 261 GLN B 635 ASN C 40 GLN C 261 GLN C 635 ASN D 40 GLN D 261 GLN D 635 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.099446 restraints weight = 22963.553| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.71 r_work: 0.2914 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20352 Z= 0.119 Angle : 0.524 8.942 27612 Z= 0.267 Chirality : 0.038 0.140 3128 Planarity : 0.004 0.033 3424 Dihedral : 11.885 164.000 3428 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.78 % Allowed : 7.84 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2384 helix: 1.85 (0.13), residues: 1524 sheet: -1.55 (0.41), residues: 128 loop : 1.00 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 593 HIS 0.004 0.001 HIS A 201 PHE 0.012 0.001 PHE D 534 TYR 0.012 0.001 TYR D 89 ARG 0.006 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1193) hydrogen bonds : angle 3.76905 ( 3363) covalent geometry : bond 0.00254 (20352) covalent geometry : angle 0.52394 (27612) *********************** 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 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7304 (tpt-90) cc_final: 0.6795 (mtm180) REVERT: A 35 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7530 (ttt90) REVERT: A 43 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7184 (mmm-85) REVERT: A 80 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: A 153 ARG cc_start: 0.8575 (mmt180) cc_final: 0.8287 (mpt-90) REVERT: A 173 VAL cc_start: 0.8228 (t) cc_final: 0.7963 (m) REVERT: A 176 GLU cc_start: 0.7349 (mp0) cc_final: 0.6938 (tt0) REVERT: A 257 GLN cc_start: 0.7589 (pt0) cc_final: 0.6916 (tp40) REVERT: A 262 LYS cc_start: 0.8543 (mttt) cc_final: 0.8067 (mttp) REVERT: A 300 LYS cc_start: 0.8196 (pttm) cc_final: 0.7896 (ptpt) REVERT: A 302 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7508 (ptm-80) REVERT: A 491 MET cc_start: 0.8172 (mmm) cc_final: 0.7826 (tpp) REVERT: B 33 ARG cc_start: 0.7341 (tpt-90) cc_final: 0.6787 (mtm180) REVERT: B 35 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7546 (ttt90) REVERT: B 43 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.7187 (mmm-85) REVERT: B 97 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6767 (mm) REVERT: B 139 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7635 (mtt-85) REVERT: B 173 VAL cc_start: 0.8216 (t) cc_final: 0.7951 (m) REVERT: B 176 GLU cc_start: 0.7328 (mp0) cc_final: 0.6935 (tt0) REVERT: B 257 GLN cc_start: 0.7559 (pt0) cc_final: 0.6974 (tp40) REVERT: B 262 LYS cc_start: 0.8545 (mttt) cc_final: 0.8074 (mttp) REVERT: B 300 LYS cc_start: 0.8187 (pttm) cc_final: 0.7899 (ptpt) REVERT: B 302 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7487 (ptm-80) REVERT: B 491 MET cc_start: 0.8172 (mmm) cc_final: 0.7826 (tpp) REVERT: C 33 ARG cc_start: 0.7338 (tpt-90) cc_final: 0.6780 (mtm180) REVERT: C 35 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7541 (ttt90) REVERT: C 43 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.7198 (mmm-85) REVERT: C 97 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6774 (mm) REVERT: C 139 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7608 (mtt-85) REVERT: C 173 VAL cc_start: 0.8210 (t) cc_final: 0.7954 (m) REVERT: C 176 GLU cc_start: 0.7337 (mp0) cc_final: 0.6949 (tt0) REVERT: C 257 GLN cc_start: 0.7586 (pt0) cc_final: 0.6926 (tp40) REVERT: C 262 LYS cc_start: 0.8546 (mttt) cc_final: 0.8068 (mttp) REVERT: C 300 LYS cc_start: 0.8179 (pttm) cc_final: 0.7891 (ptpt) REVERT: C 302 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7491 (ptm-80) REVERT: C 491 MET cc_start: 0.8175 (mmm) cc_final: 0.7828 (tpp) REVERT: D 33 ARG cc_start: 0.7338 (tpt-90) cc_final: 0.6780 (mtm180) REVERT: D 35 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7524 (ttt90) REVERT: D 43 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7210 (mmm-85) REVERT: D 139 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7613 (mtt-85) REVERT: D 173 VAL cc_start: 0.8208 (t) cc_final: 0.7944 (m) REVERT: D 176 GLU cc_start: 0.7340 (mp0) cc_final: 0.6935 (tt0) REVERT: D 257 GLN cc_start: 0.7575 (pt0) cc_final: 0.6924 (tp40) REVERT: D 262 LYS cc_start: 0.8541 (mttt) cc_final: 0.8053 (mttp) REVERT: D 300 LYS cc_start: 0.8191 (pttm) cc_final: 0.7902 (ptpt) REVERT: D 302 ARG cc_start: 0.8176 (ptp90) cc_final: 0.7494 (ptm-80) REVERT: D 491 MET cc_start: 0.8179 (mmm) cc_final: 0.7833 (tpp) outliers start: 37 outliers final: 8 residues processed: 310 average time/residue: 1.5768 time to fit residues: 541.6585 Evaluate side-chains 255 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 2.154 ------------------------------------------------------------------------------- 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 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 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 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 122 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111777 restraints weight = 22702.336| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.45 r_work: 0.2960 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20352 Z= 0.115 Angle : 0.499 6.388 27612 Z= 0.252 Chirality : 0.038 0.171 3128 Planarity : 0.004 0.034 3424 Dihedral : 11.584 164.249 3428 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.54 % Allowed : 8.85 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2384 helix: 1.98 (0.13), residues: 1520 sheet: -1.70 (0.42), residues: 128 loop : 1.05 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 593 HIS 0.003 0.001 HIS A 201 PHE 0.022 0.001 PHE D 611 TYR 0.012 0.001 TYR B 555 ARG 0.007 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1193) hydrogen bonds : angle 3.69550 ( 3363) covalent geometry : bond 0.00254 (20352) covalent geometry : angle 0.49869 (27612) *********************** 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 291 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7390 (tpt-90) cc_final: 0.6951 (mtm180) REVERT: A 74 GLN cc_start: 0.7372 (mt0) cc_final: 0.7146 (mt0) REVERT: A 80 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: A 176 GLU cc_start: 0.7415 (mp0) cc_final: 0.7082 (tt0) REVERT: A 257 GLN cc_start: 0.7547 (pt0) cc_final: 0.7111 (tp40) REVERT: A 262 LYS cc_start: 0.8522 (mttt) cc_final: 0.8137 (mttp) REVERT: A 300 LYS cc_start: 0.8276 (pttm) cc_final: 0.8005 (ptpt) REVERT: A 302 ARG cc_start: 0.8203 (ptp90) cc_final: 0.7597 (ptm160) REVERT: A 491 MET cc_start: 0.8207 (mmm) cc_final: 0.7908 (tpp) REVERT: B 33 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.6899 (mtm180) REVERT: B 43 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7309 (mmm-85) REVERT: B 97 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6966 (mm) REVERT: B 139 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7774 (mtt-85) REVERT: B 176 GLU cc_start: 0.7416 (mp0) cc_final: 0.7088 (tt0) REVERT: B 257 GLN cc_start: 0.7525 (pt0) cc_final: 0.7123 (tp40) REVERT: B 262 LYS cc_start: 0.8533 (mttt) cc_final: 0.8122 (mttp) REVERT: B 300 LYS cc_start: 0.8273 (pttm) cc_final: 0.8010 (ptpt) REVERT: B 302 ARG cc_start: 0.8195 (ptp90) cc_final: 0.7565 (ptm-80) REVERT: B 374 GLN cc_start: 0.7925 (mp-120) cc_final: 0.7652 (pm20) REVERT: B 491 MET cc_start: 0.8202 (mmm) cc_final: 0.7901 (tpp) REVERT: C 33 ARG cc_start: 0.7406 (tpt-90) cc_final: 0.6897 (mtm180) REVERT: C 43 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7296 (mmm-85) REVERT: C 97 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6953 (mm) REVERT: C 139 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7793 (mtt-85) REVERT: C 173 VAL cc_start: 0.8316 (t) cc_final: 0.8046 (m) REVERT: C 176 GLU cc_start: 0.7407 (mp0) cc_final: 0.7069 (tt0) REVERT: C 257 GLN cc_start: 0.7542 (pt0) cc_final: 0.7105 (tp40) REVERT: C 262 LYS cc_start: 0.8529 (mttt) cc_final: 0.8131 (mttp) REVERT: C 300 LYS cc_start: 0.8278 (pttm) cc_final: 0.8016 (ptpt) REVERT: C 302 ARG cc_start: 0.8195 (ptp90) cc_final: 0.7579 (ptm-80) REVERT: C 374 GLN cc_start: 0.7882 (mp-120) cc_final: 0.7663 (pm20) REVERT: C 491 MET cc_start: 0.8210 (mmm) cc_final: 0.7910 (tpp) REVERT: D 33 ARG cc_start: 0.7404 (tpt-90) cc_final: 0.6899 (mtm180) REVERT: D 43 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7308 (mmm-85) REVERT: D 139 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7789 (mtt-85) REVERT: D 176 GLU cc_start: 0.7418 (mp0) cc_final: 0.7078 (tt0) REVERT: D 257 GLN cc_start: 0.7533 (pt0) cc_final: 0.7071 (tp40) REVERT: D 262 LYS cc_start: 0.8521 (mttt) cc_final: 0.8118 (mttp) REVERT: D 300 LYS cc_start: 0.8277 (pttm) cc_final: 0.8018 (ptpt) REVERT: D 302 ARG cc_start: 0.8196 (ptp90) cc_final: 0.7580 (ptm-80) REVERT: D 382 ASP cc_start: 0.8092 (m-30) cc_final: 0.7651 (m-30) REVERT: D 491 MET cc_start: 0.8215 (mmm) cc_final: 0.7915 (tpp) outliers start: 32 outliers final: 12 residues processed: 279 average time/residue: 1.4420 time to fit residues: 450.4970 Evaluate side-chains 253 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 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 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 354 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 216 optimal weight: 0.0270 chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 40 GLN B 261 GLN C 40 GLN C 261 GLN D 40 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105841 restraints weight = 22876.647| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.46 r_work: 0.2899 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20352 Z= 0.168 Angle : 0.530 5.784 27612 Z= 0.270 Chirality : 0.039 0.139 3128 Planarity : 0.004 0.036 3424 Dihedral : 11.663 164.701 3428 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.39 % Allowed : 9.76 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2384 helix: 1.84 (0.13), residues: 1528 sheet: -1.90 (0.41), residues: 128 loop : 0.85 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 593 HIS 0.004 0.001 HIS B 201 PHE 0.014 0.002 PHE C 534 TYR 0.013 0.002 TYR D 89 ARG 0.007 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 1193) hydrogen bonds : angle 3.80692 ( 3363) covalent geometry : bond 0.00413 (20352) covalent geometry : angle 0.53008 (27612) *********************** 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 262 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7463 (tpt-90) cc_final: 0.7017 (ttp-170) REVERT: A 80 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: A 176 GLU cc_start: 0.7469 (mp0) cc_final: 0.7035 (tt0) REVERT: A 193 ASP cc_start: 0.7739 (t0) cc_final: 0.7511 (t0) REVERT: A 257 GLN cc_start: 0.7633 (pt0) cc_final: 0.7125 (tp40) REVERT: A 262 LYS cc_start: 0.8599 (mttt) cc_final: 0.8177 (mttp) REVERT: A 300 LYS cc_start: 0.8236 (pttm) cc_final: 0.7978 (ptpt) REVERT: A 302 ARG cc_start: 0.8272 (ptp90) cc_final: 0.7673 (ptm160) REVERT: A 491 MET cc_start: 0.8263 (mmm) cc_final: 0.7956 (tpp) REVERT: B 33 ARG cc_start: 0.7435 (tpt-90) cc_final: 0.7038 (ttp80) REVERT: B 35 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7599 (ttt90) REVERT: B 43 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7292 (mmm-85) REVERT: B 97 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6957 (mm) REVERT: B 139 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7829 (mtt-85) REVERT: B 176 GLU cc_start: 0.7479 (mp0) cc_final: 0.7028 (tt0) REVERT: B 257 GLN cc_start: 0.7590 (pt0) cc_final: 0.7143 (tp40) REVERT: B 262 LYS cc_start: 0.8611 (mttt) cc_final: 0.8170 (mttp) REVERT: B 300 LYS cc_start: 0.8243 (pttm) cc_final: 0.7986 (ptpt) REVERT: B 302 ARG cc_start: 0.8261 (ptp90) cc_final: 0.7664 (ptm160) REVERT: B 491 MET cc_start: 0.8258 (mmm) cc_final: 0.7944 (tpp) REVERT: B 522 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: C 33 ARG cc_start: 0.7434 (tpt-90) cc_final: 0.7040 (ttp80) REVERT: C 35 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7601 (ttt90) REVERT: C 43 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.7282 (mmm-85) REVERT: C 97 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6912 (mm) REVERT: C 139 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: C 176 GLU cc_start: 0.7482 (mp0) cc_final: 0.7027 (tt0) REVERT: C 257 GLN cc_start: 0.7619 (pt0) cc_final: 0.7163 (tp40) REVERT: C 262 LYS cc_start: 0.8602 (mttt) cc_final: 0.8172 (mttp) REVERT: C 300 LYS cc_start: 0.8246 (pttm) cc_final: 0.7990 (ptpt) REVERT: C 302 ARG cc_start: 0.8262 (ptp90) cc_final: 0.7666 (ptm160) REVERT: C 491 MET cc_start: 0.8266 (mmm) cc_final: 0.7957 (tpp) REVERT: D 33 ARG cc_start: 0.7449 (tpt-90) cc_final: 0.7055 (ttp80) REVERT: D 35 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7594 (ttt90) REVERT: D 43 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.7299 (mmm-85) REVERT: D 139 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7804 (mtt-85) REVERT: D 176 GLU cc_start: 0.7493 (mp0) cc_final: 0.7029 (tt0) REVERT: D 257 GLN cc_start: 0.7583 (pt0) cc_final: 0.7123 (tp40) REVERT: D 262 LYS cc_start: 0.8606 (mttt) cc_final: 0.8164 (mttp) REVERT: D 300 LYS cc_start: 0.8238 (pttm) cc_final: 0.7981 (ptpt) REVERT: D 302 ARG cc_start: 0.8260 (ptp90) cc_final: 0.7655 (ptm160) REVERT: D 382 ASP cc_start: 0.8136 (m-30) cc_final: 0.7741 (m-30) REVERT: D 491 MET cc_start: 0.8264 (mmm) cc_final: 0.7951 (tpp) outliers start: 29 outliers final: 13 residues processed: 250 average time/residue: 1.5098 time to fit residues: 419.8447 Evaluate side-chains 244 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 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 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 84 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 261 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112019 restraints weight = 22480.636| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.45 r_work: 0.2936 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2740 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= 0.118 Angle : 0.481 5.571 27612 Z= 0.245 Chirality : 0.037 0.127 3128 Planarity : 0.004 0.036 3424 Dihedral : 11.423 162.573 3428 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.30 % Allowed : 10.29 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.17), residues: 2384 helix: 1.99 (0.13), residues: 1520 sheet: -1.93 (0.41), residues: 128 loop : 0.95 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 PHE 0.028 0.001 PHE B 611 TYR 0.012 0.001 TYR B 555 ARG 0.006 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1193) hydrogen bonds : angle 3.70737 ( 3363) covalent geometry : bond 0.00268 (20352) covalent geometry : angle 0.48067 (27612) *********************** 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 278 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7337 (tpt-90) cc_final: 0.6926 (mtm180) REVERT: A 80 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: A 176 GLU cc_start: 0.7371 (mp0) cc_final: 0.6927 (tt0) REVERT: A 257 GLN cc_start: 0.7464 (pt0) cc_final: 0.7078 (tp40) REVERT: A 262 LYS cc_start: 0.8562 (mttt) cc_final: 0.8102 (mttp) REVERT: A 300 LYS cc_start: 0.8216 (pttm) cc_final: 0.7946 (ptpt) REVERT: A 302 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7528 (ptm160) REVERT: A 491 MET cc_start: 0.8177 (mmm) cc_final: 0.7849 (tpp) REVERT: B 33 ARG cc_start: 0.7321 (tpt-90) cc_final: 0.6873 (mtm180) REVERT: B 35 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7502 (ttt90) REVERT: B 43 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.7175 (mmm-85) REVERT: B 97 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6856 (mm) REVERT: B 139 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7732 (mtt-85) REVERT: B 173 VAL cc_start: 0.8231 (t) cc_final: 0.7934 (m) REVERT: B 176 GLU cc_start: 0.7382 (mp0) cc_final: 0.6903 (tt0) REVERT: B 257 GLN cc_start: 0.7458 (pt0) cc_final: 0.7021 (tp40) REVERT: B 262 LYS cc_start: 0.8587 (mttt) cc_final: 0.8094 (mttp) REVERT: B 300 LYS cc_start: 0.8213 (pttm) cc_final: 0.7944 (ptpt) REVERT: B 302 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7555 (ptm160) REVERT: B 374 GLN cc_start: 0.7939 (mp-120) cc_final: 0.7612 (pm20) REVERT: B 491 MET cc_start: 0.8174 (mmm) cc_final: 0.7845 (tpp) REVERT: C 33 ARG cc_start: 0.7324 (tpt-90) cc_final: 0.6884 (ttp-170) REVERT: C 35 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7511 (ttt90) REVERT: C 43 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.7172 (mmm-85) REVERT: C 97 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6893 (mm) REVERT: C 139 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7752 (mtt-85) REVERT: C 176 GLU cc_start: 0.7398 (mp0) cc_final: 0.6922 (tt0) REVERT: C 257 GLN cc_start: 0.7484 (pt0) cc_final: 0.7050 (tp40) REVERT: C 262 LYS cc_start: 0.8567 (mttt) cc_final: 0.8109 (mttp) REVERT: C 300 LYS cc_start: 0.8230 (pttm) cc_final: 0.7964 (ptpt) REVERT: C 302 ARG cc_start: 0.8162 (ptp90) cc_final: 0.7562 (ptm160) REVERT: C 374 GLN cc_start: 0.7870 (mp-120) cc_final: 0.7569 (pm20) REVERT: C 491 MET cc_start: 0.8180 (mmm) cc_final: 0.7849 (tpp) REVERT: D 33 ARG cc_start: 0.7326 (tpt-90) cc_final: 0.6887 (ttp-170) REVERT: D 35 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7508 (ttt90) REVERT: D 43 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7172 (mmm-85) REVERT: D 139 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7764 (mtt-85) REVERT: D 173 VAL cc_start: 0.8232 (t) cc_final: 0.7962 (m) REVERT: D 176 GLU cc_start: 0.7406 (mp0) cc_final: 0.6910 (tt0) REVERT: D 257 GLN cc_start: 0.7473 (pt0) cc_final: 0.7035 (tp40) REVERT: D 262 LYS cc_start: 0.8583 (mttt) cc_final: 0.8105 (mttp) REVERT: D 300 LYS cc_start: 0.8224 (pttm) cc_final: 0.7960 (ptpt) REVERT: D 302 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7509 (ptm160) REVERT: D 374 GLN cc_start: 0.7921 (mp-120) cc_final: 0.7505 (pm20) REVERT: D 382 ASP cc_start: 0.8040 (m-30) cc_final: 0.7640 (m-30) REVERT: D 491 MET cc_start: 0.8184 (mmm) cc_final: 0.7856 (tpp) outliers start: 27 outliers final: 15 residues processed: 270 average time/residue: 1.5385 time to fit residues: 463.2168 Evaluate side-chains 252 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 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 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 38 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 D 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096871 restraints weight = 22841.600| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.72 r_work: 0.2854 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20352 Z= 0.137 Angle : 0.503 5.619 27612 Z= 0.256 Chirality : 0.038 0.131 3128 Planarity : 0.004 0.038 3424 Dihedral : 11.368 161.417 3428 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.25 % Allowed : 10.53 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.17), residues: 2384 helix: 1.96 (0.13), residues: 1524 sheet: -2.01 (0.41), residues: 128 loop : 0.96 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.012 0.001 PHE A 534 TYR 0.012 0.001 TYR B 555 ARG 0.012 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 1193) hydrogen bonds : angle 3.73926 ( 3363) covalent geometry : bond 0.00327 (20352) covalent geometry : angle 0.50260 (27612) *********************** 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 264 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6793 (mtm180) REVERT: A 35 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7484 (ttt90) REVERT: A 74 GLN cc_start: 0.7587 (mt0) cc_final: 0.7199 (mt0) REVERT: A 80 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: A 176 GLU cc_start: 0.7347 (mp0) cc_final: 0.6786 (tt0) REVERT: A 257 GLN cc_start: 0.7417 (pt0) cc_final: 0.7027 (tp40) REVERT: A 262 LYS cc_start: 0.8567 (mttt) cc_final: 0.8027 (mttp) REVERT: A 300 LYS cc_start: 0.8160 (pttm) cc_final: 0.7855 (ptpt) REVERT: A 302 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7454 (ptm160) REVERT: A 491 MET cc_start: 0.8141 (mmm) cc_final: 0.7788 (tpp) REVERT: B 33 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6751 (ttp-170) REVERT: B 35 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7480 (ttt90) REVERT: B 43 ARG cc_start: 0.7324 (mmm-85) cc_final: 0.7064 (mmm-85) REVERT: B 97 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6715 (mm) REVERT: B 139 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7607 (mtt-85) REVERT: B 176 GLU cc_start: 0.7356 (mp0) cc_final: 0.6784 (tt0) REVERT: B 257 GLN cc_start: 0.7398 (pt0) cc_final: 0.6976 (tp40) REVERT: B 262 LYS cc_start: 0.8579 (mttt) cc_final: 0.8000 (mttp) REVERT: B 300 LYS cc_start: 0.8167 (pttm) cc_final: 0.7860 (ptpt) REVERT: B 302 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7439 (ptm160) REVERT: B 491 MET cc_start: 0.8143 (mmm) cc_final: 0.7785 (tpp) REVERT: B 522 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: C 33 ARG cc_start: 0.7191 (tpt-90) cc_final: 0.6742 (ttp-170) REVERT: C 35 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7483 (ttt90) REVERT: C 43 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.7058 (mmm-85) REVERT: C 97 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6689 (mm) REVERT: C 139 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7625 (mtt-85) REVERT: C 176 GLU cc_start: 0.7372 (mp0) cc_final: 0.6783 (tt0) REVERT: C 257 GLN cc_start: 0.7456 (pt0) cc_final: 0.6992 (tp40) REVERT: C 262 LYS cc_start: 0.8570 (mttt) cc_final: 0.8029 (mttp) REVERT: C 300 LYS cc_start: 0.8171 (pttm) cc_final: 0.7862 (ptpt) REVERT: C 302 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7441 (ptm160) REVERT: C 491 MET cc_start: 0.8150 (mmm) cc_final: 0.7793 (tpp) REVERT: D 33 ARG cc_start: 0.7205 (tpt-90) cc_final: 0.6764 (ttp-170) REVERT: D 35 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7493 (ttt90) REVERT: D 43 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.7061 (mmm-85) REVERT: D 139 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7645 (mtt-85) REVERT: D 176 GLU cc_start: 0.7387 (mp0) cc_final: 0.6781 (tt0) REVERT: D 257 GLN cc_start: 0.7392 (pt0) cc_final: 0.6942 (tp40) REVERT: D 262 LYS cc_start: 0.8580 (mttt) cc_final: 0.8001 (mttp) REVERT: D 300 LYS cc_start: 0.8165 (pttm) cc_final: 0.7862 (ptpt) REVERT: D 302 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7440 (ptm160) REVERT: D 382 ASP cc_start: 0.7967 (m-30) cc_final: 0.7560 (m-30) REVERT: D 491 MET cc_start: 0.8150 (mmm) cc_final: 0.7794 (tpp) outliers start: 26 outliers final: 15 residues processed: 255 average time/residue: 1.6163 time to fit residues: 458.9022 Evaluate side-chains 252 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 80 GLU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097801 restraints weight = 23011.438| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.72 r_work: 0.2868 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20352 Z= 0.127 Angle : 0.494 6.617 27612 Z= 0.251 Chirality : 0.037 0.128 3128 Planarity : 0.004 0.043 3424 Dihedral : 11.232 159.428 3428 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.30 % Allowed : 10.91 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.17), residues: 2384 helix: 2.03 (0.13), residues: 1524 sheet: -2.01 (0.41), residues: 128 loop : 0.97 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 PHE 0.030 0.002 PHE A 611 TYR 0.012 0.001 TYR B 555 ARG 0.013 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1193) hydrogen bonds : angle 3.70718 ( 3363) covalent geometry : bond 0.00298 (20352) covalent geometry : angle 0.49407 (27612) *********************** 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 259 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6794 (mtm180) REVERT: A 35 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7463 (ttt90) REVERT: A 74 GLN cc_start: 0.7629 (mt0) cc_final: 0.7234 (mt0) REVERT: A 80 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: A 97 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6819 (mm) REVERT: A 176 GLU cc_start: 0.7357 (mp0) cc_final: 0.6796 (tt0) REVERT: A 257 GLN cc_start: 0.7402 (pt0) cc_final: 0.7062 (tp40) REVERT: A 262 LYS cc_start: 0.8566 (mttt) cc_final: 0.8002 (mttp) REVERT: A 300 LYS cc_start: 0.8160 (pttm) cc_final: 0.7865 (ptpt) REVERT: A 302 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7386 (ptm160) REVERT: A 491 MET cc_start: 0.8146 (mmm) cc_final: 0.7794 (tpp) REVERT: B 33 ARG cc_start: 0.7213 (tpt-90) cc_final: 0.6788 (ttp-170) REVERT: B 35 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7468 (ttt90) REVERT: B 43 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.7066 (mmm-85) REVERT: B 97 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6766 (mm) REVERT: B 139 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7537 (mtt-85) REVERT: B 176 GLU cc_start: 0.7358 (mp0) cc_final: 0.6784 (tt0) REVERT: B 257 GLN cc_start: 0.7359 (pt0) cc_final: 0.6973 (tp40) REVERT: B 262 LYS cc_start: 0.8612 (mttt) cc_final: 0.8020 (mppt) REVERT: B 300 LYS cc_start: 0.8154 (pttm) cc_final: 0.7855 (ptpt) REVERT: B 302 ARG cc_start: 0.8082 (ptp90) cc_final: 0.7377 (ptm160) REVERT: B 374 GLN cc_start: 0.7841 (mp-120) cc_final: 0.7437 (pm20) REVERT: B 491 MET cc_start: 0.8144 (mmm) cc_final: 0.7785 (tpp) REVERT: B 522 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: C 33 ARG cc_start: 0.7201 (tpt-90) cc_final: 0.6778 (ttp-170) REVERT: C 35 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7484 (ttt90) REVERT: C 43 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.7068 (mmm-85) REVERT: C 97 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6724 (mm) REVERT: C 139 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7625 (mtt-85) REVERT: C 176 GLU cc_start: 0.7375 (mp0) cc_final: 0.6818 (tt0) REVERT: C 257 GLN cc_start: 0.7408 (pt0) cc_final: 0.7119 (tp40) REVERT: C 262 LYS cc_start: 0.8563 (mttt) cc_final: 0.8009 (mttp) REVERT: C 300 LYS cc_start: 0.8156 (pttm) cc_final: 0.7858 (ptpt) REVERT: C 302 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7382 (ptm160) REVERT: C 374 GLN cc_start: 0.7808 (mp-120) cc_final: 0.7401 (pm20) REVERT: C 491 MET cc_start: 0.8147 (mmm) cc_final: 0.7792 (tpp) REVERT: D 33 ARG cc_start: 0.7213 (tpt-90) cc_final: 0.6789 (ttp-170) REVERT: D 35 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7484 (ttt90) REVERT: D 43 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.7088 (mmm-85) REVERT: D 97 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6797 (mm) REVERT: D 139 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7633 (mtt-85) REVERT: D 176 GLU cc_start: 0.7382 (mp0) cc_final: 0.6784 (tt0) REVERT: D 257 GLN cc_start: 0.7336 (pt0) cc_final: 0.6964 (tp40) REVERT: D 262 LYS cc_start: 0.8615 (mttt) cc_final: 0.8058 (mttp) REVERT: D 300 LYS cc_start: 0.8148 (pttm) cc_final: 0.7852 (ptpt) REVERT: D 302 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7373 (ptm160) REVERT: D 374 GLN cc_start: 0.7863 (mp-120) cc_final: 0.7433 (pm20) REVERT: D 382 ASP cc_start: 0.7942 (m-30) cc_final: 0.7510 (m-30) REVERT: D 491 MET cc_start: 0.8154 (mmm) cc_final: 0.7800 (tpp) outliers start: 27 outliers final: 15 residues processed: 250 average time/residue: 1.5926 time to fit residues: 442.1570 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 D 51 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110949 restraints weight = 22488.437| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.45 r_work: 0.2902 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20352 Z= 0.137 Angle : 0.510 7.652 27612 Z= 0.259 Chirality : 0.038 0.189 3128 Planarity : 0.004 0.046 3424 Dihedral : 11.190 158.024 3428 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.35 % Allowed : 10.67 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2384 helix: 2.00 (0.13), residues: 1524 sheet: -2.09 (0.40), residues: 128 loop : 0.94 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.012 0.001 PHE A 534 TYR 0.011 0.001 TYR B 555 ARG 0.012 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1193) hydrogen bonds : angle 3.73323 ( 3363) covalent geometry : bond 0.00325 (20352) covalent geometry : angle 0.51048 (27612) *********************** 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 250 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6888 (mtm180) REVERT: A 35 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7500 (ttt90) REVERT: A 74 GLN cc_start: 0.7675 (mt0) cc_final: 0.7313 (mt0) REVERT: A 97 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6896 (mm) REVERT: A 176 GLU cc_start: 0.7487 (mp0) cc_final: 0.6932 (tt0) REVERT: A 257 GLN cc_start: 0.7439 (pt0) cc_final: 0.7184 (tp40) REVERT: A 262 LYS cc_start: 0.8567 (mttt) cc_final: 0.8048 (mttm) REVERT: A 300 LYS cc_start: 0.8223 (pttm) cc_final: 0.7958 (ptpt) REVERT: A 302 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7510 (ptm160) REVERT: A 491 MET cc_start: 0.8186 (mmm) cc_final: 0.7855 (tpp) REVERT: B 33 ARG cc_start: 0.7281 (tpt-90) cc_final: 0.6863 (ttp-170) REVERT: B 35 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7504 (ttt90) REVERT: B 43 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.7195 (mmm-85) REVERT: B 97 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6847 (mm) REVERT: B 139 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7647 (mtt-85) REVERT: B 176 GLU cc_start: 0.7444 (mp0) cc_final: 0.6913 (tt0) REVERT: B 262 LYS cc_start: 0.8606 (mttt) cc_final: 0.8082 (mppt) REVERT: B 300 LYS cc_start: 0.8234 (pttm) cc_final: 0.7965 (ptpt) REVERT: B 302 ARG cc_start: 0.8121 (ptp90) cc_final: 0.7508 (ptm160) REVERT: B 374 GLN cc_start: 0.7939 (mp-120) cc_final: 0.7535 (pm20) REVERT: B 491 MET cc_start: 0.8180 (mmm) cc_final: 0.7844 (tpp) REVERT: B 522 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 33 ARG cc_start: 0.7271 (tpt-90) cc_final: 0.6854 (ttp-170) REVERT: C 35 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7515 (ttt90) REVERT: C 43 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7168 (mmm-85) REVERT: C 97 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6841 (mm) REVERT: C 139 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7645 (mtt-85) REVERT: C 176 GLU cc_start: 0.7536 (mp0) cc_final: 0.6955 (tt0) REVERT: C 257 GLN cc_start: 0.7469 (pt0) cc_final: 0.7138 (tp40) REVERT: C 262 LYS cc_start: 0.8568 (mttt) cc_final: 0.8049 (mttm) REVERT: C 300 LYS cc_start: 0.8233 (pttm) cc_final: 0.7965 (ptpt) REVERT: C 302 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7508 (ptm160) REVERT: C 491 MET cc_start: 0.8184 (mmm) cc_final: 0.7853 (tpp) REVERT: D 33 ARG cc_start: 0.7279 (tpt-90) cc_final: 0.6863 (ttp-170) REVERT: D 35 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7509 (ttt90) REVERT: D 43 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7165 (mmm-85) REVERT: D 97 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6879 (mm) REVERT: D 139 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7721 (mtt-85) REVERT: D 176 GLU cc_start: 0.7521 (mp0) cc_final: 0.6933 (tt0) REVERT: D 257 GLN cc_start: 0.7368 (pt0) cc_final: 0.7148 (tp40) REVERT: D 262 LYS cc_start: 0.8607 (mttt) cc_final: 0.8077 (mppt) REVERT: D 300 LYS cc_start: 0.8223 (pttm) cc_final: 0.7955 (ptpt) REVERT: D 302 ARG cc_start: 0.8136 (ptp90) cc_final: 0.7488 (ptm160) REVERT: D 374 GLN cc_start: 0.7969 (mp-120) cc_final: 0.7496 (pm20) REVERT: D 382 ASP cc_start: 0.8040 (m-30) cc_final: 0.7717 (m-30) REVERT: D 491 MET cc_start: 0.8192 (mmm) cc_final: 0.7859 (tpp) outliers start: 28 outliers final: 16 residues processed: 241 average time/residue: 1.5769 time to fit residues: 421.8429 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 C 51 GLN C 261 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 = 0.3534 r_free = 0.3534 target = 0.138550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109196 restraints weight = 22410.109| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.56 r_work: 0.2892 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20352 Z= 0.149 Angle : 0.525 8.626 27612 Z= 0.265 Chirality : 0.038 0.184 3128 Planarity : 0.004 0.045 3424 Dihedral : 11.194 156.649 3428 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.25 % Allowed : 11.01 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.17), residues: 2384 helix: 1.94 (0.13), residues: 1524 sheet: -2.11 (0.40), residues: 128 loop : 0.90 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 PHE 0.035 0.002 PHE C 611 TYR 0.011 0.001 TYR D 89 ARG 0.011 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 1193) hydrogen bonds : angle 3.77502 ( 3363) covalent geometry : bond 0.00361 (20352) covalent geometry : angle 0.52455 (27612) ********************** 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 249 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7017 (ttp-170) REVERT: A 35 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7591 (ttt90) REVERT: A 74 GLN cc_start: 0.7762 (mt0) cc_final: 0.7399 (mt0) REVERT: A 176 GLU cc_start: 0.7587 (mp0) cc_final: 0.7011 (tt0) REVERT: A 257 GLN cc_start: 0.7578 (pt0) cc_final: 0.7208 (tp40) REVERT: A 262 LYS cc_start: 0.8577 (mttt) cc_final: 0.8093 (mttm) REVERT: A 300 LYS cc_start: 0.8243 (pttm) cc_final: 0.7983 (ptpt) REVERT: A 302 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7513 (ptm160) REVERT: A 491 MET cc_start: 0.8237 (mmm) cc_final: 0.7883 (tpp) REVERT: B 33 ARG cc_start: 0.7425 (tpt-90) cc_final: 0.6996 (ttp-170) REVERT: B 35 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7592 (ttt90) REVERT: B 43 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.7285 (mmm-85) REVERT: B 97 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6889 (mm) REVERT: B 139 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7683 (mtt-85) REVERT: B 176 GLU cc_start: 0.7599 (mp0) cc_final: 0.7057 (tt0) REVERT: B 262 LYS cc_start: 0.8596 (mttt) cc_final: 0.8102 (mppt) REVERT: B 300 LYS cc_start: 0.8249 (pttm) cc_final: 0.7984 (ptpt) REVERT: B 302 ARG cc_start: 0.8111 (ptp90) cc_final: 0.7529 (ptm160) REVERT: B 309 GLU cc_start: 0.8353 (mp0) cc_final: 0.7312 (mp0) REVERT: B 491 MET cc_start: 0.8236 (mmm) cc_final: 0.7887 (tpp) REVERT: B 522 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: C 33 ARG cc_start: 0.7391 (tpt-90) cc_final: 0.6956 (ttp-170) REVERT: C 35 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7604 (ttt90) REVERT: C 43 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.7270 (mmm-85) REVERT: C 97 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6897 (mm) REVERT: C 139 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7688 (mtt-85) REVERT: C 176 GLU cc_start: 0.7620 (mp0) cc_final: 0.7054 (tt0) REVERT: C 257 GLN cc_start: 0.7498 (pt0) cc_final: 0.7268 (tp40) REVERT: C 262 LYS cc_start: 0.8618 (mttt) cc_final: 0.8122 (mppt) REVERT: C 300 LYS cc_start: 0.8254 (pttm) cc_final: 0.7991 (ptpt) REVERT: C 302 ARG cc_start: 0.8106 (ptp90) cc_final: 0.7527 (ptm160) REVERT: C 491 MET cc_start: 0.8249 (mmm) cc_final: 0.7899 (tpp) REVERT: D 33 ARG cc_start: 0.7390 (tpt-90) cc_final: 0.6959 (ttp-170) REVERT: D 35 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7605 (ttt90) REVERT: D 43 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7290 (mmm-85) REVERT: D 97 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6951 (mm) REVERT: D 139 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7682 (mtt-85) REVERT: D 176 GLU cc_start: 0.7626 (mp0) cc_final: 0.7020 (tt0) REVERT: D 257 GLN cc_start: 0.7492 (pt0) cc_final: 0.7040 (mm-40) REVERT: D 262 LYS cc_start: 0.8613 (mttt) cc_final: 0.8112 (mppt) REVERT: D 300 LYS cc_start: 0.8241 (pttm) cc_final: 0.7981 (ptpt) REVERT: D 302 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7504 (ptm160) REVERT: D 382 ASP cc_start: 0.8082 (m-30) cc_final: 0.7641 (m-30) REVERT: D 491 MET cc_start: 0.8250 (mmm) cc_final: 0.7903 (tpp) outliers start: 26 outliers final: 16 residues processed: 240 average time/residue: 1.6400 time to fit residues: 437.8505 Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 35 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 0.0870 chunk 152 optimal weight: 0.0060 chunk 110 optimal weight: 0.0570 chunk 50 optimal weight: 0.0870 chunk 16 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 177 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 146 optimal weight: 0.0060 chunk 12 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.0486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 637 HIS B 51 GLN B 261 GLN B 310 GLN C 51 GLN C 582 HIS C 635 ASN D 51 GLN D 261 GLN D 635 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117821 restraints weight = 22459.137| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.44 r_work: 0.3032 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20352 Z= 0.101 Angle : 0.482 6.922 27612 Z= 0.247 Chirality : 0.036 0.254 3128 Planarity : 0.004 0.044 3424 Dihedral : 10.737 152.526 3428 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.06 % Allowed : 11.68 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.17), residues: 2384 helix: 2.28 (0.13), residues: 1524 sheet: -0.11 (0.63), residues: 68 loop : 0.75 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 583 HIS 0.004 0.001 HIS D 582 PHE 0.012 0.001 PHE C 537 TYR 0.012 0.001 TYR B 555 ARG 0.011 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1193) hydrogen bonds : angle 3.60888 ( 3363) covalent geometry : bond 0.00205 (20352) covalent geometry : angle 0.48173 (27612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14308.09 seconds wall clock time: 244 minutes 22.52 seconds (14662.52 seconds total)