Starting phenix.real_space_refine on Sun Jul 21 05:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_41040.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_41040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_41040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_41040.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4y_41040/07_2024/8t4y_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 Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.39, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 6.22 Conformation dependent library (CDL) restraints added in 3.2 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: 1.53 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: 4.45 Time building geometry restraints manager: 6.65 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: 99.31 - 106.69: 356 106.69 - 114.06: 7609 114.06 - 121.44: 7542 121.44 - 128.82: 3057 128.82 - 136.19: 116 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 2.440 nonbonded pdb=" O LYS D 468 " pdb=" OG1 THR D 472 " model vdw 2.242 2.440 nonbonded pdb=" O LYS C 468 " pdb=" OG1 THR C 472 " model vdw 2.242 2.440 nonbonded pdb=" O LYS B 468 " pdb=" OG1 THR B 472 " model vdw 2.243 2.440 nonbonded pdb=" O LEU C 450 " pdb=" NH1 ARG C 458 " model vdw 2.247 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.120 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- 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= 0.183 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.565 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: 0.2437 time to fit residues: 116.2056 Evaluate side-chains 282 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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: 8.9990 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** D 392 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN C 392 HIS ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN B 392 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13616 Z= 0.390 Angle : 0.637 6.687 18680 Z= 0.333 Chirality : 0.041 0.193 2196 Planarity : 0.004 0.033 2452 Dihedral : 11.936 166.030 2156 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 8.44 % Allowed : 27.67 % Favored : 63.89 % 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: 2.28 (0.20), residues: 1972 helix: 2.71 (0.14), residues: 1440 sheet: -0.30 (0.52), residues: 112 loop : -2.56 (0.26), residues: 420 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 0.017 0.002 PHE C 538 TYR 0.016 0.002 TYR A 439 ARG 0.005 0.001 ARG D 405 *********************** 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 356 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 280 time to evaluate : 1.475 Fit side-chains REVERT: A 175 TRP cc_start: 0.7263 (m100) cc_final: 0.6822 (m-90) REVERT: A 341 TRP cc_start: 0.7599 (p-90) cc_final: 0.7283 (t60) REVERT: A 351 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7646 (mttp) REVERT: A 401 ASP cc_start: 0.8432 (p0) cc_final: 0.8220 (p0) REVERT: A 473 MET cc_start: 0.7914 (tpp) cc_final: 0.7226 (ttm) REVERT: A 480 ASP cc_start: 0.8102 (t0) cc_final: 0.7773 (t0) REVERT: A 512 MET cc_start: 0.8693 (ttm) cc_final: 0.8460 (ttm) REVERT: D 175 TRP cc_start: 0.7264 (m100) cc_final: 0.6832 (m-90) REVERT: D 341 TRP cc_start: 0.7565 (p-90) cc_final: 0.7176 (t60) REVERT: D 401 ASP cc_start: 0.8421 (p0) cc_final: 0.8191 (p0) REVERT: D 473 MET cc_start: 0.7917 (tpp) cc_final: 0.7192 (ttm) REVERT: D 480 ASP cc_start: 0.8110 (t0) cc_final: 0.7781 (t0) REVERT: D 512 MET cc_start: 0.8686 (ttm) cc_final: 0.8456 (ttm) REVERT: C 175 TRP cc_start: 0.7362 (m100) cc_final: 0.6861 (m-90) REVERT: C 341 TRP cc_start: 0.7572 (p-90) cc_final: 0.7211 (t60) REVERT: C 401 ASP cc_start: 0.8448 (p0) cc_final: 0.8222 (p0) REVERT: C 473 MET cc_start: 0.7899 (tpp) cc_final: 0.7211 (ttm) REVERT: C 480 ASP cc_start: 0.8115 (t0) cc_final: 0.7753 (t0) REVERT: C 512 MET cc_start: 0.8695 (ttm) cc_final: 0.8461 (ttm) REVERT: B 175 TRP cc_start: 0.7252 (m100) cc_final: 0.6810 (m-90) REVERT: B 341 TRP cc_start: 0.7606 (p-90) cc_final: 0.7250 (t60) REVERT: B 351 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7634 (mttp) REVERT: B 401 ASP cc_start: 0.8444 (p0) cc_final: 0.8207 (p0) REVERT: B 473 MET cc_start: 0.7907 (tpp) cc_final: 0.7239 (ttm) REVERT: B 480 ASP cc_start: 0.8108 (t0) cc_final: 0.7749 (t0) REVERT: B 512 MET cc_start: 0.8698 (ttm) cc_final: 0.8463 (ttm) outliers start: 76 outliers final: 43 residues processed: 329 average time/residue: 0.1968 time to fit residues: 99.3278 Evaluate side-chains 302 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 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 543 LEU 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 418 MET 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 543 LEU 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 543 LEU 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 543 LEU 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 100 optimal weight: 50.0000 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 50.0000 chunk 181 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13616 Z= 0.473 Angle : 0.664 6.682 18680 Z= 0.354 Chirality : 0.041 0.168 2196 Planarity : 0.004 0.031 2452 Dihedral : 11.869 163.435 2156 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 10.89 % Allowed : 27.44 % Favored : 61.67 % 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: 2.13 (0.20), residues: 1972 helix: 2.65 (0.14), residues: 1440 sheet: 0.12 (0.59), residues: 88 loop : -2.77 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 330 HIS 0.007 0.002 HIS A 437 PHE 0.016 0.002 PHE B 483 TYR 0.028 0.002 TYR D 411 ARG 0.003 0.001 ARG D 554 *********************** 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 347 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 249 time to evaluate : 1.529 Fit side-chains REVERT: A 175 TRP cc_start: 0.7272 (m100) cc_final: 0.6803 (m-90) REVERT: A 351 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7667 (mttp) REVERT: A 401 ASP cc_start: 0.8371 (p0) cc_final: 0.8080 (p0) REVERT: A 473 MET cc_start: 0.8073 (tpp) cc_final: 0.7736 (ttp) REVERT: A 480 ASP cc_start: 0.8112 (t0) cc_final: 0.7800 (t0) REVERT: A 512 MET cc_start: 0.8804 (ttm) cc_final: 0.8585 (ttm) REVERT: D 175 TRP cc_start: 0.7286 (m100) cc_final: 0.6801 (m-90) REVERT: D 301 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8130 (mm) REVERT: D 401 ASP cc_start: 0.8353 (p0) cc_final: 0.8079 (p0) REVERT: D 473 MET cc_start: 0.8071 (tpp) cc_final: 0.7726 (ttm) REVERT: D 480 ASP cc_start: 0.8115 (t0) cc_final: 0.7805 (t0) REVERT: D 512 MET cc_start: 0.8798 (ttm) cc_final: 0.8577 (ttm) REVERT: C 175 TRP cc_start: 0.7391 (m100) cc_final: 0.6891 (m-90) REVERT: C 401 ASP cc_start: 0.8412 (p0) cc_final: 0.8143 (p0) REVERT: C 473 MET cc_start: 0.8060 (tpp) cc_final: 0.7726 (ttm) REVERT: C 480 ASP cc_start: 0.8118 (t0) cc_final: 0.7804 (t0) REVERT: C 512 MET cc_start: 0.8817 (ttm) cc_final: 0.8603 (ttm) REVERT: B 175 TRP cc_start: 0.7277 (m100) cc_final: 0.6776 (m-90) REVERT: B 301 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8143 (mm) REVERT: B 330 TRP cc_start: 0.7166 (p-90) cc_final: 0.6792 (p-90) REVERT: B 351 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7647 (mttp) REVERT: B 401 ASP cc_start: 0.8420 (p0) cc_final: 0.8128 (p0) REVERT: B 473 MET cc_start: 0.8055 (tpp) cc_final: 0.7728 (ttm) REVERT: B 480 ASP cc_start: 0.8116 (t0) cc_final: 0.7802 (t0) REVERT: B 512 MET cc_start: 0.8820 (ttm) cc_final: 0.8605 (ttm) outliers start: 98 outliers final: 65 residues processed: 309 average time/residue: 0.2108 time to fit residues: 98.2648 Evaluate side-chains 311 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 242 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 381 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 433 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 545 THR Chi-restraints excluded: chain A residue 572 VAL 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 408 GLN Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 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 D residue 594 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 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 433 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 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 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 179 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** 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** B 497 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2516 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= 0.192 Angle : 0.552 6.367 18680 Z= 0.286 Chirality : 0.039 0.163 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.983 164.400 2156 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 7.00 % Allowed : 32.67 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.20), residues: 1972 helix: 2.88 (0.13), residues: 1440 sheet: -0.07 (0.52), residues: 112 loop : -2.77 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 330 HIS 0.004 0.001 HIS C 437 PHE 0.020 0.001 PHE D 166 TYR 0.021 0.001 TYR B 558 ARG 0.003 0.000 ARG A 560 *********************** 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 327 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 1.523 Fit side-chains REVERT: A 175 TRP cc_start: 0.7305 (m100) cc_final: 0.6893 (m-90) REVERT: A 351 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7601 (mttp) REVERT: A 356 MET cc_start: 0.8238 (tmm) cc_final: 0.7968 (tmm) REVERT: A 401 ASP cc_start: 0.8365 (p0) cc_final: 0.8070 (p0) REVERT: A 405 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8191 (ttp-110) REVERT: A 427 MET cc_start: 0.8296 (mmm) cc_final: 0.7974 (mmm) REVERT: A 473 MET cc_start: 0.8134 (tpp) cc_final: 0.7458 (ttm) REVERT: A 480 ASP cc_start: 0.7895 (t0) cc_final: 0.7594 (t0) REVERT: A 512 MET cc_start: 0.8769 (ttm) cc_final: 0.8509 (ttm) REVERT: D 175 TRP cc_start: 0.7384 (m100) cc_final: 0.6965 (m-90) REVERT: D 301 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8102 (mm) REVERT: D 401 ASP cc_start: 0.8361 (p0) cc_final: 0.8052 (p0) REVERT: D 405 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8186 (ttp-110) REVERT: D 429 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7351 (tm-30) REVERT: D 473 MET cc_start: 0.8130 (tpp) cc_final: 0.7446 (ttm) REVERT: D 480 ASP cc_start: 0.7898 (t0) cc_final: 0.7593 (t0) REVERT: D 512 MET cc_start: 0.8765 (ttm) cc_final: 0.8494 (ttm) REVERT: D 529 GLU cc_start: 0.7804 (pp20) cc_final: 0.7491 (pp20) REVERT: C 175 TRP cc_start: 0.7445 (m100) cc_final: 0.6965 (m-90) REVERT: C 401 ASP cc_start: 0.8401 (p0) cc_final: 0.8091 (p0) REVERT: C 405 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8166 (ttp-110) REVERT: C 429 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7355 (tm-30) REVERT: C 473 MET cc_start: 0.8236 (tpp) cc_final: 0.7467 (ttm) REVERT: C 480 ASP cc_start: 0.7897 (t0) cc_final: 0.7596 (t0) REVERT: C 512 MET cc_start: 0.8764 (ttm) cc_final: 0.8500 (ttm) REVERT: B 175 TRP cc_start: 0.7403 (m100) cc_final: 0.6976 (m-90) REVERT: B 301 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 330 TRP cc_start: 0.7089 (p-90) cc_final: 0.6633 (p-90) REVERT: B 351 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7491 (mttp) REVERT: B 356 MET cc_start: 0.8268 (tmm) cc_final: 0.8052 (tmm) REVERT: B 401 ASP cc_start: 0.8419 (p0) cc_final: 0.8150 (p0) REVERT: B 405 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8162 (ttp-110) REVERT: B 427 MET cc_start: 0.8297 (mmm) cc_final: 0.7776 (mmm) REVERT: B 473 MET cc_start: 0.8231 (tpp) cc_final: 0.7460 (ttm) REVERT: B 480 ASP cc_start: 0.7932 (t0) cc_final: 0.7611 (t0) REVERT: B 512 MET cc_start: 0.8726 (ttm) cc_final: 0.8484 (ttm) outliers start: 63 outliers final: 34 residues processed: 299 average time/residue: 0.2299 time to fit residues: 104.4947 Evaluate side-chains 302 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 517 HIS 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 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 461 ILE Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 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 461 ILE Chi-restraints excluded: chain B residue 517 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 2 optimal weight: 0.0050 chunk 143 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 173 optimal weight: 0.9990 chunk 48 optimal weight: 50.0000 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13616 Z= 0.244 Angle : 0.562 6.438 18680 Z= 0.293 Chirality : 0.039 0.157 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.834 162.300 2156 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 9.56 % Allowed : 31.33 % 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: 2.53 (0.20), residues: 1972 helix: 2.97 (0.13), residues: 1440 sheet: -0.15 (0.50), residues: 112 loop : -2.81 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 330 HIS 0.005 0.001 HIS A 437 PHE 0.021 0.002 PHE D 166 TYR 0.025 0.001 TYR A 411 ARG 0.003 0.000 ARG D 560 *********************** 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 354 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 268 time to evaluate : 1.623 Fit side-chains REVERT: A 175 TRP cc_start: 0.7335 (m100) cc_final: 0.6915 (m-90) REVERT: A 351 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7696 (mttp) REVERT: A 356 MET cc_start: 0.8225 (tmm) cc_final: 0.7909 (tmm) REVERT: A 401 ASP cc_start: 0.8408 (p0) cc_final: 0.8096 (p0) REVERT: A 405 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8227 (ttp-110) REVERT: A 429 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 473 MET cc_start: 0.8183 (tpp) cc_final: 0.7543 (ttm) REVERT: A 480 ASP cc_start: 0.7965 (t0) cc_final: 0.7677 (t0) REVERT: A 487 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7865 (ttm) REVERT: A 512 MET cc_start: 0.8835 (ttm) cc_final: 0.8531 (ttm) REVERT: A 529 GLU cc_start: 0.7708 (pp20) cc_final: 0.7354 (pp20) REVERT: D 175 TRP cc_start: 0.7392 (m100) cc_final: 0.6932 (m-90) REVERT: D 301 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7957 (mm) REVERT: D 356 MET cc_start: 0.8185 (tmm) cc_final: 0.7908 (tmm) REVERT: D 401 ASP cc_start: 0.8396 (p0) cc_final: 0.7981 (p0) REVERT: D 405 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8405 (ttp-110) REVERT: D 429 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 473 MET cc_start: 0.8184 (tpp) cc_final: 0.7537 (ttm) REVERT: D 480 ASP cc_start: 0.7966 (t0) cc_final: 0.7676 (t0) REVERT: D 512 MET cc_start: 0.8831 (ttm) cc_final: 0.8529 (ttm) REVERT: D 529 GLU cc_start: 0.7739 (pp20) cc_final: 0.7363 (pp20) REVERT: C 175 TRP cc_start: 0.7450 (m100) cc_final: 0.6973 (m-90) REVERT: C 356 MET cc_start: 0.8187 (tmm) cc_final: 0.7917 (tmm) REVERT: C 401 ASP cc_start: 0.8427 (p0) cc_final: 0.8120 (p0) REVERT: C 405 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8215 (ttp-110) REVERT: C 429 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 473 MET cc_start: 0.8269 (tpp) cc_final: 0.7535 (ttm) REVERT: C 480 ASP cc_start: 0.7940 (t0) cc_final: 0.7651 (t0) REVERT: C 487 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7874 (ttm) REVERT: C 512 MET cc_start: 0.8834 (ttm) cc_final: 0.8528 (ttm) REVERT: B 175 TRP cc_start: 0.7421 (m100) cc_final: 0.6995 (m-90) REVERT: B 301 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 356 MET cc_start: 0.8267 (tmm) cc_final: 0.7998 (tmm) REVERT: B 401 ASP cc_start: 0.8426 (p0) cc_final: 0.8205 (p0) REVERT: B 405 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8437 (ttp-110) REVERT: B 429 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 473 MET cc_start: 0.8267 (tpp) cc_final: 0.7531 (ttm) REVERT: B 480 ASP cc_start: 0.7914 (t0) cc_final: 0.7596 (t0) REVERT: B 512 MET cc_start: 0.8830 (ttm) cc_final: 0.8527 (ttm) REVERT: B 529 GLU cc_start: 0.7712 (pp20) cc_final: 0.7365 (pp20) outliers start: 86 outliers final: 61 residues processed: 321 average time/residue: 0.2161 time to fit residues: 105.6035 Evaluate side-chains 331 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 265 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 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 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 487 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 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 517 HIS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 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 487 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 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 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 495 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 50.0000 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2682 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= 0.179 Angle : 0.545 6.761 18680 Z= 0.280 Chirality : 0.038 0.156 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.905 163.707 2156 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.78 % Allowed : 34.33 % Favored : 58.89 % 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: 2.66 (0.20), residues: 1972 helix: 3.10 (0.13), residues: 1432 sheet: -0.14 (0.50), residues: 112 loop : -2.76 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 330 HIS 0.003 0.001 HIS B 437 PHE 0.021 0.001 PHE D 166 TYR 0.016 0.001 TYR C 411 ARG 0.003 0.000 ARG A 560 *********************** 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 342 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 1.728 Fit side-chains REVERT: A 175 TRP cc_start: 0.7387 (m100) cc_final: 0.6963 (m-90) REVERT: A 351 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7627 (mttp) REVERT: A 356 MET cc_start: 0.8260 (tmm) cc_final: 0.7922 (tmm) REVERT: A 401 ASP cc_start: 0.8334 (p0) cc_final: 0.8013 (p0) REVERT: A 405 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8228 (ttp-110) REVERT: A 429 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 473 MET cc_start: 0.8195 (tpp) cc_final: 0.7490 (ttp) REVERT: A 480 ASP cc_start: 0.7825 (t0) cc_final: 0.7532 (t0) REVERT: A 512 MET cc_start: 0.8709 (ttm) cc_final: 0.8458 (ttm) REVERT: A 529 GLU cc_start: 0.7583 (pp20) cc_final: 0.7175 (pp20) REVERT: D 175 TRP cc_start: 0.7485 (m100) cc_final: 0.7001 (m-90) REVERT: D 301 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7890 (mm) REVERT: D 356 MET cc_start: 0.8185 (tmm) cc_final: 0.7884 (tmm) REVERT: D 401 ASP cc_start: 0.8306 (p0) cc_final: 0.7959 (p0) REVERT: D 405 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8226 (ttp-110) REVERT: D 429 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 473 MET cc_start: 0.8159 (tpp) cc_final: 0.7456 (ttp) REVERT: D 480 ASP cc_start: 0.7849 (t0) cc_final: 0.7574 (t0) REVERT: D 512 MET cc_start: 0.8757 (ttm) cc_final: 0.8388 (ttm) REVERT: D 529 GLU cc_start: 0.7774 (pp20) cc_final: 0.7484 (pp20) REVERT: C 175 TRP cc_start: 0.7415 (m100) cc_final: 0.6901 (m-90) REVERT: C 356 MET cc_start: 0.8193 (tmm) cc_final: 0.7896 (tmm) REVERT: C 401 ASP cc_start: 0.8335 (p0) cc_final: 0.7992 (p0) REVERT: C 405 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8217 (ttp-110) REVERT: C 429 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 473 MET cc_start: 0.8171 (tpp) cc_final: 0.7474 (ttp) REVERT: C 480 ASP cc_start: 0.7824 (t0) cc_final: 0.7535 (t0) REVERT: C 512 MET cc_start: 0.8709 (ttm) cc_final: 0.8461 (ttm) REVERT: C 529 GLU cc_start: 0.7671 (pp20) cc_final: 0.7333 (pp20) REVERT: B 175 TRP cc_start: 0.7460 (m100) cc_final: 0.6979 (m-90) REVERT: B 301 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 356 MET cc_start: 0.8272 (tmm) cc_final: 0.7976 (tmm) REVERT: B 401 ASP cc_start: 0.8355 (p0) cc_final: 0.8134 (p0) REVERT: B 405 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8440 (ttp-110) REVERT: B 429 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7243 (tm-30) REVERT: B 473 MET cc_start: 0.8154 (tpp) cc_final: 0.7438 (ttp) REVERT: B 480 ASP cc_start: 0.7834 (t0) cc_final: 0.7547 (t0) REVERT: B 512 MET cc_start: 0.8778 (ttm) cc_final: 0.8413 (ttm) REVERT: B 529 GLU cc_start: 0.7584 (pp20) cc_final: 0.7179 (pp20) outliers start: 61 outliers final: 43 residues processed: 318 average time/residue: 0.2203 time to fit residues: 105.4038 Evaluate side-chains 312 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 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 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 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 451 ASN 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 C residue 166 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.0370 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 478 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN B 465 ASN B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2754 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= 0.178 Angle : 0.545 7.141 18680 Z= 0.280 Chirality : 0.038 0.154 2196 Planarity : 0.003 0.033 2452 Dihedral : 11.894 163.812 2156 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.89 % Allowed : 37.00 % Favored : 58.11 % 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: 2.77 (0.20), residues: 1972 helix: 3.19 (0.13), residues: 1432 sheet: -0.09 (0.50), residues: 112 loop : -2.77 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 330 HIS 0.006 0.001 HIS D 421 PHE 0.019 0.001 PHE C 166 TYR 0.018 0.001 TYR A 411 ARG 0.002 0.000 ARG A 560 *********************** 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 317 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 1.751 Fit side-chains REVERT: A 175 TRP cc_start: 0.7427 (m100) cc_final: 0.6961 (m-90) REVERT: A 351 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7619 (mttp) REVERT: A 356 MET cc_start: 0.8262 (tmm) cc_final: 0.7900 (tmm) REVERT: A 401 ASP cc_start: 0.8329 (p0) cc_final: 0.8000 (p0) REVERT: A 405 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8227 (ttp-110) REVERT: A 429 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7203 (tm-30) REVERT: A 473 MET cc_start: 0.8163 (tpp) cc_final: 0.7460 (ttp) REVERT: A 480 ASP cc_start: 0.7806 (t0) cc_final: 0.7522 (t0) REVERT: A 529 GLU cc_start: 0.7660 (pp20) cc_final: 0.7254 (pp20) REVERT: D 175 TRP cc_start: 0.7347 (m100) cc_final: 0.6844 (m-90) REVERT: D 301 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (mm) REVERT: D 356 MET cc_start: 0.8174 (tmm) cc_final: 0.7845 (tmm) REVERT: D 401 ASP cc_start: 0.8309 (p0) cc_final: 0.7980 (p0) REVERT: D 405 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8229 (ttp-110) REVERT: D 429 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7157 (tm-30) REVERT: D 473 MET cc_start: 0.8146 (tpp) cc_final: 0.7432 (ttp) REVERT: D 480 ASP cc_start: 0.7822 (t0) cc_final: 0.7554 (t0) REVERT: D 529 GLU cc_start: 0.7720 (pp20) cc_final: 0.7376 (pp20) REVERT: C 175 TRP cc_start: 0.7458 (m100) cc_final: 0.6935 (m-90) REVERT: C 356 MET cc_start: 0.8190 (tmm) cc_final: 0.7869 (tmm) REVERT: C 401 ASP cc_start: 0.8337 (p0) cc_final: 0.8009 (p0) REVERT: C 405 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8219 (ttp-110) REVERT: C 429 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7158 (tm-30) REVERT: C 473 MET cc_start: 0.8157 (tpp) cc_final: 0.7449 (ttp) REVERT: C 480 ASP cc_start: 0.7782 (t0) cc_final: 0.7505 (t0) REVERT: C 529 GLU cc_start: 0.7658 (pp20) cc_final: 0.7349 (pp20) REVERT: B 175 TRP cc_start: 0.7493 (m100) cc_final: 0.7004 (m-90) REVERT: B 299 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B 301 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 356 MET cc_start: 0.8220 (tmm) cc_final: 0.7896 (tmm) REVERT: B 401 ASP cc_start: 0.8352 (p0) cc_final: 0.8130 (p0) REVERT: B 405 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8439 (ttp-110) REVERT: B 429 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 473 MET cc_start: 0.8170 (tpp) cc_final: 0.7464 (ttp) REVERT: B 480 ASP cc_start: 0.7799 (t0) cc_final: 0.7507 (t0) REVERT: B 487 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: B 512 MET cc_start: 0.8757 (ttm) cc_final: 0.8375 (ttm) REVERT: B 529 GLU cc_start: 0.7666 (pp20) cc_final: 0.7259 (pp20) outliers start: 44 outliers final: 27 residues processed: 295 average time/residue: 0.2113 time to fit residues: 94.2592 Evaluate side-chains 299 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS 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 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.0050 chunk 58 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** C 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13616 Z= 0.164 Angle : 0.538 6.308 18680 Z= 0.277 Chirality : 0.038 0.154 2196 Planarity : 0.003 0.033 2452 Dihedral : 11.888 163.736 2156 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.33 % Allowed : 36.56 % 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: 2.90 (0.20), residues: 1972 helix: 3.28 (0.13), residues: 1432 sheet: 0.06 (0.50), residues: 112 loop : -2.74 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 330 HIS 0.005 0.001 HIS B 437 PHE 0.017 0.001 PHE C 166 TYR 0.022 0.001 TYR B 558 ARG 0.002 0.000 ARG A 560 *********************** 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 313 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.838 Fit side-chains REVERT: A 175 TRP cc_start: 0.7419 (m100) cc_final: 0.6954 (m-90) REVERT: A 351 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7600 (mttp) REVERT: A 356 MET cc_start: 0.8280 (tmm) cc_final: 0.7916 (tmm) REVERT: A 401 ASP cc_start: 0.8345 (p0) cc_final: 0.7993 (p0) REVERT: A 405 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8222 (ttp-110) REVERT: A 429 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 473 MET cc_start: 0.8246 (tpp) cc_final: 0.7364 (ttp) REVERT: A 480 ASP cc_start: 0.7727 (t0) cc_final: 0.7464 (t0) REVERT: A 529 GLU cc_start: 0.7584 (pp20) cc_final: 0.7190 (pp20) REVERT: D 175 TRP cc_start: 0.7332 (m100) cc_final: 0.6809 (m-90) REVERT: D 299 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8222 (t80) REVERT: D 301 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 356 MET cc_start: 0.8222 (tmm) cc_final: 0.7882 (tmm) REVERT: D 401 ASP cc_start: 0.8290 (p0) cc_final: 0.7965 (p0) REVERT: D 405 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8216 (ttp-110) REVERT: D 429 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7124 (tm-30) REVERT: D 473 MET cc_start: 0.8250 (tpp) cc_final: 0.7370 (ttp) REVERT: D 480 ASP cc_start: 0.7752 (t0) cc_final: 0.7487 (t0) REVERT: D 494 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7300 (mt-10) REVERT: D 529 GLU cc_start: 0.7748 (pp20) cc_final: 0.7474 (pp20) REVERT: C 175 TRP cc_start: 0.7448 (m100) cc_final: 0.6923 (m-90) REVERT: C 356 MET cc_start: 0.8185 (tmm) cc_final: 0.7838 (tmm) REVERT: C 401 ASP cc_start: 0.8339 (p0) cc_final: 0.8018 (p0) REVERT: C 405 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8191 (ttp-110) REVERT: C 429 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7102 (tm-30) REVERT: C 473 MET cc_start: 0.8172 (tpp) cc_final: 0.7351 (ttp) REVERT: C 480 ASP cc_start: 0.7729 (t0) cc_final: 0.7462 (t0) REVERT: C 529 GLU cc_start: 0.7590 (pp20) cc_final: 0.7193 (pp20) REVERT: B 175 TRP cc_start: 0.7487 (m100) cc_final: 0.6957 (m-90) REVERT: B 301 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7957 (mm) REVERT: B 356 MET cc_start: 0.8258 (tmm) cc_final: 0.7923 (tmm) REVERT: B 401 ASP cc_start: 0.8359 (p0) cc_final: 0.8102 (p0) REVERT: B 405 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8436 (ttp-110) REVERT: B 429 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 473 MET cc_start: 0.8210 (tpp) cc_final: 0.7393 (ttp) REVERT: B 480 ASP cc_start: 0.7734 (t0) cc_final: 0.7464 (t0) REVERT: B 529 GLU cc_start: 0.7591 (pp20) cc_final: 0.7199 (pp20) outliers start: 39 outliers final: 20 residues processed: 294 average time/residue: 0.2425 time to fit residues: 107.9376 Evaluate side-chains 295 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain 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 451 ASN Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** D 497 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13616 Z= 0.333 Angle : 0.606 6.515 18680 Z= 0.320 Chirality : 0.039 0.136 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.791 163.039 2156 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.22 % Allowed : 35.67 % Favored : 58.11 % 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: 2.79 (0.20), residues: 1972 helix: 3.21 (0.13), residues: 1432 sheet: -0.12 (0.49), residues: 112 loop : -2.74 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 330 HIS 0.008 0.002 HIS C 437 PHE 0.017 0.002 PHE B 350 TYR 0.023 0.002 TYR D 411 ARG 0.004 0.001 ARG C 560 *********************** 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 322 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 1.639 Fit side-chains REVERT: A 175 TRP cc_start: 0.7420 (m100) cc_final: 0.6933 (m-90) REVERT: A 351 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7731 (mttp) REVERT: A 356 MET cc_start: 0.8256 (tmm) cc_final: 0.7845 (tmm) REVERT: A 401 ASP cc_start: 0.8326 (p0) cc_final: 0.7930 (p0) REVERT: A 405 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8435 (ttp-110) REVERT: A 429 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 473 MET cc_start: 0.8272 (tpp) cc_final: 0.7686 (ttp) REVERT: A 480 ASP cc_start: 0.7923 (t0) cc_final: 0.7648 (t0) REVERT: A 512 MET cc_start: 0.8858 (ttm) cc_final: 0.8647 (ttm) REVERT: A 529 GLU cc_start: 0.7516 (pp20) cc_final: 0.6936 (pp20) REVERT: D 175 TRP cc_start: 0.7361 (m100) cc_final: 0.6822 (m-90) REVERT: D 301 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7973 (mm) REVERT: D 401 ASP cc_start: 0.8351 (p0) cc_final: 0.7942 (p0) REVERT: D 405 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.8419 (ttp-110) REVERT: D 429 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7207 (tm-30) REVERT: D 473 MET cc_start: 0.8260 (tpp) cc_final: 0.7672 (ttp) REVERT: D 480 ASP cc_start: 0.7919 (t0) cc_final: 0.7642 (t0) REVERT: D 512 MET cc_start: 0.8934 (ttm) cc_final: 0.8703 (ttm) REVERT: C 175 TRP cc_start: 0.7460 (m100) cc_final: 0.6917 (m-90) REVERT: C 301 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 356 MET cc_start: 0.8187 (tmm) cc_final: 0.7807 (tmm) REVERT: C 401 ASP cc_start: 0.8368 (p0) cc_final: 0.7991 (p0) REVERT: C 405 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8401 (ttp-110) REVERT: C 429 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 473 MET cc_start: 0.8273 (tpp) cc_final: 0.7678 (ttp) REVERT: C 480 ASP cc_start: 0.7924 (t0) cc_final: 0.7650 (t0) REVERT: C 512 MET cc_start: 0.8855 (ttm) cc_final: 0.8642 (ttm) REVERT: C 529 GLU cc_start: 0.7576 (pp20) cc_final: 0.7026 (pp20) REVERT: B 175 TRP cc_start: 0.7513 (m100) cc_final: 0.6968 (m-90) REVERT: B 299 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 301 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7967 (mm) REVERT: B 356 MET cc_start: 0.8207 (tmm) cc_final: 0.7814 (tmm) REVERT: B 401 ASP cc_start: 0.8337 (p0) cc_final: 0.8096 (p0) REVERT: B 405 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8472 (ttp-110) REVERT: B 429 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 473 MET cc_start: 0.8315 (tpp) cc_final: 0.7736 (ttp) REVERT: B 480 ASP cc_start: 0.7905 (t0) cc_final: 0.7633 (t0) REVERT: B 529 GLU cc_start: 0.7526 (pp20) cc_final: 0.6959 (pp20) outliers start: 56 outliers final: 44 residues processed: 300 average time/residue: 0.2105 time to fit residues: 96.0400 Evaluate side-chains 316 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 426 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 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 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 451 ASN 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 519 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 433 ASP 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 465 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 451 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 50.0000 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 97 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 chunk 169 optimal weight: 0.0020 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 517 HIS D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS B 465 ASN B 517 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13616 Z= 0.227 Angle : 0.588 7.323 18680 Z= 0.305 Chirality : 0.038 0.137 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.896 164.098 2156 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.22 % Allowed : 36.78 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.19), residues: 1972 helix: 3.20 (0.13), residues: 1432 sheet: -0.01 (0.49), residues: 112 loop : -2.70 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 330 HIS 0.008 0.002 HIS A 517 PHE 0.017 0.001 PHE C 166 TYR 0.025 0.001 TYR B 558 ARG 0.002 0.000 ARG C 560 ********************** 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 305 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 1.562 Fit side-chains REVERT: A 175 TRP cc_start: 0.7421 (m100) cc_final: 0.6896 (m-90) REVERT: A 299 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8284 (t80) REVERT: A 351 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7717 (mttp) REVERT: A 356 MET cc_start: 0.8271 (tmm) cc_final: 0.7891 (tmm) REVERT: A 401 ASP cc_start: 0.8326 (p0) cc_final: 0.7981 (p0) REVERT: A 405 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8228 (ttp-110) REVERT: A 429 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 473 MET cc_start: 0.8266 (tpp) cc_final: 0.7609 (ttm) REVERT: A 480 ASP cc_start: 0.7847 (t0) cc_final: 0.7570 (t0) REVERT: A 512 MET cc_start: 0.8774 (ttm) cc_final: 0.8563 (ttm) REVERT: A 529 GLU cc_start: 0.7548 (pp20) cc_final: 0.7014 (pp20) REVERT: D 175 TRP cc_start: 0.7366 (m100) cc_final: 0.6831 (m-90) REVERT: D 299 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8245 (t80) REVERT: D 301 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7962 (mm) REVERT: D 401 ASP cc_start: 0.8347 (p0) cc_final: 0.7983 (p0) REVERT: D 405 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8199 (ttp-110) REVERT: D 429 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 473 MET cc_start: 0.8258 (tpp) cc_final: 0.7589 (ttm) REVERT: D 480 ASP cc_start: 0.7841 (t0) cc_final: 0.7565 (t0) REVERT: D 512 MET cc_start: 0.8884 (ttm) cc_final: 0.8657 (ttm) REVERT: D 544 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8636 (mt) REVERT: C 175 TRP cc_start: 0.7455 (m100) cc_final: 0.6915 (m-90) REVERT: C 299 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8289 (t80) REVERT: C 301 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8077 (mm) REVERT: C 356 MET cc_start: 0.8191 (tmm) cc_final: 0.7825 (tmm) REVERT: C 401 ASP cc_start: 0.8365 (p0) cc_final: 0.7996 (p0) REVERT: C 405 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: C 429 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7250 (tm-30) REVERT: C 473 MET cc_start: 0.8267 (tpp) cc_final: 0.7607 (ttp) REVERT: C 480 ASP cc_start: 0.7845 (t0) cc_final: 0.7571 (t0) REVERT: C 512 MET cc_start: 0.8769 (ttm) cc_final: 0.8556 (ttm) REVERT: C 529 GLU cc_start: 0.7516 (pp20) cc_final: 0.6988 (pp20) REVERT: B 175 TRP cc_start: 0.7511 (m100) cc_final: 0.6967 (m-90) REVERT: B 301 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 356 MET cc_start: 0.8213 (tmm) cc_final: 0.7835 (tmm) REVERT: B 401 ASP cc_start: 0.8334 (p0) cc_final: 0.8096 (p0) REVERT: B 405 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.8459 (ttp-110) REVERT: B 429 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7318 (tm-30) REVERT: B 473 MET cc_start: 0.8278 (tpp) cc_final: 0.7623 (ttp) REVERT: B 480 ASP cc_start: 0.7837 (t0) cc_final: 0.7570 (t0) REVERT: B 529 GLU cc_start: 0.7553 (pp20) cc_final: 0.7025 (pp20) REVERT: B 544 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8635 (mt) outliers start: 38 outliers final: 26 residues processed: 289 average time/residue: 0.2135 time to fit residues: 92.8609 Evaluate side-chains 299 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS 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 451 ASN Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 451 ASN 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 543 LEU Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 50.0000 chunk 146 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 517 HIS D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104116 restraints weight = 23552.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108038 restraints weight = 14245.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110139 restraints weight = 8836.518| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13616 Z= 0.237 Angle : 0.580 6.432 18680 Z= 0.303 Chirality : 0.038 0.138 2196 Planarity : 0.003 0.032 2452 Dihedral : 11.867 163.920 2156 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.89 % Allowed : 37.78 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.20), residues: 1972 helix: 3.21 (0.13), residues: 1432 sheet: -0.02 (0.49), residues: 112 loop : -2.68 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 330 HIS 0.008 0.002 HIS A 517 PHE 0.016 0.001 PHE C 166 TYR 0.023 0.001 TYR B 558 ARG 0.003 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.42 seconds wall clock time: 49 minutes 11.79 seconds (2951.79 seconds total)