Starting phenix.real_space_refine on Thu May 15 17:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4y_41040/05_2025/8t4y_41040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4y_41040/05_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_41040/05_2025/8t4y_41040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4y_41040/05_2025/8t4y_41040.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4y_41040/05_2025/8t4y_41040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4y_41040/05_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-5687/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: 7.69, per 1000 atoms: 0.58 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 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: 1.47 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: 4.03 Time building geometry restraints manager: 3.89 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: 0.11 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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 : 1.357 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: 0.2282 time to fit residues: 109.1584 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 : 1.319 ------------------------------------------------------------------------------- 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 = 70)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101549 restraints weight = 24000.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104823 restraints weight = 14168.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107029 restraints weight = 10056.447| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- 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 : 11.870 165.408 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 : 1.394 Fit side-chains REVERT: A 175 TRP cc_start: 0.7128 (m100) cc_final: 0.6785 (m-90) REVERT: A 351 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8231 (mttp) REVERT: A 401 ASP cc_start: 0.8458 (p0) cc_final: 0.8203 (p0) REVERT: A 473 MET cc_start: 0.7754 (tpp) cc_final: 0.7131 (ttm) REVERT: A 530 MET cc_start: 0.6398 (ptm) cc_final: 0.6119 (ptm) REVERT: D 175 TRP cc_start: 0.7100 (m100) cc_final: 0.6774 (m-90) REVERT: D 401 ASP cc_start: 0.8422 (p0) cc_final: 0.8148 (p0) REVERT: D 473 MET cc_start: 0.7751 (tpp) cc_final: 0.7114 (ttm) REVERT: D 530 MET cc_start: 0.6372 (ptm) cc_final: 0.6089 (ptm) REVERT: C 175 TRP cc_start: 0.7202 (m100) cc_final: 0.6792 (m-90) REVERT: C 401 ASP cc_start: 0.8410 (p0) cc_final: 0.8128 (p0) REVERT: C 473 MET cc_start: 0.7740 (tpp) cc_final: 0.7110 (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: 0.8502 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: B 401 ASP cc_start: 0.8419 (p0) cc_final: 0.8122 (p0) REVERT: B 473 MET cc_start: 0.7740 (tpp) cc_final: 0.7118 (ttm) REVERT: B 530 MET cc_start: 0.6414 (ptm) cc_final: 0.6136 (ptm) outliers start: 85 outliers final: 51 residues processed: 339 average time/residue: 0.1910 time to fit residues: 100.3261 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 : 1.481 ------------------------------------------------------------------------------- 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: 0.6980 chunk 159 optimal weight: 50.0000 chunk 120 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 98 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 47 optimal weight: 50.0000 chunk 133 optimal weight: 0.6980 chunk 63 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101074 restraints weight = 23853.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104226 restraints weight = 14316.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106410 restraints weight = 10251.575| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13616 Z= 0.233 Angle : 0.618 6.607 18680 Z= 0.326 Chirality : 0.041 0.177 2196 Planarity : 0.004 0.031 2452 Dihedral : 11.885 164.311 2156 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 9.00 % Allowed : 28.22 % Favored : 62.78 % 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: 2.39 (0.20), residues: 1972 helix: 2.80 (0.13), residues: 1456 sheet: -0.37 (0.53), residues: 112 loop : -2.75 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 330 HIS 0.005 0.002 HIS B 437 PHE 0.013 0.002 PHE A 538 TYR 0.025 0.002 TYR D 411 ARG 0.003 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1153) hydrogen bonds : angle 3.81298 ( 3411) covalent geometry : bond 0.00527 (13616) covalent geometry : angle 0.61796 (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 334 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 253 time to evaluate : 1.367 Fit side-chains REVERT: A 175 TRP cc_start: 0.7129 (m100) cc_final: 0.6774 (m-90) REVERT: A 330 TRP cc_start: 0.7315 (p-90) cc_final: 0.7070 (p90) REVERT: A 351 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8196 (mttp) REVERT: A 401 ASP cc_start: 0.8305 (p0) cc_final: 0.7930 (p0) REVERT: A 473 MET cc_start: 0.7984 (tpp) cc_final: 0.7461 (ttm) REVERT: A 530 MET cc_start: 0.6310 (ptm) cc_final: 0.6066 (ptm) REVERT: D 175 TRP cc_start: 0.7102 (m100) cc_final: 0.6764 (m-90) REVERT: D 401 ASP cc_start: 0.8276 (p0) cc_final: 0.7955 (p0) REVERT: D 427 MET cc_start: 0.8520 (mmm) cc_final: 0.8055 (mmm) REVERT: D 473 MET cc_start: 0.8042 (tpp) cc_final: 0.7494 (ttm) REVERT: C 175 TRP cc_start: 0.7201 (m100) cc_final: 0.6780 (m-90) REVERT: C 401 ASP cc_start: 0.8336 (p0) cc_final: 0.7991 (p0) REVERT: C 473 MET cc_start: 0.8020 (tpp) cc_final: 0.7479 (ttm) REVERT: B 175 TRP cc_start: 0.7161 (m100) cc_final: 0.6783 (m-90) REVERT: B 351 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8285 (mttp) REVERT: B 401 ASP cc_start: 0.8355 (p0) cc_final: 0.7992 (p0) REVERT: B 473 MET cc_start: 0.7976 (tpp) cc_final: 0.7455 (ttm) REVERT: B 530 MET cc_start: 0.6327 (ptm) cc_final: 0.6034 (ptm) outliers start: 81 outliers final: 48 residues processed: 304 average time/residue: 0.2087 time to fit residues: 95.7807 Evaluate side-chains 303 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR 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 594 ILE Chi-restraints excluded: chain D residue 301 LEU 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 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 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: 4.9990 chunk 173 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 109 optimal weight: 40.0000 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102890 restraints weight = 23761.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106121 restraints weight = 13966.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108375 restraints weight = 9926.645| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2515 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= 0.151 Angle : 0.567 6.508 18680 Z= 0.296 Chirality : 0.039 0.163 2196 Planarity : 0.003 0.031 2452 Dihedral : 11.976 165.335 2156 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 8.67 % Allowed : 29.44 % Favored : 61.89 % 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: 2.53 (0.20), residues: 1972 helix: 2.91 (0.13), residues: 1456 sheet: -0.28 (0.52), residues: 112 loop : -2.76 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 330 HIS 0.005 0.001 HIS D 437 PHE 0.017 0.001 PHE C 166 TYR 0.027 0.001 TYR B 411 ARG 0.003 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 1153) hydrogen bonds : angle 3.59877 ( 3411) covalent geometry : bond 0.00335 (13616) covalent geometry : angle 0.56691 (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 339 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 261 time to evaluate : 1.479 Fit side-chains REVERT: A 175 TRP cc_start: 0.7209 (m100) cc_final: 0.6868 (m-90) REVERT: A 351 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (mttp) REVERT: A 401 ASP cc_start: 0.8301 (p0) cc_final: 0.8099 (p0) REVERT: A 405 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8367 (ttp-110) REVERT: A 427 MET cc_start: 0.8424 (mmm) cc_final: 0.8090 (mmm) REVERT: A 473 MET cc_start: 0.7972 (tpp) cc_final: 0.7387 (ttp) REVERT: D 175 TRP cc_start: 0.7273 (m100) cc_final: 0.6939 (m-90) REVERT: D 301 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 401 ASP cc_start: 0.8331 (p0) cc_final: 0.7897 (p0) REVERT: D 429 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 473 MET cc_start: 0.7974 (tpp) cc_final: 0.7379 (ttp) REVERT: C 175 TRP cc_start: 0.7267 (m100) cc_final: 0.6864 (m-90) REVERT: C 356 MET cc_start: 0.8725 (tmm) cc_final: 0.8496 (tmm) REVERT: C 401 ASP cc_start: 0.8342 (p0) cc_final: 0.8129 (p0) REVERT: C 405 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8361 (ttp-110) REVERT: C 429 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 473 MET cc_start: 0.8016 (tpp) cc_final: 0.7364 (ttp) REVERT: B 175 TRP cc_start: 0.7272 (m100) cc_final: 0.6929 (m-90) REVERT: B 301 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 330 TRP cc_start: 0.7435 (p90) cc_final: 0.7201 (p-90) REVERT: B 351 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: B 356 MET cc_start: 0.8773 (tmm) cc_final: 0.8535 (tmm) REVERT: B 401 ASP cc_start: 0.8337 (p0) cc_final: 0.8121 (p0) REVERT: B 405 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8389 (ttp-110) REVERT: B 427 MET cc_start: 0.8433 (mmm) cc_final: 0.8114 (mmm) REVERT: B 473 MET cc_start: 0.8009 (tpp) cc_final: 0.7363 (ttp) REVERT: B 530 MET cc_start: 0.6259 (ptm) cc_final: 0.6038 (ptm) outliers start: 78 outliers final: 51 residues processed: 309 average time/residue: 0.2071 time to fit residues: 96.9105 Evaluate side-chains 304 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 461 ILE 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 572 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 301 LEU 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 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 572 VAL 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 377 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 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 572 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 394 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 168 optimal weight: 20.0000 chunk 148 optimal weight: 40.0000 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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 416 GLN ** 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 = 0.4147 r_free = 0.4147 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104261 restraints weight = 23615.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107543 restraints weight = 13899.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109640 restraints weight = 9853.124| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2618 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= 0.143 Angle : 0.567 6.409 18680 Z= 0.295 Chirality : 0.039 0.158 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.853 162.974 2156 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 8.67 % Allowed : 29.78 % 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: 2.70 (0.20), residues: 1972 helix: 3.05 (0.13), residues: 1456 sheet: -0.01 (0.52), residues: 112 loop : -2.79 (0.26), residues: 404 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 0.021 0.002 PHE C 166 TYR 0.024 0.001 TYR D 411 ARG 0.006 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 1153) hydrogen bonds : angle 3.48523 ( 3411) covalent geometry : bond 0.00317 (13616) covalent geometry : angle 0.56740 (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 344 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 266 time to evaluate : 1.365 Fit side-chains REVERT: A 175 TRP cc_start: 0.7228 (m100) cc_final: 0.6911 (m-90) REVERT: A 299 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7726 (t80) REVERT: A 351 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8176 (mttp) REVERT: A 356 MET cc_start: 0.8719 (tmm) cc_final: 0.8453 (tmm) REVERT: A 401 ASP cc_start: 0.8270 (p0) cc_final: 0.8040 (p0) REVERT: A 405 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8307 (ttp-110) REVERT: A 473 MET cc_start: 0.8037 (tpp) cc_final: 0.7466 (ttp) REVERT: D 175 TRP cc_start: 0.7280 (m100) cc_final: 0.6900 (m-90) REVERT: D 301 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (mm) REVERT: D 356 MET cc_start: 0.8686 (tmm) cc_final: 0.8439 (tmm) REVERT: D 401 ASP cc_start: 0.8297 (p0) cc_final: 0.8089 (p0) REVERT: D 429 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 473 MET cc_start: 0.8033 (tpp) cc_final: 0.7455 (ttp) REVERT: C 175 TRP cc_start: 0.7288 (m100) cc_final: 0.6897 (m-90) REVERT: C 356 MET cc_start: 0.8705 (tmm) cc_final: 0.8430 (tmm) REVERT: C 401 ASP cc_start: 0.8311 (p0) cc_final: 0.8071 (p0) REVERT: C 405 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8397 (ttp-110) REVERT: C 429 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 473 MET cc_start: 0.8018 (tpp) cc_final: 0.7441 (ttp) REVERT: B 175 TRP cc_start: 0.7317 (m100) cc_final: 0.6931 (m-90) REVERT: B 299 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7701 (t80) REVERT: B 301 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (mm) REVERT: B 330 TRP cc_start: 0.7445 (p90) cc_final: 0.7221 (p-90) REVERT: B 351 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8168 (mttp) REVERT: B 356 MET cc_start: 0.8750 (tmm) cc_final: 0.8478 (tmm) REVERT: B 401 ASP cc_start: 0.8306 (p0) cc_final: 0.8071 (p0) REVERT: B 405 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8337 (ttp-110) REVERT: B 427 MET cc_start: 0.8323 (mmm) cc_final: 0.7927 (mmm) REVERT: B 473 MET cc_start: 0.8014 (tpp) cc_final: 0.7441 (ttp) outliers start: 78 outliers final: 57 residues processed: 314 average time/residue: 0.1973 time to fit residues: 93.9826 Evaluate side-chains 325 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 HIS 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 462 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 572 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 301 LEU 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 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 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 572 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 166 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 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 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 C residue 543 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU 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 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: 2.9990 chunk 1 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 416 GLN ** 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 = 0.4142 r_free = 0.4142 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103623 restraints weight = 23919.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106853 restraints weight = 14029.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109105 restraints weight = 9955.476| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13616 Z= 0.156 Angle : 0.573 6.366 18680 Z= 0.299 Chirality : 0.039 0.151 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.841 163.181 2156 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 9.11 % Allowed : 29.33 % 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: 2.79 (0.20), residues: 1972 helix: 3.11 (0.13), residues: 1456 sheet: -0.05 (0.52), residues: 112 loop : -2.74 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 330 HIS 0.005 0.001 HIS A 437 PHE 0.021 0.002 PHE C 166 TYR 0.023 0.001 TYR B 411 ARG 0.006 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 1153) hydrogen bonds : angle 3.46495 ( 3411) covalent geometry : bond 0.00350 (13616) covalent geometry : angle 0.57266 (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 360 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 278 time to evaluate : 1.382 Fit side-chains REVERT: A 175 TRP cc_start: 0.7326 (m100) cc_final: 0.6969 (m-90) REVERT: A 351 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: A 356 MET cc_start: 0.8736 (tmm) cc_final: 0.8430 (tmm) REVERT: A 401 ASP cc_start: 0.8314 (p0) cc_final: 0.8113 (p0) REVERT: A 429 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 460 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 473 MET cc_start: 0.8067 (tpp) cc_final: 0.7531 (ttp) REVERT: D 175 TRP cc_start: 0.7334 (m100) cc_final: 0.6899 (m-90) REVERT: D 301 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (mm) REVERT: D 356 MET cc_start: 0.8682 (tmm) cc_final: 0.8399 (tmm) REVERT: D 429 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7427 (tm-30) REVERT: D 460 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6924 (tm-30) REVERT: D 473 MET cc_start: 0.8062 (tpp) cc_final: 0.7507 (ttp) REVERT: C 175 TRP cc_start: 0.7288 (m100) cc_final: 0.6861 (m-90) REVERT: C 356 MET cc_start: 0.8709 (tmm) cc_final: 0.8387 (tmm) REVERT: C 401 ASP cc_start: 0.8340 (p0) cc_final: 0.8135 (p0) REVERT: C 429 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 473 MET cc_start: 0.8046 (tpp) cc_final: 0.7499 (ttp) REVERT: B 175 TRP cc_start: 0.7349 (m100) cc_final: 0.6949 (m-90) REVERT: B 301 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 351 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: B 356 MET cc_start: 0.8744 (tmm) cc_final: 0.8428 (tmm) REVERT: B 401 ASP cc_start: 0.8321 (p0) cc_final: 0.8077 (p0) REVERT: B 405 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8397 (ttp-110) REVERT: B 429 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7496 (tm-30) REVERT: B 473 MET cc_start: 0.8064 (tpp) cc_final: 0.7527 (ttp) REVERT: B 487 MET cc_start: 0.8136 (ttm) cc_final: 0.7812 (ttm) outliers start: 82 outliers final: 68 residues processed: 334 average time/residue: 0.2024 time to fit residues: 103.4097 Evaluate side-chains 335 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 421 HIS 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 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 A residue 543 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 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 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 D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL 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 394 THR 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 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 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE 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 408 GLN 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 457 LEU Chi-restraints excluded: chain B residue 461 ILE 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 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.159897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103334 restraints weight = 23607.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106616 restraints weight = 13889.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108708 restraints weight = 9813.468| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13616 Z= 0.172 Angle : 0.596 8.229 18680 Z= 0.311 Chirality : 0.039 0.147 2196 Planarity : 0.003 0.034 2452 Dihedral : 11.872 163.322 2156 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 10.11 % Allowed : 30.11 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.81 (0.19), residues: 1972 helix: 3.12 (0.13), residues: 1456 sheet: -0.03 (0.51), residues: 112 loop : -2.72 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 330 HIS 0.007 0.001 HIS D 421 PHE 0.017 0.002 PHE D 166 TYR 0.023 0.001 TYR D 411 ARG 0.008 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 1153) hydrogen bonds : angle 3.46485 ( 3411) covalent geometry : bond 0.00388 (13616) covalent geometry : angle 0.59553 (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 358 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 267 time to evaluate : 1.585 Fit side-chains REVERT: A 175 TRP cc_start: 0.7329 (m100) cc_final: 0.6936 (m-90) REVERT: A 299 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 351 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8245 (mttp) REVERT: A 356 MET cc_start: 0.8749 (tmm) cc_final: 0.8421 (tmm) REVERT: A 401 ASP cc_start: 0.8317 (p0) cc_final: 0.8097 (p0) REVERT: A 429 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 473 MET cc_start: 0.8090 (tpp) cc_final: 0.7584 (ttp) REVERT: D 175 TRP cc_start: 0.7281 (m100) cc_final: 0.6849 (m-90) REVERT: D 301 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (mm) REVERT: D 356 MET cc_start: 0.8679 (tmm) cc_final: 0.8369 (tmm) REVERT: D 401 ASP cc_start: 0.8260 (p0) cc_final: 0.7973 (p0) REVERT: D 429 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7402 (tm-30) REVERT: D 473 MET cc_start: 0.8065 (tpp) cc_final: 0.7565 (ttp) REVERT: C 175 TRP cc_start: 0.7304 (m100) cc_final: 0.6882 (m-90) REVERT: C 356 MET cc_start: 0.8703 (tmm) cc_final: 0.8357 (tmm) REVERT: C 401 ASP cc_start: 0.8339 (p0) cc_final: 0.8133 (p0) REVERT: C 429 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 473 MET cc_start: 0.8055 (tpp) cc_final: 0.7557 (ttp) REVERT: B 175 TRP cc_start: 0.7348 (m100) cc_final: 0.6950 (m-90) REVERT: B 301 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 351 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: B 356 MET cc_start: 0.8747 (tmm) cc_final: 0.8402 (tmm) REVERT: B 401 ASP cc_start: 0.8350 (p0) cc_final: 0.8096 (p0) REVERT: B 405 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8405 (ttp-110) REVERT: B 429 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 473 MET cc_start: 0.8088 (tpp) cc_final: 0.7584 (ttp) outliers start: 91 outliers final: 70 residues processed: 323 average time/residue: 0.2024 time to fit residues: 99.5429 Evaluate side-chains 337 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 262 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 HIS 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 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 544 LEU Chi-restraints excluded: chain A residue 572 VAL 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 301 LEU 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 462 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE 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 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 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 544 LEU Chi-restraints excluded: chain C residue 572 VAL 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 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 418 MET 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 457 LEU 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 544 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.159582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102750 restraints weight = 23732.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106045 restraints weight = 13880.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108131 restraints weight = 9783.124| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13616 Z= 0.181 Angle : 0.606 7.041 18680 Z= 0.319 Chirality : 0.039 0.142 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.845 162.844 2156 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 10.78 % Allowed : 29.56 % Favored : 59.67 % 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: 2.79 (0.19), residues: 1972 helix: 3.11 (0.13), residues: 1456 sheet: -0.02 (0.51), residues: 112 loop : -2.71 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 330 HIS 0.005 0.001 HIS D 421 PHE 0.017 0.002 PHE D 166 TYR 0.022 0.001 TYR D 411 ARG 0.007 0.001 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 1153) hydrogen bonds : angle 3.47982 ( 3411) covalent geometry : bond 0.00410 (13616) covalent geometry : angle 0.60616 (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 366 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 269 time to evaluate : 1.383 Fit side-chains REVERT: A 175 TRP cc_start: 0.7335 (m100) cc_final: 0.6939 (m-90) REVERT: A 351 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8266 (mttp) REVERT: A 356 MET cc_start: 0.8770 (tmm) cc_final: 0.8430 (tmm) REVERT: A 401 ASP cc_start: 0.8342 (p0) cc_final: 0.8137 (p0) REVERT: A 429 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 473 MET cc_start: 0.8065 (tpp) cc_final: 0.7607 (ttp) REVERT: D 175 TRP cc_start: 0.7172 (m100) cc_final: 0.6756 (m-90) REVERT: D 299 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7669 (t80) REVERT: D 301 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8121 (mm) REVERT: D 356 MET cc_start: 0.8683 (tmm) cc_final: 0.8358 (tmm) REVERT: D 401 ASP cc_start: 0.8298 (p0) cc_final: 0.7922 (p0) REVERT: D 429 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 473 MET cc_start: 0.8048 (tpp) cc_final: 0.7585 (ttp) REVERT: C 175 TRP cc_start: 0.7331 (m100) cc_final: 0.6887 (m-90) REVERT: C 356 MET cc_start: 0.8705 (tmm) cc_final: 0.8332 (tmm) REVERT: C 429 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 473 MET cc_start: 0.8019 (tpp) cc_final: 0.7554 (ttp) REVERT: B 175 TRP cc_start: 0.7367 (m100) cc_final: 0.6930 (m-90) REVERT: B 301 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 351 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: B 356 MET cc_start: 0.8722 (tmm) cc_final: 0.8360 (tmm) REVERT: B 401 ASP cc_start: 0.8377 (p0) cc_final: 0.8116 (p0) REVERT: B 405 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8406 (ttp-110) REVERT: B 429 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 473 MET cc_start: 0.8053 (tpp) cc_final: 0.7588 (ttp) outliers start: 97 outliers final: 76 residues processed: 332 average time/residue: 0.2045 time to fit residues: 103.8238 Evaluate side-chains 346 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 265 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 421 HIS 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 462 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 VAL 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 301 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE 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 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 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 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET 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 457 LEU Chi-restraints excluded: chain B residue 461 ILE 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 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 Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 0.1980 chunk 198 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 149 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.158961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102110 restraints weight = 23264.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105300 restraints weight = 13716.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107552 restraints weight = 9699.813| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13616 Z= 0.203 Angle : 0.628 7.509 18680 Z= 0.332 Chirality : 0.040 0.138 2196 Planarity : 0.004 0.036 2452 Dihedral : 11.863 163.048 2156 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 10.22 % Allowed : 31.22 % Favored : 58.56 % 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: 2.73 (0.19), residues: 1972 helix: 3.04 (0.13), residues: 1456 sheet: 0.02 (0.51), residues: 112 loop : -2.68 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 330 HIS 0.005 0.001 HIS D 421 PHE 0.016 0.002 PHE D 166 TYR 0.022 0.001 TYR D 411 ARG 0.008 0.001 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1153) hydrogen bonds : angle 3.53511 ( 3411) covalent geometry : bond 0.00460 (13616) covalent geometry : angle 0.62825 (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 356 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 264 time to evaluate : 1.495 Fit side-chains REVERT: A 175 TRP cc_start: 0.7304 (m100) cc_final: 0.6886 (m-90) REVERT: A 299 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 351 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8289 (mttp) REVERT: A 356 MET cc_start: 0.8761 (tmm) cc_final: 0.8414 (tmm) REVERT: A 429 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 473 MET cc_start: 0.8063 (tpp) cc_final: 0.7635 (ttp) REVERT: D 175 TRP cc_start: 0.7146 (m100) cc_final: 0.6736 (m-90) REVERT: D 299 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7702 (t80) REVERT: D 301 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8157 (mm) REVERT: D 356 MET cc_start: 0.8690 (tmm) cc_final: 0.8358 (tmm) REVERT: D 401 ASP cc_start: 0.8306 (p0) cc_final: 0.7953 (p0) REVERT: D 406 GLN cc_start: 0.8771 (mt0) cc_final: 0.8432 (mt0) REVERT: D 429 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 473 MET cc_start: 0.8032 (tpp) cc_final: 0.7606 (ttp) REVERT: C 175 TRP cc_start: 0.7295 (m100) cc_final: 0.6872 (m-90) REVERT: C 299 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 356 MET cc_start: 0.8733 (tmm) cc_final: 0.8347 (tmm) REVERT: C 401 ASP cc_start: 0.8221 (p0) cc_final: 0.7915 (p0) REVERT: C 429 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 473 MET cc_start: 0.7999 (tpp) cc_final: 0.7550 (ttp) REVERT: B 175 TRP cc_start: 0.7319 (m100) cc_final: 0.6905 (m-90) REVERT: B 299 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 301 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8178 (mm) REVERT: B 330 TRP cc_start: 0.7671 (p-90) cc_final: 0.7305 (p90) REVERT: B 351 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 356 MET cc_start: 0.8738 (tmm) cc_final: 0.8373 (tmm) REVERT: B 401 ASP cc_start: 0.8395 (p0) cc_final: 0.8188 (p0) REVERT: B 429 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 473 MET cc_start: 0.8035 (tpp) cc_final: 0.7607 (ttp) outliers start: 92 outliers final: 73 residues processed: 321 average time/residue: 0.2062 time to fit residues: 101.3460 Evaluate side-chains 342 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 261 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 MET 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 457 LEU Chi-restraints excluded: chain A residue 461 ILE 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 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 VAL 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 301 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE 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 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 GLN 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 462 VAL Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET 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 457 LEU 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 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 Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 5.9990 chunk 37 optimal weight: 0.0060 chunk 120 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 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 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.160803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104033 restraints weight = 23614.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107338 restraints weight = 13781.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109616 restraints weight = 9728.105| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2966 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= 0.141 Angle : 0.606 7.062 18680 Z= 0.317 Chirality : 0.039 0.142 2196 Planarity : 0.003 0.045 2452 Dihedral : 11.920 163.364 2156 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 8.67 % Allowed : 32.67 % Favored : 58.67 % 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: 2.80 (0.19), residues: 1972 helix: 3.09 (0.13), residues: 1456 sheet: 0.05 (0.51), residues: 112 loop : -2.64 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 330 HIS 0.004 0.001 HIS C 437 PHE 0.023 0.001 PHE B 350 TYR 0.021 0.001 TYR D 411 ARG 0.009 0.001 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 1153) hydrogen bonds : angle 3.45696 ( 3411) covalent geometry : bond 0.00314 (13616) covalent geometry : angle 0.60640 (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 344 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 266 time to evaluate : 1.612 Fit side-chains REVERT: A 175 TRP cc_start: 0.7305 (m100) cc_final: 0.6873 (m-90) REVERT: A 351 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (mttp) REVERT: A 356 MET cc_start: 0.8733 (tmm) cc_final: 0.8402 (tmm) REVERT: A 406 GLN cc_start: 0.8689 (mt0) cc_final: 0.8479 (mt0) REVERT: A 429 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 473 MET cc_start: 0.8054 (tpp) cc_final: 0.7574 (ttp) REVERT: D 175 TRP cc_start: 0.7146 (m100) cc_final: 0.6733 (m-90) REVERT: D 299 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7667 (t80) REVERT: D 301 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (mm) REVERT: D 356 MET cc_start: 0.8668 (tmm) cc_final: 0.8348 (tmm) REVERT: D 401 ASP cc_start: 0.8284 (p0) cc_final: 0.7923 (p0) REVERT: D 406 GLN cc_start: 0.8750 (mt0) cc_final: 0.8405 (mt0) REVERT: D 429 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7430 (tm-30) REVERT: D 473 MET cc_start: 0.8042 (tpp) cc_final: 0.7560 (ttp) REVERT: C 175 TRP cc_start: 0.7299 (m100) cc_final: 0.6872 (m-90) REVERT: C 299 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 356 MET cc_start: 0.8678 (tmm) cc_final: 0.8313 (tmm) REVERT: C 401 ASP cc_start: 0.8181 (p0) cc_final: 0.7869 (p0) REVERT: C 406 GLN cc_start: 0.8714 (mt0) cc_final: 0.8488 (mt0) REVERT: C 429 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 473 MET cc_start: 0.8026 (tpp) cc_final: 0.7537 (ttp) REVERT: C 544 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 175 TRP cc_start: 0.7321 (m100) cc_final: 0.6904 (m-90) REVERT: B 299 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7688 (t80) REVERT: B 301 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 351 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (mttp) REVERT: B 356 MET cc_start: 0.8712 (tmm) cc_final: 0.8364 (tmm) REVERT: B 401 ASP cc_start: 0.8342 (p0) cc_final: 0.8136 (p0) REVERT: B 429 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 473 MET cc_start: 0.8060 (tpp) cc_final: 0.7577 (ttp) outliers start: 78 outliers final: 65 residues processed: 312 average time/residue: 0.2238 time to fit residues: 107.9641 Evaluate side-chains 334 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 261 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 457 LEU 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 572 VAL 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 301 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE 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 372 LEU 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 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 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 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 457 LEU Chi-restraints excluded: chain B residue 461 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 138 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 133 optimal weight: 0.0670 chunk 123 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.5730 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.162206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106012 restraints weight = 23602.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109372 restraints weight = 13715.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111659 restraints weight = 9625.021| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13616 Z= 0.126 Angle : 0.601 7.692 18680 Z= 0.312 Chirality : 0.038 0.145 2196 Planarity : 0.003 0.039 2452 Dihedral : 11.923 165.265 2156 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.22 % Allowed : 34.67 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.19), residues: 1972 helix: 3.13 (0.13), residues: 1456 sheet: 0.05 (0.48), residues: 120 loop : -2.62 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 330 HIS 0.004 0.001 HIS C 437 PHE 0.017 0.001 PHE D 166 TYR 0.019 0.001 TYR B 558 ARG 0.009 0.001 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 1153) hydrogen bonds : angle 3.39325 ( 3411) covalent geometry : bond 0.00276 (13616) covalent geometry : angle 0.60080 (18680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4811.28 seconds wall clock time: 84 minutes 10.73 seconds (5050.73 seconds total)