Starting phenix.real_space_refine on Thu Aug 6 04:11:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4y_41040/08_2026/8t4y_41040.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 68 5.16 5 C 8436 2.51 5 N 2400 2.21 5 O 2440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13348 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "C" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "B" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.24 Number of scatterers: 13348 At special positions: 0 Unit cell: (109.686, 109.686, 125.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 4 15.00 O 2440 8.00 N 2400 7.00 C 8436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 792.5 milliseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 76.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.685A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 369 through 401 removed outlier: 4.215A pdb=" N TRP A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.909A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.683A pdb=" N ILE D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 270 through 286 Processing helix chain 'D' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 369 through 401 removed outlier: 4.216A pdb=" N TRP D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.907A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 595 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU C 147 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.684A pdb=" N ILE C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 270 through 286 Processing helix chain 'C' and resid 295 through 323 removed outlier: 3.777A pdb=" N PHE C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 369 through 401 removed outlier: 4.216A pdb=" N TRP C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.907A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.074A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 595 Processing helix chain 'C' and resid 598 through 611 Processing helix chain 'C' and resid 615 through 635 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.684A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 369 through 401 removed outlier: 4.217A pdb=" N TRP B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.908A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 598 through 611 Processing helix chain 'B' and resid 615 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.885A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 564 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.539A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.884A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 564 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.538A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.885A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 564 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.540A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.884A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 564 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.540A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4532 1.34 - 1.46: 2902 1.46 - 1.58: 6062 1.58 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 13616 Sorted by residual: bond pdb=" C4' CMP C 901 " pdb=" C5' CMP C 901 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C PRO B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C PRO D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C PRO A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.58e+00 bond pdb=" C4' CMP B 901 " pdb=" C5' CMP B 901 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.00e-02 2.50e+03 1.55e+00 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18333 2.06 - 4.13: 241 4.13 - 6.19: 60 6.19 - 8.25: 30 8.25 - 10.32: 16 Bond angle restraints: 18680 Sorted by residual: angle pdb=" N TYR A 361 " pdb=" CA TYR A 361 " pdb=" C TYR A 361 " ideal model delta sigma weight residual 112.59 105.66 6.93 1.22e+00 6.72e-01 3.22e+01 angle pdb=" N TYR B 361 " pdb=" CA TYR B 361 " pdb=" C TYR B 361 " ideal model delta sigma weight residual 112.59 105.72 6.87 1.22e+00 6.72e-01 3.17e+01 angle pdb=" N TYR C 361 " pdb=" CA TYR C 361 " pdb=" C TYR C 361 " ideal model delta sigma weight residual 112.59 105.87 6.72 1.22e+00 6.72e-01 3.04e+01 angle pdb=" N TYR D 361 " pdb=" CA TYR D 361 " pdb=" C TYR D 361 " ideal model delta sigma weight residual 112.59 106.05 6.54 1.22e+00 6.72e-01 2.88e+01 angle pdb=" C1' CMP C 901 " pdb=" C2' CMP C 901 " pdb=" C3' CMP C 901 " ideal model delta sigma weight residual 111.00 100.68 10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 18675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 7763 32.50 - 64.99: 205 64.99 - 97.49: 4 97.49 - 129.99: 4 129.99 - 162.48: 4 Dihedral angle restraints: 7980 sinusoidal: 2092 harmonic: 5888 Sorted by residual: dihedral pdb=" C3' CMP D 901 " pdb=" O3' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.48 -162.48 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C3' CMP B 901 " pdb=" O3' CMP B 901 " pdb=" P CMP B 901 " pdb=" O1P CMP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.46 -162.46 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C3' CMP C 901 " pdb=" O3' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.41 -162.41 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1883 0.059 - 0.118: 298 0.118 - 0.176: 7 0.176 - 0.235: 0 0.235 - 0.294: 8 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CG LEU D 301 " pdb=" CB LEU D 301 " pdb=" CD1 LEU D 301 " pdb=" CD2 LEU D 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU C 301 " pdb=" CB LEU C 301 " pdb=" CD1 LEU C 301 " pdb=" CD2 LEU C 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU B 301 " pdb=" CB LEU B 301 " pdb=" CD1 LEU B 301 " pdb=" CD2 LEU B 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2193 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 365 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 366 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 365 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 366 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 365 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 366 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 366 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 366 " 0.030 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2830 2.77 - 3.31: 13832 3.31 - 3.84: 23003 3.84 - 4.37: 21192 4.37 - 4.90: 38766 Nonbonded interactions: 99623 Sorted by model distance: nonbonded pdb=" O LYS A 468 " pdb=" OG1 THR A 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS D 468 " pdb=" OG1 THR D 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS C 468 " pdb=" OG1 THR C 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS B 468 " pdb=" OG1 THR B 472 " model vdw 2.243 3.040 nonbonded pdb=" O LEU C 450 " pdb=" NH1 ARG C 458 " model vdw 2.247 3.120 ... (remaining 99618 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.003 0.034 13616 Z= 0.141 Angle : 0.708 10.318 18680 Z= 0.345 Chirality : 0.042 0.294 2196 Planarity : 0.004 0.056 2452 Dihedral : 15.654 162.481 4148 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 34.22 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.20), residues: 1972 helix: 2.74 (0.13), residues: 1400 sheet: -0.64 (0.48), residues: 120 loop : -2.56 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.012 0.001 TYR D 417 PHE 0.006 0.001 PHE A 538 TRP 0.004 0.001 TRP D 221 HIS 0.003 0.001 HIS D 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (13616) covalent geometry : angle 0.70788 / 0.35 (18680) hydrogen bonds : bond 0.10201 / 7.38 ( 1153) hydrogen bonds : angle 4.61124 / 3.43 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.407 Fit side-chains REVERT: A 175 TRP cc_start: 0.7277 (m100) cc_final: 0.6799 (m-90) REVERT: A 341 TRP cc_start: 0.7569 (p-90) cc_final: 0.7291 (t60) REVERT: A 411 TYR cc_start: 0.6907 (t80) cc_final: 0.6646 (t80) REVERT: A 429 GLN cc_start: 0.7228 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 433 ASP cc_start: 0.8840 (t0) cc_final: 0.8559 (t70) REVERT: A 473 MET cc_start: 0.7962 (tpp) cc_final: 0.7439 (ttm) REVERT: A 480 ASP cc_start: 0.8389 (t0) cc_final: 0.8158 (t0) REVERT: A 558 TYR cc_start: 0.7711 (m-80) cc_final: 0.7432 (m-80) REVERT: A 589 ASP cc_start: 0.9072 (t0) cc_final: 0.8833 (t70) REVERT: D 175 TRP cc_start: 0.7298 (m100) cc_final: 0.6784 (m-90) REVERT: D 341 TRP cc_start: 0.7576 (p-90) cc_final: 0.7179 (t60) REVERT: D 411 TYR cc_start: 0.6938 (t80) cc_final: 0.6654 (t80) REVERT: D 429 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6981 (tm-30) REVERT: D 433 ASP cc_start: 0.8820 (t0) cc_final: 0.8601 (t70) REVERT: D 473 MET cc_start: 0.7923 (tpp) cc_final: 0.7401 (ttm) REVERT: D 480 ASP cc_start: 0.8333 (t0) cc_final: 0.8112 (t0) REVERT: D 589 ASP cc_start: 0.9045 (t0) cc_final: 0.8801 (t70) REVERT: C 175 TRP cc_start: 0.7360 (m100) cc_final: 0.6886 (m-90) REVERT: C 341 TRP cc_start: 0.7568 (p-90) cc_final: 0.7206 (t60) REVERT: C 411 TYR cc_start: 0.6931 (t80) cc_final: 0.6623 (t80) REVERT: C 433 ASP cc_start: 0.8819 (t0) cc_final: 0.8566 (t70) REVERT: C 473 MET cc_start: 0.8025 (tpp) cc_final: 0.7431 (ttm) REVERT: C 480 ASP cc_start: 0.8406 (t0) cc_final: 0.8179 (t0) REVERT: C 589 ASP cc_start: 0.9080 (t0) cc_final: 0.8832 (t70) REVERT: B 175 TRP cc_start: 0.7202 (m100) cc_final: 0.6739 (m-90) REVERT: B 341 TRP cc_start: 0.7573 (p-90) cc_final: 0.7262 (t60) REVERT: B 411 TYR cc_start: 0.6938 (t80) cc_final: 0.6656 (t80) REVERT: B 429 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6982 (tm-30) REVERT: B 433 ASP cc_start: 0.8793 (t0) cc_final: 0.8523 (t70) REVERT: B 473 MET cc_start: 0.8025 (tpp) cc_final: 0.7456 (ttm) REVERT: B 480 ASP cc_start: 0.8398 (t0) cc_final: 0.8169 (t0) REVERT: B 558 TYR cc_start: 0.7717 (m-80) cc_final: 0.7443 (m-80) REVERT: B 589 ASP cc_start: 0.9087 (t0) cc_final: 0.8850 (t70) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.0935 time to fit residues: 45.7191 Evaluate side-chains 282 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN C 392 HIS ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN B 392 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.164339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112913 restraints weight = 24592.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113219 restraints weight = 15043.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113499 restraints weight = 9707.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113973 restraints weight = 9421.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114311 restraints weight = 8737.611| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13616 Z= 0.147 Angle : 0.603 8.160 18680 Z= 0.293 Chirality : 0.041 0.203 2196 Planarity : 0.004 0.034 2452 Dihedral : 10.974 177.435 2156 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.56 % Allowed : 29.00 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.20), residues: 1972 helix: 2.93 (0.13), residues: 1432 sheet: -0.31 (0.51), residues: 112 loop : -2.52 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 405 TYR 0.010 0.001 TYR C 411 PHE 0.009 0.001 PHE B 464 TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (13616) covalent geometry : angle 0.60301 / 0.29 (18680) hydrogen bonds : bond 0.03191 / 2.36 ( 1153) hydrogen bonds : angle 3.72856 / 2.77 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 0.409 Fit side-chains REVERT: A 175 TRP cc_start: 0.7187 (m100) cc_final: 0.6782 (m-90) REVERT: A 351 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8062 (mttp) REVERT: A 379 MET cc_start: 0.9163 (mtm) cc_final: 0.8940 (mtm) REVERT: A 411 TYR cc_start: 0.7331 (t80) cc_final: 0.7059 (t80) REVERT: A 473 MET cc_start: 0.7757 (tpp) cc_final: 0.6901 (ttm) REVERT: A 480 ASP cc_start: 0.8096 (t0) cc_final: 0.7862 (t0) REVERT: A 494 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7341 (mt-10) REVERT: D 175 TRP cc_start: 0.7268 (m100) cc_final: 0.6844 (m-90) REVERT: D 341 TRP cc_start: 0.7426 (p-90) cc_final: 0.7132 (t60) REVERT: D 401 ASP cc_start: 0.8430 (p0) cc_final: 0.8215 (p0) REVERT: D 411 TYR cc_start: 0.7306 (t80) cc_final: 0.7029 (t80) REVERT: D 473 MET cc_start: 0.7740 (tpp) cc_final: 0.6853 (ttm) REVERT: D 480 ASP cc_start: 0.8106 (t0) cc_final: 0.7878 (t0) REVERT: D 494 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7353 (mt-10) REVERT: C 175 TRP cc_start: 0.7318 (m100) cc_final: 0.6854 (m-90) REVERT: C 341 TRP cc_start: 0.7442 (p-90) cc_final: 0.7205 (t60) REVERT: C 411 TYR cc_start: 0.7379 (t80) cc_final: 0.7057 (t80) REVERT: C 473 MET cc_start: 0.7730 (tpp) cc_final: 0.6855 (ttm) REVERT: C 480 ASP cc_start: 0.8125 (t0) cc_final: 0.7917 (t0) REVERT: B 175 TRP cc_start: 0.7281 (m100) cc_final: 0.6806 (m-90) REVERT: B 330 TRP cc_start: 0.6584 (p-90) cc_final: 0.6383 (p-90) REVERT: B 341 TRP cc_start: 0.7475 (p-90) cc_final: 0.7224 (t60) REVERT: B 347 TYR cc_start: 0.8019 (m-10) cc_final: 0.7812 (m-10) REVERT: B 351 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7923 (mmtp) REVERT: B 411 TYR cc_start: 0.7361 (t80) cc_final: 0.7038 (t80) REVERT: B 473 MET cc_start: 0.7773 (tpp) cc_final: 0.6924 (ttm) REVERT: B 480 ASP cc_start: 0.8122 (t0) cc_final: 0.7903 (t0) outliers start: 50 outliers final: 27 residues processed: 317 average time/residue: 0.0799 time to fit residues: 39.3722 Evaluate side-chains 295 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 172 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN A 482 ASN A 497 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 482 ASN D 497 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 482 ASN C 497 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 482 ASN B 497 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110346 restraints weight = 24605.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113516 restraints weight = 16450.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114855 restraints weight = 10402.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115058 restraints weight = 9173.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115481 restraints weight = 9193.392| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13616 Z= 0.123 Angle : 0.589 7.904 18680 Z= 0.283 Chirality : 0.039 0.184 2196 Planarity : 0.003 0.033 2452 Dihedral : 11.115 179.607 2156 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.56 % Allowed : 31.00 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.20), residues: 1972 helix: 3.09 (0.13), residues: 1432 sheet: -0.31 (0.49), residues: 120 loop : -2.56 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 405 TYR 0.008 0.001 TYR A 411 PHE 0.007 0.001 PHE D 538 TRP 0.014 0.001 TRP C 330 HIS 0.004 0.001 HIS D 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13616) covalent geometry : angle 0.58918 / 0.28 (18680) hydrogen bonds : bond 0.02960 / 2.21 ( 1153) hydrogen bonds : angle 3.53896 / 2.62 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.398 Fit side-chains REVERT: A 175 TRP cc_start: 0.7093 (m100) cc_final: 0.6746 (m-90) REVERT: A 351 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8194 (mttp) REVERT: A 379 MET cc_start: 0.9069 (mtm) cc_final: 0.8834 (mtm) REVERT: A 411 TYR cc_start: 0.7304 (t80) cc_final: 0.7073 (t80) REVERT: A 473 MET cc_start: 0.7969 (tpp) cc_final: 0.7047 (ttp) REVERT: D 175 TRP cc_start: 0.7179 (m100) cc_final: 0.6768 (m-90) REVERT: D 405 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8334 (ttp-110) REVERT: D 411 TYR cc_start: 0.7234 (t80) cc_final: 0.7003 (t80) REVERT: D 429 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 473 MET cc_start: 0.7955 (tpp) cc_final: 0.7007 (ttp) REVERT: C 175 TRP cc_start: 0.7206 (m100) cc_final: 0.6801 (m-90) REVERT: C 411 TYR cc_start: 0.7303 (t80) cc_final: 0.7084 (t80) REVERT: C 473 MET cc_start: 0.7936 (tpp) cc_final: 0.7003 (ttp) REVERT: B 175 TRP cc_start: 0.7255 (m100) cc_final: 0.6827 (m-90) REVERT: B 301 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 347 TYR cc_start: 0.8039 (m-10) cc_final: 0.7821 (m-10) REVERT: B 351 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8014 (mmtp) REVERT: B 411 TYR cc_start: 0.7326 (t80) cc_final: 0.7108 (t80) REVERT: B 429 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 473 MET cc_start: 0.7966 (tpp) cc_final: 0.7034 (ttp) outliers start: 59 outliers final: 25 residues processed: 304 average time/residue: 0.0901 time to fit residues: 42.6184 Evaluate side-chains 285 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 50.0000 chunk 189 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 98 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN A 497 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 497 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098435 restraints weight = 23817.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101501 restraints weight = 14233.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103643 restraints weight = 10207.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105062 restraints weight = 8265.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105873 restraints weight = 7245.146| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 13616 Z= 0.353 Angle : 0.733 9.667 18680 Z= 0.375 Chirality : 0.044 0.213 2196 Planarity : 0.005 0.042 2452 Dihedral : 11.329 176.697 2156 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 10.89 % Allowed : 27.56 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.20), residues: 1972 helix: 2.80 (0.13), residues: 1456 sheet: 0.49 (0.60), residues: 88 loop : -3.02 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 405 TYR 0.022 0.002 TYR A 411 PHE 0.024 0.003 PHE D 538 TRP 0.012 0.001 TRP C 330 HIS 0.008 0.002 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.35 (13616) covalent geometry : angle 0.73301 / 0.38 (18680) hydrogen bonds : bond 0.04067 / 3.00 ( 1153) hydrogen bonds : angle 3.93888 / 2.92 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 265 time to evaluate : 0.585 Fit side-chains REVERT: A 175 TRP cc_start: 0.7134 (m100) cc_final: 0.6777 (m-90) REVERT: A 301 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8153 (mm) REVERT: A 351 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8167 (mttp) REVERT: A 401 ASP cc_start: 0.8320 (p0) cc_final: 0.7999 (p0) REVERT: A 416 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 473 MET cc_start: 0.8028 (tpp) cc_final: 0.7580 (ttm) REVERT: A 529 GLU cc_start: 0.7564 (pp20) cc_final: 0.7271 (pp20) REVERT: D 175 TRP cc_start: 0.7202 (m100) cc_final: 0.6851 (m-90) REVERT: D 401 ASP cc_start: 0.8329 (p0) cc_final: 0.8006 (p0) REVERT: D 427 MET cc_start: 0.8569 (mmm) cc_final: 0.8241 (mmm) REVERT: D 473 MET cc_start: 0.8039 (tpp) cc_final: 0.7575 (ttm) REVERT: C 175 TRP cc_start: 0.7193 (m100) cc_final: 0.6774 (m-90) REVERT: C 401 ASP cc_start: 0.8345 (p0) cc_final: 0.8002 (p0) REVERT: C 427 MET cc_start: 0.8601 (mmm) cc_final: 0.8255 (mmm) REVERT: C 473 MET cc_start: 0.8025 (tpp) cc_final: 0.7572 (ttm) REVERT: B 175 TRP cc_start: 0.7214 (m100) cc_final: 0.6845 (m-90) REVERT: B 301 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8155 (mm) REVERT: B 351 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: B 401 ASP cc_start: 0.8331 (p0) cc_final: 0.7957 (p0) REVERT: B 416 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8726 (tm-30) REVERT: B 429 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 473 MET cc_start: 0.8024 (tpp) cc_final: 0.7566 (ttm) REVERT: B 529 GLU cc_start: 0.7557 (pp20) cc_final: 0.7273 (pp20) outliers start: 98 outliers final: 68 residues processed: 320 average time/residue: 0.0956 time to fit residues: 46.8922 Evaluate side-chains 323 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 408 GLN Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 36 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 192 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 159 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 497 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN B 465 ASN B 497 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.160807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103888 restraints weight = 23990.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107187 restraints weight = 14146.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109387 restraints weight = 10035.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111007 restraints weight = 8066.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111780 restraints weight = 7027.040| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13616 Z= 0.126 Angle : 0.611 8.097 18680 Z= 0.297 Chirality : 0.040 0.199 2196 Planarity : 0.003 0.030 2452 Dihedral : 9.498 148.057 2156 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 7.11 % Allowed : 32.33 % Favored : 60.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.20), residues: 1972 helix: 3.04 (0.13), residues: 1456 sheet: -0.06 (0.53), residues: 112 loop : -2.92 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 405 TYR 0.012 0.001 TYR C 411 PHE 0.017 0.001 PHE A 166 TRP 0.011 0.001 TRP A 330 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13616) covalent geometry : angle 0.61139 / 0.30 (18680) hydrogen bonds : bond 0.02983 / 2.22 ( 1153) hydrogen bonds : angle 3.51303 / 2.59 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 0.427 Fit side-chains REVERT: A 175 TRP cc_start: 0.7160 (m100) cc_final: 0.6847 (m-90) REVERT: A 301 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 351 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8144 (mttp) REVERT: A 356 MET cc_start: 0.8658 (tmm) cc_final: 0.8433 (tmm) REVERT: A 379 MET cc_start: 0.9034 (mtm) cc_final: 0.8799 (mtm) REVERT: A 416 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 429 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 473 MET cc_start: 0.7910 (tpp) cc_final: 0.7394 (ttp) REVERT: A 529 GLU cc_start: 0.7426 (pp20) cc_final: 0.7191 (pp20) REVERT: D 175 TRP cc_start: 0.7296 (m100) cc_final: 0.6866 (m-90) REVERT: D 429 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7410 (tm-30) REVERT: D 473 MET cc_start: 0.7917 (tpp) cc_final: 0.7385 (ttp) REVERT: D 530 MET cc_start: 0.6444 (ptm) cc_final: 0.5478 (ptm) REVERT: C 175 TRP cc_start: 0.7303 (m100) cc_final: 0.6919 (m-90) REVERT: C 401 ASP cc_start: 0.8281 (p0) cc_final: 0.8059 (p0) REVERT: C 405 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8412 (ttp-110) REVERT: C 473 MET cc_start: 0.7953 (tpp) cc_final: 0.7443 (ttp) REVERT: C 530 MET cc_start: 0.6456 (ptm) cc_final: 0.5499 (ptm) REVERT: B 175 TRP cc_start: 0.7297 (m100) cc_final: 0.6900 (m-90) REVERT: B 301 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8081 (mm) REVERT: B 330 TRP cc_start: 0.7146 (p-90) cc_final: 0.6880 (p-90) REVERT: B 351 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: B 429 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 473 MET cc_start: 0.7953 (tpp) cc_final: 0.7452 (ttp) REVERT: B 529 GLU cc_start: 0.7386 (pp20) cc_final: 0.7146 (pp20) outliers start: 64 outliers final: 34 residues processed: 303 average time/residue: 0.0905 time to fit residues: 42.5331 Evaluate side-chains 297 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 50.0000 chunk 185 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 158 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN A 478 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 478 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 478 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 478 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099625 restraints weight = 23546.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102796 restraints weight = 13788.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104842 restraints weight = 9799.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106454 restraints weight = 7910.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107180 restraints weight = 6902.845| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13616 Z= 0.245 Angle : 0.685 9.564 18680 Z= 0.340 Chirality : 0.041 0.163 2196 Planarity : 0.004 0.038 2452 Dihedral : 8.705 132.491 2156 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 9.22 % Allowed : 29.67 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.20), residues: 1972 helix: 3.00 (0.13), residues: 1456 sheet: -0.08 (0.52), residues: 112 loop : -2.90 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 560 TYR 0.015 0.002 TYR C 411 PHE 0.021 0.002 PHE A 166 TRP 0.011 0.001 TRP D 330 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (13616) covalent geometry : angle 0.68506 / 0.34 (18680) hydrogen bonds : bond 0.03467 / 2.57 ( 1153) hydrogen bonds : angle 3.65667 / 2.69 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 269 time to evaluate : 0.522 Fit side-chains REVERT: A 175 TRP cc_start: 0.7294 (m100) cc_final: 0.6961 (m-90) REVERT: A 299 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 301 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 351 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: A 416 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 427 MET cc_start: 0.8581 (mmm) cc_final: 0.8087 (mmm) REVERT: A 429 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 473 MET cc_start: 0.8028 (tpp) cc_final: 0.7631 (ttm) REVERT: D 175 TRP cc_start: 0.7280 (m100) cc_final: 0.6825 (m-90) REVERT: D 429 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 473 MET cc_start: 0.8053 (tpp) cc_final: 0.7639 (ttm) REVERT: C 175 TRP cc_start: 0.7281 (m100) cc_final: 0.6845 (m-90) REVERT: C 401 ASP cc_start: 0.8372 (p0) cc_final: 0.7892 (p0) REVERT: C 473 MET cc_start: 0.8021 (tpp) cc_final: 0.7626 (ttm) REVERT: B 175 TRP cc_start: 0.7325 (m100) cc_final: 0.6935 (m-90) REVERT: B 301 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 351 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8114 (mttp) REVERT: B 429 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 473 MET cc_start: 0.8023 (tpp) cc_final: 0.7628 (ttm) REVERT: B 487 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8017 (ttm) outliers start: 83 outliers final: 64 residues processed: 311 average time/residue: 0.0920 time to fit residues: 44.3616 Evaluate side-chains 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 408 GLN Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 0.0570 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 overall best weight: 2.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098197 restraints weight = 23611.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101352 restraints weight = 13908.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103501 restraints weight = 9914.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104720 restraints weight = 8017.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105882 restraints weight = 7035.060| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13616 Z= 0.272 Angle : 0.722 9.842 18680 Z= 0.359 Chirality : 0.042 0.240 2196 Planarity : 0.004 0.035 2452 Dihedral : 8.575 128.718 2156 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 9.22 % Allowed : 29.89 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.19), residues: 1972 helix: 2.89 (0.13), residues: 1456 sheet: 0.17 (0.55), residues: 88 loop : -3.01 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 405 TYR 0.015 0.002 TYR C 411 PHE 0.019 0.002 PHE A 166 TRP 0.023 0.001 TRP B 330 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 (13616) covalent geometry : angle 0.72152 / 0.36 (18680) hydrogen bonds : bond 0.03584 / 2.66 ( 1153) hydrogen bonds : angle 3.78660 / 2.79 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 0.510 Fit side-chains REVERT: A 175 TRP cc_start: 0.7314 (m100) cc_final: 0.6937 (m-90) REVERT: A 301 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 330 TRP cc_start: 0.7859 (p-90) cc_final: 0.7514 (p90) REVERT: A 351 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8235 (mttp) REVERT: A 401 ASP cc_start: 0.8371 (p0) cc_final: 0.8003 (p0) REVERT: A 406 GLN cc_start: 0.8755 (mt0) cc_final: 0.8548 (mt0) REVERT: A 416 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 473 MET cc_start: 0.8095 (tpp) cc_final: 0.7776 (ttm) REVERT: D 175 TRP cc_start: 0.7227 (m100) cc_final: 0.6793 (m-90) REVERT: D 401 ASP cc_start: 0.8370 (p0) cc_final: 0.8061 (p0) REVERT: D 406 GLN cc_start: 0.8789 (mt0) cc_final: 0.8576 (mt0) REVERT: D 429 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 473 MET cc_start: 0.8103 (tpp) cc_final: 0.7777 (ttm) REVERT: C 175 TRP cc_start: 0.7324 (m100) cc_final: 0.6861 (m-90) REVERT: C 299 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 401 ASP cc_start: 0.8396 (p0) cc_final: 0.7965 (p0) REVERT: C 473 MET cc_start: 0.8081 (tpp) cc_final: 0.7770 (ttm) REVERT: B 175 TRP cc_start: 0.7326 (m100) cc_final: 0.6922 (m-90) REVERT: B 301 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 351 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8306 (mttp) REVERT: B 401 ASP cc_start: 0.8368 (p0) cc_final: 0.7954 (p0) REVERT: B 429 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 473 MET cc_start: 0.8086 (tpp) cc_final: 0.7777 (ttm) outliers start: 83 outliers final: 67 residues processed: 309 average time/residue: 0.0943 time to fit residues: 45.0532 Evaluate side-chains 332 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 408 GLN Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 138 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 152 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.160623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103712 restraints weight = 23570.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106962 restraints weight = 13873.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109207 restraints weight = 9900.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110723 restraints weight = 7982.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111513 restraints weight = 6966.642| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13616 Z= 0.126 Angle : 0.645 8.499 18680 Z= 0.312 Chirality : 0.040 0.230 2196 Planarity : 0.003 0.031 2452 Dihedral : 8.600 131.582 2156 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.56 % Allowed : 33.44 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.20), residues: 1972 helix: 3.04 (0.13), residues: 1456 sheet: -0.05 (0.51), residues: 112 loop : -2.85 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 405 TYR 0.012 0.001 TYR C 411 PHE 0.017 0.001 PHE B 166 TRP 0.018 0.001 TRP B 330 HIS 0.011 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13616) covalent geometry : angle 0.64530 / 0.31 (18680) hydrogen bonds : bond 0.02896 / 2.16 ( 1153) hydrogen bonds : angle 3.49128 / 2.56 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.475 Fit side-chains REVERT: A 175 TRP cc_start: 0.7318 (m100) cc_final: 0.6899 (m-90) REVERT: A 301 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 351 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8182 (mttp) REVERT: A 406 GLN cc_start: 0.8646 (mt0) cc_final: 0.8435 (mt0) REVERT: A 429 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 473 MET cc_start: 0.8043 (tpp) cc_final: 0.7595 (ttp) REVERT: D 175 TRP cc_start: 0.7159 (m100) cc_final: 0.6748 (m-90) REVERT: D 406 GLN cc_start: 0.8656 (mt0) cc_final: 0.8450 (mt0) REVERT: D 429 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 473 MET cc_start: 0.8062 (tpp) cc_final: 0.7595 (ttp) REVERT: C 175 TRP cc_start: 0.7296 (m100) cc_final: 0.6876 (m-90) REVERT: C 406 GLN cc_start: 0.8669 (mt0) cc_final: 0.8434 (mt0) REVERT: C 429 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7369 (tm-30) REVERT: C 473 MET cc_start: 0.8016 (tpp) cc_final: 0.7554 (ttp) REVERT: B 175 TRP cc_start: 0.7288 (m100) cc_final: 0.6876 (m-90) REVERT: B 301 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8120 (mm) REVERT: B 351 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: B 429 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 473 MET cc_start: 0.8013 (tpp) cc_final: 0.7584 (ttp) outliers start: 50 outliers final: 39 residues processed: 294 average time/residue: 0.0840 time to fit residues: 38.9843 Evaluate side-chains 306 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 50 optimal weight: 50.0000 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.160259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103575 restraints weight = 23727.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107899 restraints weight = 14579.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108653 restraints weight = 9102.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109660 restraints weight = 8338.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109710 restraints weight = 7677.293| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13616 Z= 0.146 Angle : 0.661 9.234 18680 Z= 0.321 Chirality : 0.040 0.309 2196 Planarity : 0.003 0.035 2452 Dihedral : 8.638 132.532 2156 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.89 % Allowed : 34.22 % Favored : 59.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.20), residues: 1972 helix: 3.09 (0.13), residues: 1456 sheet: -0.03 (0.50), residues: 112 loop : -2.79 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 405 TYR 0.012 0.001 TYR C 411 PHE 0.016 0.001 PHE B 166 TRP 0.024 0.001 TRP B 330 HIS 0.014 0.002 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (13616) covalent geometry : angle 0.66052 / 0.32 (18680) hydrogen bonds : bond 0.02927 / 2.19 ( 1153) hydrogen bonds : angle 3.48308 / 2.55 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.482 Fit side-chains REVERT: A 175 TRP cc_start: 0.7350 (m100) cc_final: 0.6897 (m-90) REVERT: A 299 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (t80) REVERT: A 301 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8155 (mm) REVERT: A 351 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8244 (mttp) REVERT: A 379 MET cc_start: 0.9038 (mtm) cc_final: 0.8681 (mtm) REVERT: A 406 GLN cc_start: 0.8743 (mt0) cc_final: 0.8521 (mt0) REVERT: A 429 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 473 MET cc_start: 0.8104 (tpp) cc_final: 0.7640 (ttp) REVERT: D 175 TRP cc_start: 0.7185 (m100) cc_final: 0.6746 (m-90) REVERT: D 406 GLN cc_start: 0.8741 (mt0) cc_final: 0.8517 (mt0) REVERT: D 429 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 473 MET cc_start: 0.8113 (tpp) cc_final: 0.7642 (ttp) REVERT: C 175 TRP cc_start: 0.7331 (m100) cc_final: 0.6882 (m-90) REVERT: C 406 GLN cc_start: 0.8747 (mt0) cc_final: 0.8521 (mt0) REVERT: C 429 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 473 MET cc_start: 0.8091 (tpp) cc_final: 0.7624 (ttp) REVERT: B 175 TRP cc_start: 0.7318 (m100) cc_final: 0.6876 (m-90) REVERT: B 301 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 351 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8221 (mttp) REVERT: B 429 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7379 (tm-30) REVERT: B 473 MET cc_start: 0.8088 (tpp) cc_final: 0.7645 (ttp) outliers start: 53 outliers final: 37 residues processed: 295 average time/residue: 0.0906 time to fit residues: 41.7777 Evaluate side-chains 309 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN A 478 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099610 restraints weight = 23190.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102702 restraints weight = 13765.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104856 restraints weight = 9866.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105963 restraints weight = 7998.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107103 restraints weight = 7071.328| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13616 Z= 0.242 Angle : 0.719 9.639 18680 Z= 0.358 Chirality : 0.042 0.304 2196 Planarity : 0.004 0.031 2452 Dihedral : 8.585 130.139 2156 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.56 % Allowed : 34.67 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.20), residues: 1972 helix: 2.98 (0.13), residues: 1456 sheet: 0.35 (0.53), residues: 88 loop : -2.89 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 405 TYR 0.015 0.001 TYR C 411 PHE 0.016 0.002 PHE D 514 TRP 0.026 0.001 TRP B 330 HIS 0.006 0.002 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (13616) covalent geometry : angle 0.71919 / 0.36 (18680) hydrogen bonds : bond 0.03430 / 2.54 ( 1153) hydrogen bonds : angle 3.67367 / 2.70 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.365 Fit side-chains REVERT: A 175 TRP cc_start: 0.7297 (m100) cc_final: 0.6835 (m-90) REVERT: A 301 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 351 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8341 (mttp) REVERT: A 379 MET cc_start: 0.9019 (mtm) cc_final: 0.8690 (mtm) REVERT: A 401 ASP cc_start: 0.8253 (p0) cc_final: 0.7950 (p0) REVERT: A 429 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 473 MET cc_start: 0.8094 (tpp) cc_final: 0.7877 (ttp) REVERT: D 175 TRP cc_start: 0.7160 (m100) cc_final: 0.6724 (m-90) REVERT: D 401 ASP cc_start: 0.8245 (p0) cc_final: 0.7997 (p0) REVERT: D 406 GLN cc_start: 0.8733 (mt0) cc_final: 0.8531 (mt0) REVERT: D 429 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 473 MET cc_start: 0.8108 (tpp) cc_final: 0.7883 (ttp) REVERT: C 175 TRP cc_start: 0.7208 (m100) cc_final: 0.6792 (m-90) REVERT: C 299 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7756 (t80) REVERT: C 401 ASP cc_start: 0.8268 (p0) cc_final: 0.7971 (p0) REVERT: C 406 GLN cc_start: 0.8738 (mt0) cc_final: 0.8534 (mt0) REVERT: C 429 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 473 MET cc_start: 0.8067 (tpp) cc_final: 0.7801 (ttp) REVERT: B 175 TRP cc_start: 0.7316 (m100) cc_final: 0.6872 (m-90) REVERT: B 299 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (t80) REVERT: B 301 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8162 (mm) REVERT: B 351 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8336 (mttp) REVERT: B 401 ASP cc_start: 0.8305 (p0) cc_final: 0.8032 (p0) REVERT: B 429 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 473 MET cc_start: 0.8062 (tpp) cc_final: 0.7790 (ttp) outliers start: 50 outliers final: 35 residues processed: 286 average time/residue: 0.0845 time to fit residues: 38.0737 Evaluate side-chains 304 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 158 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 112 optimal weight: 40.0000 chunk 147 optimal weight: 50.0000 chunk 115 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 HIS C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.159819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103184 restraints weight = 23342.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107018 restraints weight = 14352.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108079 restraints weight = 9043.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109597 restraints weight = 8309.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109066 restraints weight = 9313.154| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13616 Z= 0.160 Angle : 0.681 11.147 18680 Z= 0.331 Chirality : 0.041 0.322 2196 Planarity : 0.003 0.034 2452 Dihedral : 8.590 131.175 2156 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.11 % Allowed : 35.11 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.20), residues: 1972 helix: 3.01 (0.13), residues: 1456 sheet: -0.04 (0.50), residues: 112 loop : -2.81 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 405 TYR 0.013 0.001 TYR C 411 PHE 0.016 0.001 PHE B 166 TRP 0.024 0.001 TRP B 330 HIS 0.009 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13616) covalent geometry : angle 0.68107 / 0.33 (18680) hydrogen bonds : bond 0.02997 / 2.24 ( 1153) hydrogen bonds : angle 3.52059 / 2.58 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.49 seconds wall clock time: 42 minutes 1.88 seconds (2521.88 seconds total)