Starting phenix.real_space_refine on Thu Jul 31 11:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4y_41040/07_2025/8t4y_41040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4y_41040/07_2025/8t4y_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_41040/07_2025/8t4y_41040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4y_41040/07_2025/8t4y_41040.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4y_41040/07_2025/8t4y_41040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4y_41040/07_2025/8t4y_41040.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 17, 'ARG:plan': 15} 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: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 17, 'ARG:plan': 15} 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: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 17, 'ARG:plan': 15} 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: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 436 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 9.95, per 1000 atoms: 0.75 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: 3.94 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.49 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: 5.00 Time building geometry restraints manager: 4.74 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=" 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=" C PRO C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.54e+00 bond pdb=" CA PRO B 366 " pdb=" C PRO B 366 " ideal model delta sigma weight residual 1.520 1.537 -0.017 1.42e-02 4.96e+03 1.44e+00 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18330 1.99 - 3.99: 258 3.99 - 5.98: 56 5.98 - 7.97: 28 7.97 - 9.97: 8 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=" O1P CMP A 901 " pdb=" P CMP A 901 " pdb=" O2P CMP A 901 " ideal model delta sigma weight residual 109.50 119.47 -9.97 3.00e+00 1.11e-01 1.10e+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: 0 97.49 - 129.99: 4 129.99 - 162.48: 8 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: 1887 0.059 - 0.118: 298 0.118 - 0.176: 7 0.176 - 0.235: 0 0.235 - 0.294: 4 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 217.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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:4.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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= 0.139 Angle : 0.663 9.968 18680 Z= 0.340 Chirality : 0.040 0.294 2196 Planarity : 0.004 0.056 2452 Dihedral : 16.197 162.481 4148 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (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 TRP 0.004 0.001 TRP D 221 HIS 0.003 0.001 HIS D 355 PHE 0.006 0.001 PHE A 538 TYR 0.012 0.001 TYR D 417 ARG 0.002 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.10201 ( 1153) hydrogen bonds : angle 4.61124 ( 3411) covalent geometry : bond 0.00271 (13616) covalent geometry : angle 0.66309 (18680) *********************** 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 : 1.675 Fit side-chains REVERT: A 175 TRP cc_start: 0.7277 (m100) cc_final: 0.6798 (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: 0.7229 (tm-30) cc_final: 0.7006 (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: 0.7180 (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: 0.8405 (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: 0.7222 (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: 0.7442 (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: 0.2999 time to fit residues: 144.2651 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 : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN 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** B 497 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101560 restraints weight = 24000.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104775 restraints weight = 14165.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107002 restraints weight = 10090.731| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1885 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= 0.273 Angle : 0.650 6.952 18680 Z= 0.342 Chirality : 0.042 0.191 2196 Planarity : 0.004 0.040 2452 Dihedral : 11.870 165.407 2156 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 9.44 % Allowed : 25.78 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.20), residues: 1972 helix: 2.70 (0.13), residues: 1456 sheet: 0.06 (0.58), residues: 88 loop : -2.86 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 330 HIS 0.007 0.002 HIS A 517 PHE 0.018 0.002 PHE A 538 TYR 0.016 0.002 TYR A 439 ARG 0.005 0.001 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1153) hydrogen bonds : angle 3.93491 ( 3411) covalent geometry : bond 0.00615 (13616) covalent geometry : angle 0.65046 (18680) *********************** 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 370 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 285 time to evaluate : 1.793 Fit side-chains REVERT: A 175 TRP cc_start: 0.7128 (m100) cc_final: 0.6785 (m-90) REVERT: A 351 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: A 401 ASP cc_start: 0.8461 (p0) cc_final: 0.8206 (p0) REVERT: A 473 MET cc_start: 0.7757 (tpp) cc_final: 0.7134 (ttm) REVERT: A 530 MET cc_start: 0.6397 (ptm) cc_final: 0.6119 (ptm) REVERT: D 175 TRP cc_start: 0.7102 (m100) cc_final: 0.6776 (m-90) REVERT: D 401 ASP cc_start: 0.8423 (p0) cc_final: 0.8147 (p0) REVERT: D 473 MET cc_start: 0.7756 (tpp) cc_final: 0.7117 (ttm) REVERT: D 530 MET cc_start: 0.6372 (ptm) cc_final: 0.6088 (ptm) REVERT: C 175 TRP cc_start: 0.7202 (m100) cc_final: 0.6793 (m-90) REVERT: C 401 ASP cc_start: 0.8409 (p0) cc_final: 0.8127 (p0) REVERT: C 473 MET cc_start: 0.7744 (tpp) cc_final: 0.7112 (ttm) REVERT: C 530 MET cc_start: 0.6371 (ptm) cc_final: 0.6102 (ptm) REVERT: B 175 TRP cc_start: 0.7112 (m100) cc_final: 0.6772 (m-90) REVERT: B 351 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8158 (mttp) REVERT: B 401 ASP cc_start: 0.8420 (p0) cc_final: 0.8123 (p0) REVERT: B 473 MET cc_start: 0.7745 (tpp) cc_final: 0.7120 (ttm) REVERT: B 530 MET cc_start: 0.6413 (ptm) cc_final: 0.6135 (ptm) outliers start: 85 outliers final: 51 residues processed: 339 average time/residue: 0.2036 time to fit residues: 106.5295 Evaluate side-chains 305 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 426 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 545 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 408 GLN Chi-restraints excluded: chain D residue 426 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 545 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 377 LEU 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 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 545 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 381 VAL 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 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 543 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 0.3980 chunk 159 optimal weight: 40.0000 chunk 120 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 98 optimal weight: 50.0000 chunk 62 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 47 optimal weight: 50.0000 chunk 133 optimal weight: 0.6980 chunk 63 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** 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 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100133 restraints weight = 23885.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103347 restraints weight = 14345.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105484 restraints weight = 10264.535| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13616 Z= 0.257 Angle : 0.632 6.599 18680 Z= 0.335 Chirality : 0.041 0.173 2196 Planarity : 0.004 0.031 2452 Dihedral : 11.876 164.266 2156 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 10.00 % Allowed : 27.11 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.20), residues: 1972 helix: 2.77 (0.13), residues: 1456 sheet: 0.03 (0.58), residues: 88 loop : -2.88 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 330 HIS 0.006 0.002 HIS B 437 PHE 0.014 0.002 PHE B 538 TYR 0.027 0.002 TYR D 411 ARG 0.003 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1153) hydrogen bonds : angle 3.85794 ( 3411) covalent geometry : bond 0.00581 (13616) covalent geometry : angle 0.63195 (18680) *********************** 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 342 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 252 time to evaluate : 1.651 Fit side-chains REVERT: A 175 TRP cc_start: 0.7139 (m100) cc_final: 0.6776 (m-90) REVERT: A 330 TRP cc_start: 0.7338 (p-90) cc_final: 0.7093 (p90) REVERT: A 351 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8213 (mttp) REVERT: A 401 ASP cc_start: 0.8329 (p0) cc_final: 0.7963 (p0) REVERT: A 473 MET cc_start: 0.7984 (tpp) cc_final: 0.7508 (ttm) REVERT: A 530 MET cc_start: 0.6422 (ptm) cc_final: 0.6174 (ptm) REVERT: D 175 TRP cc_start: 0.7110 (m100) cc_final: 0.6764 (m-90) REVERT: D 401 ASP cc_start: 0.8292 (p0) cc_final: 0.7975 (p0) REVERT: D 473 MET cc_start: 0.7964 (tpp) cc_final: 0.7488 (ttm) REVERT: C 175 TRP cc_start: 0.7213 (m100) cc_final: 0.6784 (m-90) REVERT: C 401 ASP cc_start: 0.8343 (p0) cc_final: 0.8006 (p0) REVERT: C 473 MET cc_start: 0.7955 (tpp) cc_final: 0.7478 (ttm) REVERT: B 175 TRP cc_start: 0.7173 (m100) cc_final: 0.6784 (m-90) REVERT: B 351 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: B 401 ASP cc_start: 0.8345 (p0) cc_final: 0.7985 (p0) REVERT: B 473 MET cc_start: 0.7947 (tpp) cc_final: 0.7489 (ttm) REVERT: B 530 MET cc_start: 0.6340 (ptm) cc_final: 0.6054 (ptm) outliers start: 90 outliers final: 53 residues processed: 312 average time/residue: 0.2553 time to fit residues: 121.8564 Evaluate side-chains 306 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 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 394 THR Chi-restraints excluded: chain D residue 426 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 495 VAL 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 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 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 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 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 545 THR 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 408 GLN 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 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 109 optimal weight: 40.0000 chunk 92 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** 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 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.160663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103655 restraints weight = 23697.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106912 restraints weight = 14033.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109188 restraints weight = 9968.673| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2532 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= 0.137 Angle : 0.566 6.478 18680 Z= 0.294 Chirality : 0.039 0.198 2196 Planarity : 0.003 0.031 2452 Dihedral : 11.994 165.649 2156 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.78 % Allowed : 30.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.20), residues: 1972 helix: 2.91 (0.13), residues: 1456 sheet: -0.21 (0.52), residues: 112 loop : -2.79 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 330 HIS 0.004 0.001 HIS D 437 PHE 0.022 0.001 PHE A 166 TYR 0.028 0.001 TYR B 411 ARG 0.003 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 1153) hydrogen bonds : angle 3.57875 ( 3411) covalent geometry : bond 0.00300 (13616) covalent geometry : angle 0.56567 (18680) *********************** 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 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 1.483 Fit side-chains REVERT: A 175 TRP cc_start: 0.7191 (m100) cc_final: 0.6863 (m-90) REVERT: A 351 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8150 (mttp) REVERT: A 356 MET cc_start: 0.8689 (tmm) cc_final: 0.8472 (tmm) REVERT: A 401 ASP cc_start: 0.8271 (p0) cc_final: 0.8042 (p0) REVERT: A 405 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8355 (ttp-110) REVERT: A 427 MET cc_start: 0.8383 (mmm) cc_final: 0.8066 (mmm) REVERT: A 473 MET cc_start: 0.7944 (tpp) cc_final: 0.7361 (ttp) REVERT: D 175 TRP cc_start: 0.7256 (m100) cc_final: 0.6936 (m-90) REVERT: D 401 ASP cc_start: 0.8301 (p0) cc_final: 0.7865 (p0) REVERT: D 429 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7464 (tm-30) REVERT: D 473 MET cc_start: 0.7947 (tpp) cc_final: 0.7347 (ttp) REVERT: C 175 TRP cc_start: 0.7249 (m100) cc_final: 0.6863 (m-90) REVERT: C 356 MET cc_start: 0.8719 (tmm) cc_final: 0.8497 (tmm) REVERT: C 401 ASP cc_start: 0.8301 (p0) cc_final: 0.7834 (p0) REVERT: C 405 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8313 (ttp-110) REVERT: C 429 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 473 MET cc_start: 0.7940 (tpp) cc_final: 0.7352 (ttp) REVERT: B 175 TRP cc_start: 0.7254 (m100) cc_final: 0.6921 (m-90) REVERT: B 301 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 330 TRP cc_start: 0.7424 (p90) cc_final: 0.7204 (p-90) REVERT: B 351 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8156 (mttp) REVERT: B 356 MET cc_start: 0.8773 (tmm) cc_final: 0.8542 (tmm) REVERT: B 401 ASP cc_start: 0.8297 (p0) cc_final: 0.8083 (p0) REVERT: B 405 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8385 (ttp-110) REVERT: B 427 MET cc_start: 0.8383 (mmm) cc_final: 0.8065 (mmm) REVERT: B 473 MET cc_start: 0.7990 (tpp) cc_final: 0.7428 (ttp) outliers start: 70 outliers final: 40 residues processed: 305 average time/residue: 0.2159 time to fit residues: 100.4154 Evaluate side-chains 295 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 461 ILE Chi-restraints excluded: chain A residue 517 HIS 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 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 461 ILE 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 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 301 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 461 ILE Chi-restraints excluded: chain C residue 462 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 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 394 THR 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 461 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 60 optimal weight: 40.0000 chunk 168 optimal weight: 0.0270 chunk 148 optimal weight: 50.0000 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** A 482 ASN ** 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 478 ASN ** C 482 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104623 restraints weight = 23764.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107955 restraints weight = 13885.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110256 restraints weight = 9803.893| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13616 Z= 0.134 Angle : 0.564 6.357 18680 Z= 0.292 Chirality : 0.039 0.158 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.856 162.793 2156 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 7.89 % Allowed : 29.78 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.20), residues: 1972 helix: 3.15 (0.13), residues: 1432 sheet: -0.04 (0.52), residues: 112 loop : -2.60 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 330 HIS 0.004 0.001 HIS C 437 PHE 0.021 0.002 PHE A 166 TYR 0.023 0.001 TYR D 411 ARG 0.007 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 1153) hydrogen bonds : angle 3.45861 ( 3411) covalent geometry : bond 0.00295 (13616) covalent geometry : angle 0.56354 (18680) *********************** 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 342 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 271 time to evaluate : 1.554 Fit side-chains REVERT: A 175 TRP cc_start: 0.7222 (m100) cc_final: 0.6908 (m-90) REVERT: A 299 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 351 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8216 (mttp) REVERT: A 356 MET cc_start: 0.8707 (tmm) cc_final: 0.8445 (tmm) REVERT: A 401 ASP cc_start: 0.8251 (p0) cc_final: 0.8015 (p0) REVERT: A 405 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8309 (ttp-110) REVERT: A 427 MET cc_start: 0.8302 (mmm) cc_final: 0.7930 (mmm) REVERT: A 473 MET cc_start: 0.8017 (tpp) cc_final: 0.7457 (ttp) REVERT: D 175 TRP cc_start: 0.7293 (m100) cc_final: 0.6875 (m-90) REVERT: D 356 MET cc_start: 0.8673 (tmm) cc_final: 0.8424 (tmm) REVERT: D 401 ASP cc_start: 0.8293 (p0) cc_final: 0.8069 (p0) REVERT: D 429 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7417 (tm-30) REVERT: D 473 MET cc_start: 0.8014 (tpp) cc_final: 0.7441 (ttp) REVERT: C 175 TRP cc_start: 0.7282 (m100) cc_final: 0.6897 (m-90) REVERT: C 356 MET cc_start: 0.8698 (tmm) cc_final: 0.8427 (tmm) REVERT: C 401 ASP cc_start: 0.8300 (p0) cc_final: 0.8060 (p0) REVERT: C 405 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8380 (ttp-110) REVERT: C 429 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 473 MET cc_start: 0.8000 (tpp) cc_final: 0.7421 (ttp) REVERT: B 175 TRP cc_start: 0.7308 (m100) cc_final: 0.6925 (m-90) REVERT: B 299 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7680 (t80) REVERT: B 301 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 330 TRP cc_start: 0.7445 (p90) cc_final: 0.7229 (p-90) REVERT: B 351 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8151 (mttp) REVERT: B 356 MET cc_start: 0.8741 (tmm) cc_final: 0.8474 (tmm) REVERT: B 401 ASP cc_start: 0.8301 (p0) cc_final: 0.8064 (p0) REVERT: B 405 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8368 (ttp-110) REVERT: B 473 MET cc_start: 0.7997 (tpp) cc_final: 0.7413 (ttp) outliers start: 71 outliers final: 53 residues processed: 312 average time/residue: 0.2034 time to fit residues: 96.2861 Evaluate side-chains 324 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 451 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 462 VAL 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 A residue 543 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 166 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 461 ILE Chi-restraints excluded: chain D residue 462 VAL 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 543 LEU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 377 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 461 ILE Chi-restraints excluded: chain C residue 462 VAL 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 C residue 543 LEU Chi-restraints excluded: chain C residue 594 ILE 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 451 ASN Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106272 restraints weight = 23918.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109648 restraints weight = 13886.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111901 restraints weight = 9752.949| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2691 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= 0.123 Angle : 0.564 7.194 18680 Z= 0.290 Chirality : 0.039 0.234 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.872 163.289 2156 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.00 % Allowed : 31.00 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.20), residues: 1972 helix: 3.27 (0.13), residues: 1432 sheet: -0.09 (0.51), residues: 112 loop : -2.54 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 330 HIS 0.004 0.001 HIS C 437 PHE 0.020 0.001 PHE A 166 TYR 0.020 0.001 TYR B 411 ARG 0.008 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 1153) hydrogen bonds : angle 3.38278 ( 3411) covalent geometry : bond 0.00268 (13616) covalent geometry : angle 0.56376 (18680) *********************** 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 348 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 1.398 Fit side-chains REVERT: A 175 TRP cc_start: 0.7271 (m100) cc_final: 0.6946 (m-90) REVERT: A 351 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: A 356 MET cc_start: 0.8689 (tmm) cc_final: 0.8400 (tmm) REVERT: A 401 ASP cc_start: 0.8183 (p0) cc_final: 0.7920 (p0) REVERT: A 405 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8290 (ttp-110) REVERT: A 429 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 473 MET cc_start: 0.7904 (tpp) cc_final: 0.7329 (ttp) REVERT: D 175 TRP cc_start: 0.7291 (m100) cc_final: 0.6891 (m-90) REVERT: D 356 MET cc_start: 0.8660 (tmm) cc_final: 0.8392 (tmm) REVERT: D 429 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 473 MET cc_start: 0.7946 (tpp) cc_final: 0.7296 (ttp) REVERT: C 175 TRP cc_start: 0.7277 (m100) cc_final: 0.6888 (m-90) REVERT: C 299 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7582 (t80) REVERT: C 356 MET cc_start: 0.8688 (tmm) cc_final: 0.8392 (tmm) REVERT: C 401 ASP cc_start: 0.8218 (p0) cc_final: 0.7961 (p0) REVERT: C 405 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8365 (ttp-110) REVERT: C 429 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 473 MET cc_start: 0.7928 (tpp) cc_final: 0.7304 (ttp) REVERT: C 494 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7474 (mt-10) REVERT: B 175 TRP cc_start: 0.7265 (m100) cc_final: 0.6895 (m-90) REVERT: B 301 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 351 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 356 MET cc_start: 0.8688 (tmm) cc_final: 0.8389 (tmm) REVERT: B 401 ASP cc_start: 0.8236 (p0) cc_final: 0.7968 (p0) REVERT: B 405 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8372 (ttp-110) REVERT: B 429 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 473 MET cc_start: 0.7897 (tpp) cc_final: 0.7280 (ttp) REVERT: B 487 MET cc_start: 0.8086 (ttm) cc_final: 0.7723 (ttm) outliers start: 63 outliers final: 45 residues processed: 321 average time/residue: 0.2155 time to fit residues: 105.2892 Evaluate side-chains 319 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 465 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 299 PHE 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 462 VAL Chi-restraints excluded: chain D residue 465 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 D residue 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 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 465 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 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 421 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 163 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS C 465 ASN ** C 482 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.161941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106014 restraints weight = 23798.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109314 restraints weight = 13851.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111489 restraints weight = 9760.839| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2751 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= 0.126 Angle : 0.575 7.416 18680 Z= 0.295 Chirality : 0.039 0.202 2196 Planarity : 0.003 0.033 2452 Dihedral : 11.872 163.789 2156 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 7.11 % Allowed : 31.67 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.20), residues: 1972 helix: 3.30 (0.13), residues: 1432 sheet: -0.01 (0.51), residues: 112 loop : -2.48 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 330 HIS 0.006 0.001 HIS A 421 PHE 0.020 0.001 PHE A 166 TYR 0.021 0.001 TYR A 558 ARG 0.007 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 1153) hydrogen bonds : angle 3.34818 ( 3411) covalent geometry : bond 0.00278 (13616) covalent geometry : angle 0.57544 (18680) *********************** 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 340 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 1.557 Fit side-chains REVERT: A 175 TRP cc_start: 0.7281 (m100) cc_final: 0.6876 (m-90) REVERT: A 299 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 351 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: A 356 MET cc_start: 0.8707 (tmm) cc_final: 0.8392 (tmm) REVERT: A 401 ASP cc_start: 0.8196 (p0) cc_final: 0.7930 (p0) REVERT: A 405 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8336 (ttp-110) REVERT: A 429 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 473 MET cc_start: 0.7883 (tpp) cc_final: 0.7309 (ttp) REVERT: D 175 TRP cc_start: 0.7250 (m100) cc_final: 0.6842 (m-90) REVERT: D 356 MET cc_start: 0.8654 (tmm) cc_final: 0.8365 (tmm) REVERT: D 429 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7267 (tm-30) REVERT: D 473 MET cc_start: 0.7881 (tpp) cc_final: 0.7296 (ttp) REVERT: C 175 TRP cc_start: 0.7246 (m100) cc_final: 0.6856 (m-90) REVERT: C 299 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 356 MET cc_start: 0.8683 (tmm) cc_final: 0.8355 (tmm) REVERT: C 401 ASP cc_start: 0.8238 (p0) cc_final: 0.8023 (p0) REVERT: C 429 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 473 MET cc_start: 0.7862 (tpp) cc_final: 0.7304 (ttp) REVERT: C 494 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7589 (mt-10) REVERT: B 175 TRP cc_start: 0.7290 (m100) cc_final: 0.6920 (m-90) REVERT: B 301 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 351 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8257 (mttp) REVERT: B 356 MET cc_start: 0.8715 (tmm) cc_final: 0.8387 (tmm) REVERT: B 401 ASP cc_start: 0.8223 (p0) cc_final: 0.7967 (p0) REVERT: B 405 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8383 (ttp-110) REVERT: B 429 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 473 MET cc_start: 0.7903 (tpp) cc_final: 0.7308 (ttp) outliers start: 64 outliers final: 39 residues processed: 316 average time/residue: 0.2057 time to fit residues: 98.7271 Evaluate side-chains 310 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 VAL 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 D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 462 VAL 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 543 LEU 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 301 LEU Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL 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 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 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.162294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106240 restraints weight = 23747.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109618 restraints weight = 13809.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111915 restraints weight = 9678.171| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2792 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= 0.129 Angle : 0.579 8.081 18680 Z= 0.299 Chirality : 0.039 0.285 2196 Planarity : 0.003 0.041 2452 Dihedral : 11.858 163.755 2156 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.33 % Allowed : 33.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.20), residues: 1972 helix: 3.34 (0.13), residues: 1432 sheet: 0.03 (0.50), residues: 112 loop : -2.47 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 330 HIS 0.007 0.001 HIS D 421 PHE 0.018 0.001 PHE B 166 TYR 0.018 0.001 TYR A 558 ARG 0.008 0.000 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 1153) hydrogen bonds : angle 3.34009 ( 3411) covalent geometry : bond 0.00285 (13616) covalent geometry : angle 0.57887 (18680) *********************** 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: 48 poor density : 273 time to evaluate : 1.369 Fit side-chains REVERT: A 175 TRP cc_start: 0.7297 (m100) cc_final: 0.6881 (m-90) REVERT: A 299 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 351 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8233 (mttp) REVERT: A 356 MET cc_start: 0.8709 (tmm) cc_final: 0.8376 (tmm) REVERT: A 401 ASP cc_start: 0.8256 (p0) cc_final: 0.7972 (p0) REVERT: A 405 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8378 (ttp-110) REVERT: A 429 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 473 MET cc_start: 0.8068 (tpp) cc_final: 0.7432 (ttp) REVERT: D 175 TRP cc_start: 0.7260 (m100) cc_final: 0.6827 (m-90) REVERT: D 356 MET cc_start: 0.8662 (tmm) cc_final: 0.8341 (tmm) REVERT: D 429 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 473 MET cc_start: 0.8066 (tpp) cc_final: 0.7431 (ttp) REVERT: D 494 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7493 (mt-10) REVERT: C 175 TRP cc_start: 0.7270 (m100) cc_final: 0.6864 (m-90) REVERT: C 299 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7653 (t80) REVERT: C 356 MET cc_start: 0.8675 (tmm) cc_final: 0.8327 (tmm) REVERT: C 401 ASP cc_start: 0.8312 (p0) cc_final: 0.8074 (p0) REVERT: C 429 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7334 (tm-30) REVERT: C 473 MET cc_start: 0.8053 (tpp) cc_final: 0.7421 (ttp) REVERT: C 494 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7614 (mt-10) REVERT: B 175 TRP cc_start: 0.7315 (m100) cc_final: 0.6900 (m-90) REVERT: B 301 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 330 TRP cc_start: 0.7421 (p90) cc_final: 0.7126 (p-90) REVERT: B 351 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: B 356 MET cc_start: 0.8717 (tmm) cc_final: 0.8367 (tmm) REVERT: B 401 ASP cc_start: 0.8309 (p0) cc_final: 0.8034 (p0) REVERT: B 405 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8397 (ttp-110) REVERT: B 429 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 473 MET cc_start: 0.8081 (tpp) cc_final: 0.7435 (ttp) outliers start: 48 outliers final: 39 residues processed: 297 average time/residue: 0.2053 time to fit residues: 93.3903 Evaluate side-chains 311 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 451 ASN Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 465 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 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE 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 462 VAL Chi-restraints excluded: chain C residue 465 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 C residue 543 LEU 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 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL 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 80 optimal weight: 0.9980 chunk 168 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 38 optimal weight: 0.7980 chunk 198 optimal weight: 40.0000 chunk 10 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 135 optimal weight: 0.5980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 478 ASN ** B 482 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.162465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106347 restraints weight = 23418.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109588 restraints weight = 13647.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111936 restraints weight = 9627.299| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13616 Z= 0.132 Angle : 0.589 8.792 18680 Z= 0.304 Chirality : 0.039 0.285 2196 Planarity : 0.003 0.035 2452 Dihedral : 11.856 163.989 2156 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.44 % Allowed : 34.33 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.20), residues: 1972 helix: 3.37 (0.13), residues: 1432 sheet: -0.06 (0.47), residues: 120 loop : -2.45 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 330 HIS 0.005 0.001 HIS D 437 PHE 0.021 0.001 PHE B 350 TYR 0.017 0.001 TYR A 558 ARG 0.009 0.000 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 1153) hydrogen bonds : angle 3.33131 ( 3411) covalent geometry : bond 0.00294 (13616) covalent geometry : angle 0.58896 (18680) *********************** 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 320 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.356 Fit side-chains REVERT: A 175 TRP cc_start: 0.7301 (m100) cc_final: 0.6879 (m-90) REVERT: A 299 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 351 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8243 (mttp) REVERT: A 356 MET cc_start: 0.8723 (tmm) cc_final: 0.8365 (tmm) REVERT: A 401 ASP cc_start: 0.8259 (p0) cc_final: 0.7981 (p0) REVERT: A 405 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8385 (ttp-110) REVERT: A 429 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 473 MET cc_start: 0.8052 (tpp) cc_final: 0.7409 (ttp) REVERT: D 175 TRP cc_start: 0.7264 (m100) cc_final: 0.6827 (m-90) REVERT: D 356 MET cc_start: 0.8665 (tmm) cc_final: 0.8332 (tmm) REVERT: D 401 ASP cc_start: 0.8231 (p0) cc_final: 0.7966 (p0) REVERT: D 406 GLN cc_start: 0.8742 (mt0) cc_final: 0.8413 (mt0) REVERT: D 429 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7303 (tm-30) REVERT: D 473 MET cc_start: 0.8049 (tpp) cc_final: 0.7405 (ttp) REVERT: D 494 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7508 (mt-10) REVERT: C 175 TRP cc_start: 0.7286 (m100) cc_final: 0.6876 (m-90) REVERT: C 356 MET cc_start: 0.8677 (tmm) cc_final: 0.8304 (tmm) REVERT: C 429 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 460 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6976 (tm-30) REVERT: C 473 MET cc_start: 0.8043 (tpp) cc_final: 0.7392 (ttp) REVERT: C 494 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7628 (mt-10) REVERT: B 175 TRP cc_start: 0.7321 (m100) cc_final: 0.6902 (m-90) REVERT: B 301 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 330 TRP cc_start: 0.7424 (p90) cc_final: 0.7204 (p-90) REVERT: B 351 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: B 356 MET cc_start: 0.8712 (tmm) cc_final: 0.8348 (tmm) REVERT: B 401 ASP cc_start: 0.8304 (p0) cc_final: 0.8033 (p0) REVERT: B 405 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8389 (ttp-110) REVERT: B 429 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 473 MET cc_start: 0.8054 (tpp) cc_final: 0.7420 (ttp) outliers start: 49 outliers final: 40 residues processed: 294 average time/residue: 0.2094 time to fit residues: 93.9962 Evaluate side-chains 312 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 451 ASN Chi-restraints excluded: chain A residue 462 VAL 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 D residue 299 PHE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 462 VAL 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 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE 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 462 VAL Chi-restraints excluded: chain C residue 465 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 C residue 543 LEU Chi-restraints excluded: chain B residue 166 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 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 478 ASN ** C 482 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106918 restraints weight = 23478.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110253 restraints weight = 13623.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112598 restraints weight = 9571.465| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13616 Z= 0.129 Angle : 0.599 10.098 18680 Z= 0.308 Chirality : 0.039 0.313 2196 Planarity : 0.003 0.039 2452 Dihedral : 11.858 164.221 2156 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.22 % Allowed : 34.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.19), residues: 1972 helix: 3.27 (0.13), residues: 1456 sheet: -0.01 (0.47), residues: 120 loop : -2.64 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 330 HIS 0.005 0.001 HIS D 437 PHE 0.017 0.001 PHE B 166 TYR 0.017 0.001 TYR A 558 ARG 0.009 0.000 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 1153) hydrogen bonds : angle 3.32373 ( 3411) covalent geometry : bond 0.00285 (13616) covalent geometry : angle 0.59875 (18680) ********************** 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 320 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 1.844 Fit side-chains REVERT: A 175 TRP cc_start: 0.7232 (m100) cc_final: 0.6833 (m-90) REVERT: A 299 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 351 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8287 (mttp) REVERT: A 356 MET cc_start: 0.8713 (tmm) cc_final: 0.8370 (tmm) REVERT: A 401 ASP cc_start: 0.8199 (p0) cc_final: 0.7924 (p0) REVERT: A 405 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8362 (ttp-110) REVERT: A 429 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 473 MET cc_start: 0.8030 (tpp) cc_final: 0.7452 (ttp) REVERT: D 175 TRP cc_start: 0.7090 (m100) cc_final: 0.6726 (m-90) REVERT: D 356 MET cc_start: 0.8659 (tmm) cc_final: 0.8334 (tmm) REVERT: D 401 ASP cc_start: 0.8174 (p0) cc_final: 0.7889 (p0) REVERT: D 406 GLN cc_start: 0.8646 (mt0) cc_final: 0.8329 (mt0) REVERT: D 429 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 473 MET cc_start: 0.8023 (tpp) cc_final: 0.7454 (ttp) REVERT: D 494 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7497 (mt-10) REVERT: C 175 TRP cc_start: 0.7238 (m100) cc_final: 0.6843 (m-90) REVERT: C 301 LEU cc_start: 0.8465 (mm) cc_final: 0.8253 (mm) REVERT: C 356 MET cc_start: 0.8683 (tmm) cc_final: 0.8316 (tmm) REVERT: C 406 GLN cc_start: 0.8618 (mt0) cc_final: 0.8310 (mt0) REVERT: C 429 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7362 (tm-30) REVERT: C 473 MET cc_start: 0.8010 (tpp) cc_final: 0.7439 (ttp) REVERT: C 494 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7605 (mt-10) REVERT: B 175 TRP cc_start: 0.7282 (m100) cc_final: 0.6886 (m-90) REVERT: B 301 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 351 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8233 (mttp) REVERT: B 356 MET cc_start: 0.8695 (tmm) cc_final: 0.8336 (tmm) REVERT: B 401 ASP cc_start: 0.8229 (p0) cc_final: 0.7968 (p0) REVERT: B 429 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 473 MET cc_start: 0.7966 (tpp) cc_final: 0.7359 (ttp) outliers start: 47 outliers final: 37 residues processed: 298 average time/residue: 0.2295 time to fit residues: 104.6999 Evaluate side-chains 309 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 VAL 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 594 ILE Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 462 VAL 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 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 465 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 C residue 543 LEU 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 426 ASP 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 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 133 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 165 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 478 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.163361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107830 restraints weight = 23440.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111262 restraints weight = 13556.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113599 restraints weight = 9457.074| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13616 Z= 0.123 Angle : 0.602 11.286 18680 Z= 0.308 Chirality : 0.039 0.327 2196 Planarity : 0.003 0.038 2452 Dihedral : 11.863 164.531 2156 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.22 % Allowed : 34.33 % Favored : 60.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.20), residues: 1972 helix: 3.39 (0.13), residues: 1432 sheet: 0.08 (0.47), residues: 120 loop : -2.40 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 330 HIS 0.004 0.001 HIS D 437 PHE 0.017 0.001 PHE B 166 TYR 0.021 0.001 TYR D 411 ARG 0.009 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.02608 ( 1153) hydrogen bonds : angle 3.31222 ( 3411) covalent geometry : bond 0.00269 (13616) covalent geometry : angle 0.60175 (18680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5783.12 seconds wall clock time: 102 minutes 28.44 seconds (6148.44 seconds total)