Starting phenix.real_space_refine on Thu Sep 18 02:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4y_41040/09_2025/8t4y_41040.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 68 5.16 5 C 8436 2.51 5 N 2400 2.21 5 O 2440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13348 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "C" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "B" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3315 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 673 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 16, 'ARG:plan': 15, 'GLN:plan1': 13, 'GLU:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 10, 'TYR:plan': 5, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 436 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'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: 3.57, per 1000 atoms: 0.27 Number of scatterers: 13348 At special positions: 0 Unit cell: (109.686, 109.686, 125.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 4 15.00 O 2440 8.00 N 2400 7.00 C 8436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 719.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 76.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.685A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 369 through 401 removed outlier: 4.215A pdb=" N TRP A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.909A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.683A pdb=" N ILE D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 270 through 286 Processing helix chain 'D' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 369 through 401 removed outlier: 4.216A pdb=" N TRP D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.907A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 595 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU C 147 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.684A pdb=" N ILE C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 270 through 286 Processing helix chain 'C' and resid 295 through 323 removed outlier: 3.777A pdb=" N PHE C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 369 through 401 removed outlier: 4.216A pdb=" N TRP C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.907A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.074A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 595 Processing helix chain 'C' and resid 598 through 611 Processing helix chain 'C' and resid 615 through 635 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 139 through 167 removed outlier: 5.142A pdb=" N LEU B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 195 removed outlier: 3.700A pdb=" N PHE B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.684A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 270 through 286 Processing helix chain 'B' and resid 295 through 323 removed outlier: 3.778A pdb=" N PHE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 369 through 401 removed outlier: 4.217A pdb=" N TRP B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.908A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.075A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 598 through 611 Processing helix chain 'B' and resid 615 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.885A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 564 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.539A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.884A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 564 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.538A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.885A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 564 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.540A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.884A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 564 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.540A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4532 1.34 - 1.46: 2902 1.46 - 1.58: 6062 1.58 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 13616 Sorted by residual: bond pdb=" C PRO B 326 " pdb=" N PRO B 327 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C PRO D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C PRO A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.58e+00 bond pdb=" C PRO C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.54e+00 bond pdb=" CA PRO B 366 " pdb=" C PRO B 366 " ideal model delta sigma weight residual 1.520 1.537 -0.017 1.42e-02 4.96e+03 1.44e+00 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18330 1.99 - 3.99: 258 3.99 - 5.98: 56 5.98 - 7.97: 28 7.97 - 9.97: 8 Bond angle restraints: 18680 Sorted by residual: angle pdb=" N TYR A 361 " pdb=" CA TYR A 361 " pdb=" C TYR A 361 " ideal model delta sigma weight residual 112.59 105.66 6.93 1.22e+00 6.72e-01 3.22e+01 angle pdb=" N TYR B 361 " pdb=" CA TYR B 361 " pdb=" C TYR B 361 " ideal model delta sigma weight residual 112.59 105.72 6.87 1.22e+00 6.72e-01 3.17e+01 angle pdb=" N TYR C 361 " pdb=" CA TYR C 361 " pdb=" C TYR C 361 " ideal model delta sigma weight residual 112.59 105.87 6.72 1.22e+00 6.72e-01 3.04e+01 angle pdb=" N TYR D 361 " pdb=" CA TYR D 361 " pdb=" C TYR D 361 " ideal model delta sigma weight residual 112.59 106.05 6.54 1.22e+00 6.72e-01 2.88e+01 angle pdb=" O1P CMP A 901 " pdb=" P CMP A 901 " pdb=" O2P CMP A 901 " ideal model delta sigma weight residual 109.50 119.47 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 18675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 7763 32.50 - 64.99: 205 64.99 - 97.49: 0 97.49 - 129.99: 4 129.99 - 162.48: 8 Dihedral angle restraints: 7980 sinusoidal: 2092 harmonic: 5888 Sorted by residual: dihedral pdb=" C3' CMP D 901 " pdb=" O3' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.48 -162.48 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C3' CMP B 901 " pdb=" O3' CMP B 901 " pdb=" P CMP B 901 " pdb=" O1P CMP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.46 -162.46 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C3' CMP C 901 " pdb=" O3' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual -60.00 102.41 -162.41 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1887 0.059 - 0.118: 298 0.118 - 0.176: 7 0.176 - 0.235: 0 0.235 - 0.294: 4 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CG LEU D 301 " pdb=" CB LEU D 301 " pdb=" CD1 LEU D 301 " pdb=" CD2 LEU D 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU C 301 " pdb=" CB LEU C 301 " pdb=" CD1 LEU C 301 " pdb=" CD2 LEU C 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU B 301 " pdb=" CB LEU B 301 " pdb=" CD1 LEU B 301 " pdb=" CD2 LEU B 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2193 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 365 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 366 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 365 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 366 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 365 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 366 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 366 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 366 " 0.030 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2830 2.77 - 3.31: 13832 3.31 - 3.84: 23003 3.84 - 4.37: 21192 4.37 - 4.90: 38766 Nonbonded interactions: 99623 Sorted by model distance: nonbonded pdb=" O LYS A 468 " pdb=" OG1 THR A 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS D 468 " pdb=" OG1 THR D 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS C 468 " pdb=" OG1 THR C 472 " model vdw 2.242 3.040 nonbonded pdb=" O LYS B 468 " pdb=" OG1 THR B 472 " model vdw 2.243 3.040 nonbonded pdb=" O LEU C 450 " pdb=" NH1 ARG C 458 " model vdw 2.247 3.120 ... (remaining 99618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13616 Z= 0.139 Angle : 0.663 9.968 18680 Z= 0.340 Chirality : 0.040 0.294 2196 Planarity : 0.004 0.056 2452 Dihedral : 16.197 162.481 4148 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 34.22 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.20), residues: 1972 helix: 2.74 (0.13), residues: 1400 sheet: -0.64 (0.48), residues: 120 loop : -2.56 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.012 0.001 TYR D 417 PHE 0.006 0.001 PHE A 538 TRP 0.004 0.001 TRP D 221 HIS 0.003 0.001 HIS D 355 Details of bonding type rmsd covalent geometry : bond 0.00271 (13616) covalent geometry : angle 0.66309 (18680) hydrogen bonds : bond 0.10201 ( 1153) hydrogen bonds : angle 4.61124 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.549 Fit side-chains REVERT: A 175 TRP cc_start: 0.7277 (m100) cc_final: 0.6799 (m-90) REVERT: A 341 TRP cc_start: 0.7569 (p-90) cc_final: 0.7291 (t60) REVERT: A 411 TYR cc_start: 0.6907 (t80) cc_final: 0.6646 (t80) REVERT: A 429 GLN cc_start: 0.7229 (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: 0.7443 (m-80) REVERT: B 589 ASP cc_start: 0.9087 (t0) cc_final: 0.8850 (t70) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1183 time to fit residues: 56.8081 Evaluate side-chains 282 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.164371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108297 restraints weight = 24610.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111570 restraints weight = 14743.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113879 restraints weight = 10520.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115312 restraints weight = 8447.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116456 restraints weight = 7329.479| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13616 Z= 0.145 Angle : 0.568 6.842 18680 Z= 0.290 Chirality : 0.040 0.207 2196 Planarity : 0.004 0.033 2452 Dihedral : 11.966 166.094 2156 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.56 % Allowed : 28.78 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.20), residues: 1972 helix: 2.92 (0.13), residues: 1432 sheet: -0.32 (0.51), residues: 112 loop : -2.51 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 405 TYR 0.010 0.001 TYR C 411 PHE 0.009 0.001 PHE C 464 TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00322 (13616) covalent geometry : angle 0.56761 (18680) hydrogen bonds : bond 0.03261 ( 1153) hydrogen bonds : angle 3.74528 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.613 Fit side-chains REVERT: A 175 TRP cc_start: 0.7082 (m100) cc_final: 0.6757 (m-90) REVERT: A 351 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: A 379 MET cc_start: 0.9028 (mtm) cc_final: 0.8810 (mtm) REVERT: A 411 TYR cc_start: 0.7358 (t80) cc_final: 0.7088 (t80) REVERT: A 473 MET cc_start: 0.7619 (tpp) cc_final: 0.6821 (ttm) REVERT: D 175 TRP cc_start: 0.7151 (m100) cc_final: 0.6806 (m-90) REVERT: D 411 TYR cc_start: 0.7324 (t80) cc_final: 0.7066 (t80) REVERT: D 473 MET cc_start: 0.7613 (tpp) cc_final: 0.6799 (ttm) REVERT: D 530 MET cc_start: 0.5892 (ptm) cc_final: 0.5677 (ptm) REVERT: C 175 TRP cc_start: 0.7201 (m100) cc_final: 0.6816 (m-90) REVERT: C 411 TYR cc_start: 0.7396 (t80) cc_final: 0.7086 (t80) REVERT: C 473 MET cc_start: 0.7596 (tpp) cc_final: 0.6773 (ttm) REVERT: B 175 TRP cc_start: 0.7175 (m100) cc_final: 0.6782 (m-90) REVERT: B 351 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8083 (mmtp) REVERT: B 411 TYR cc_start: 0.7387 (t80) cc_final: 0.7075 (t80) REVERT: B 473 MET cc_start: 0.7637 (tpp) cc_final: 0.6850 (ttm) outliers start: 50 outliers final: 28 residues processed: 316 average time/residue: 0.1006 time to fit residues: 48.6829 Evaluate side-chains 291 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 461 ILE Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 120 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 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 C 497 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 482 ASN B 497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.164094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107520 restraints weight = 24505.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110834 restraints weight = 14608.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113164 restraints weight = 10406.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114565 restraints weight = 8350.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115733 restraints weight = 7269.772| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13616 Z= 0.132 Angle : 0.551 6.458 18680 Z= 0.282 Chirality : 0.039 0.181 2196 Planarity : 0.003 0.033 2452 Dihedral : 11.888 164.971 2156 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.89 % Allowed : 30.33 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.20), residues: 1972 helix: 3.10 (0.13), residues: 1432 sheet: -0.23 (0.51), residues: 112 loop : -2.54 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.008 0.001 TYR B 411 PHE 0.008 0.001 PHE C 538 TRP 0.014 0.001 TRP C 330 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00284 (13616) covalent geometry : angle 0.55142 (18680) hydrogen bonds : bond 0.03022 ( 1153) hydrogen bonds : angle 3.55953 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 0.516 Fit side-chains REVERT: A 175 TRP cc_start: 0.7054 (m100) cc_final: 0.6740 (m-90) REVERT: A 351 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8245 (mttp) REVERT: A 379 MET cc_start: 0.9005 (mtm) cc_final: 0.8763 (mtm) REVERT: A 411 TYR cc_start: 0.7321 (t80) cc_final: 0.7100 (t80) REVERT: A 429 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 473 MET cc_start: 0.7882 (tpp) cc_final: 0.7023 (ttp) REVERT: D 175 TRP cc_start: 0.7131 (m100) cc_final: 0.6756 (m-90) REVERT: D 411 TYR cc_start: 0.7289 (t80) cc_final: 0.7076 (t80) REVERT: D 473 MET cc_start: 0.7875 (tpp) cc_final: 0.6976 (ttp) REVERT: C 175 TRP cc_start: 0.7155 (m100) cc_final: 0.6788 (m-90) REVERT: C 411 TYR cc_start: 0.7338 (t80) cc_final: 0.7107 (t80) REVERT: C 473 MET cc_start: 0.7869 (tpp) cc_final: 0.6989 (ttp) REVERT: B 175 TRP cc_start: 0.7215 (m100) cc_final: 0.6821 (m-90) REVERT: B 301 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 351 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8087 (mmtp) REVERT: B 473 MET cc_start: 0.7876 (tpp) cc_final: 0.7009 (ttp) outliers start: 62 outliers final: 29 residues processed: 303 average time/residue: 0.1021 time to fit residues: 47.7196 Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 50.0000 chunk 189 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 98 optimal weight: 50.0000 chunk 122 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN B 465 ASN B 497 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098516 restraints weight = 23805.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101523 restraints weight = 14295.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103594 restraints weight = 10291.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105008 restraints weight = 8349.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105697 restraints weight = 7307.181| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 13616 Z= 0.345 Angle : 0.703 6.754 18680 Z= 0.376 Chirality : 0.043 0.205 2196 Planarity : 0.004 0.039 2452 Dihedral : 11.851 164.953 2156 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 10.11 % Allowed : 27.33 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.20), residues: 1972 helix: 2.79 (0.13), residues: 1456 sheet: 0.32 (0.59), residues: 88 loop : -2.98 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 405 TYR 0.042 0.002 TYR B 411 PHE 0.023 0.003 PHE B 538 TRP 0.012 0.001 TRP C 330 HIS 0.008 0.002 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00783 (13616) covalent geometry : angle 0.70261 (18680) hydrogen bonds : bond 0.04015 ( 1153) hydrogen bonds : angle 3.96223 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 263 time to evaluate : 0.525 Fit side-chains REVERT: A 175 TRP cc_start: 0.7127 (m100) cc_final: 0.6773 (m-90) REVERT: A 301 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 351 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8174 (mttp) REVERT: A 401 ASP cc_start: 0.8322 (p0) cc_final: 0.7976 (p0) REVERT: A 416 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 429 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 473 MET cc_start: 0.8076 (tpp) cc_final: 0.7595 (ttm) REVERT: A 529 GLU cc_start: 0.7461 (pp20) cc_final: 0.7195 (pp20) REVERT: D 175 TRP cc_start: 0.7198 (m100) cc_final: 0.6849 (m-90) REVERT: D 401 ASP cc_start: 0.8337 (p0) cc_final: 0.8003 (p0) REVERT: D 427 MET cc_start: 0.8568 (mmm) cc_final: 0.8230 (mmm) REVERT: D 473 MET cc_start: 0.8077 (tpp) cc_final: 0.7587 (ttm) REVERT: C 175 TRP cc_start: 0.7184 (m100) cc_final: 0.6768 (m-90) REVERT: C 401 ASP cc_start: 0.8352 (p0) cc_final: 0.7995 (p0) REVERT: C 427 MET cc_start: 0.8567 (mmm) cc_final: 0.8235 (mmm) REVERT: C 473 MET cc_start: 0.8068 (tpp) cc_final: 0.7580 (ttm) REVERT: C 529 GLU cc_start: 0.7488 (pp20) cc_final: 0.7211 (pp20) REVERT: B 175 TRP cc_start: 0.7209 (m100) cc_final: 0.6847 (m-90) REVERT: B 301 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 351 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (mttp) REVERT: B 401 ASP cc_start: 0.8345 (p0) cc_final: 0.7963 (p0) REVERT: B 416 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8704 (tm-30) REVERT: B 473 MET cc_start: 0.8065 (tpp) cc_final: 0.7582 (ttm) outliers start: 91 outliers final: 67 residues processed: 314 average time/residue: 0.1036 time to fit residues: 49.3014 Evaluate side-chains 321 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 250 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 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 465 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 408 GLN Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 433 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 36 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 159 optimal weight: 40.0000 chunk 125 optimal weight: 0.9980 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 465 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103352 restraints weight = 24052.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106608 restraints weight = 14293.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108721 restraints weight = 10205.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110428 restraints weight = 8206.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111183 restraints weight = 7143.329| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13616 Z= 0.135 Angle : 0.571 6.374 18680 Z= 0.295 Chirality : 0.039 0.192 2196 Planarity : 0.003 0.030 2452 Dihedral : 11.980 164.999 2156 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 7.78 % Allowed : 30.44 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.20), residues: 1972 helix: 3.00 (0.13), residues: 1456 sheet: -0.05 (0.53), residues: 112 loop : -2.90 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 405 TYR 0.016 0.001 TYR B 411 PHE 0.018 0.001 PHE D 166 TRP 0.010 0.001 TRP A 330 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00295 (13616) covalent geometry : angle 0.57084 (18680) hydrogen bonds : bond 0.03070 ( 1153) hydrogen bonds : angle 3.54990 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 0.548 Fit side-chains REVERT: A 175 TRP cc_start: 0.7172 (m100) cc_final: 0.6848 (m-90) REVERT: A 301 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 379 MET cc_start: 0.9039 (mtm) cc_final: 0.8810 (mtm) REVERT: A 405 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8349 (ttp-110) REVERT: A 429 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 473 MET cc_start: 0.7880 (tpp) cc_final: 0.7382 (ttp) REVERT: D 175 TRP cc_start: 0.7306 (m100) cc_final: 0.6866 (m-90) REVERT: D 473 MET cc_start: 0.7945 (tpp) cc_final: 0.7416 (ttp) REVERT: C 175 TRP cc_start: 0.7302 (m100) cc_final: 0.6914 (m-90) REVERT: C 473 MET cc_start: 0.7998 (tpp) cc_final: 0.7477 (ttp) REVERT: B 175 TRP cc_start: 0.7313 (m100) cc_final: 0.6913 (m-90) REVERT: B 301 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 351 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: B 356 MET cc_start: 0.8726 (tmm) cc_final: 0.8519 (tmm) REVERT: B 429 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 473 MET cc_start: 0.7905 (tpp) cc_final: 0.7403 (ttp) outliers start: 70 outliers final: 44 residues processed: 296 average time/residue: 0.1027 time to fit residues: 46.4324 Evaluate side-chains 300 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 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 465 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 50.0000 chunk 185 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 158 optimal weight: 50.0000 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 478 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.158674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101411 restraints weight = 23641.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104558 restraints weight = 14063.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106722 restraints weight = 10088.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108048 restraints weight = 8159.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109118 restraints weight = 7127.732| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13616 Z= 0.199 Angle : 0.607 6.579 18680 Z= 0.318 Chirality : 0.040 0.254 2196 Planarity : 0.003 0.036 2452 Dihedral : 11.851 162.786 2156 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 9.11 % Allowed : 29.67 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.20), residues: 1972 helix: 3.03 (0.13), residues: 1456 sheet: -0.00 (0.53), residues: 112 loop : -2.89 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 405 TYR 0.015 0.001 TYR B 411 PHE 0.021 0.002 PHE D 166 TRP 0.010 0.001 TRP D 330 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00452 (13616) covalent geometry : angle 0.60735 (18680) hydrogen bonds : bond 0.03228 ( 1153) hydrogen bonds : angle 3.57890 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 270 time to evaluate : 0.530 Fit side-chains REVERT: A 175 TRP cc_start: 0.7239 (m100) cc_final: 0.6912 (m-90) REVERT: A 299 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 301 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 351 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: A 356 MET cc_start: 0.8693 (tmm) cc_final: 0.8416 (tmm) REVERT: A 379 MET cc_start: 0.9105 (mtm) cc_final: 0.8890 (mtm) REVERT: A 401 ASP cc_start: 0.8286 (p0) cc_final: 0.7919 (p0) REVERT: A 405 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8418 (ttp-110) REVERT: A 427 MET cc_start: 0.8545 (mmm) cc_final: 0.8225 (mmm) REVERT: A 429 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 473 MET cc_start: 0.8010 (tpp) cc_final: 0.7542 (ttp) REVERT: D 175 TRP cc_start: 0.7319 (m100) cc_final: 0.6892 (m-90) REVERT: D 401 ASP cc_start: 0.8305 (p0) cc_final: 0.7938 (p0) REVERT: D 405 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8410 (ttp-110) REVERT: D 429 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 473 MET cc_start: 0.8012 (tpp) cc_final: 0.7536 (ttp) REVERT: C 175 TRP cc_start: 0.7323 (m100) cc_final: 0.6903 (m-90) REVERT: C 401 ASP cc_start: 0.8320 (p0) cc_final: 0.7924 (p0) REVERT: C 405 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8367 (ttp-110) REVERT: C 429 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 473 MET cc_start: 0.7986 (tpp) cc_final: 0.7487 (ttp) REVERT: B 175 TRP cc_start: 0.7349 (m100) cc_final: 0.6945 (m-90) REVERT: B 301 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 351 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8207 (mttp) REVERT: B 356 MET cc_start: 0.8751 (tmm) cc_final: 0.8477 (tmm) REVERT: B 416 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 429 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 473 MET cc_start: 0.8004 (tpp) cc_final: 0.7519 (ttp) outliers start: 82 outliers final: 62 residues processed: 316 average time/residue: 0.1004 time to fit residues: 48.6196 Evaluate side-chains 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 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 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 572 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 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 465 ASN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 572 VAL 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 394 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 27 optimal weight: 0.7980 chunk 118 optimal weight: 0.0970 chunk 70 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098545 restraints weight = 23521.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101676 restraints weight = 13886.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103679 restraints weight = 9904.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105271 restraints weight = 8000.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106018 restraints weight = 6981.493| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13616 Z= 0.288 Angle : 0.665 8.161 18680 Z= 0.351 Chirality : 0.041 0.193 2196 Planarity : 0.004 0.036 2452 Dihedral : 11.862 163.242 2156 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 9.22 % Allowed : 29.56 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.19), residues: 1972 helix: 2.91 (0.13), residues: 1456 sheet: 0.28 (0.57), residues: 88 loop : -3.05 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 405 TYR 0.017 0.002 TYR B 411 PHE 0.020 0.002 PHE D 166 TRP 0.019 0.001 TRP B 330 HIS 0.006 0.002 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00656 (13616) covalent geometry : angle 0.66451 (18680) hydrogen bonds : bond 0.03591 ( 1153) hydrogen bonds : angle 3.77447 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 267 time to evaluate : 0.519 Fit side-chains REVERT: A 175 TRP cc_start: 0.7303 (m100) cc_final: 0.6928 (m-90) REVERT: A 301 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 401 ASP cc_start: 0.8336 (p0) cc_final: 0.7906 (p0) REVERT: A 405 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8455 (ttp-110) REVERT: A 429 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 473 MET cc_start: 0.8028 (tpp) cc_final: 0.7728 (ttm) REVERT: A 529 GLU cc_start: 0.7486 (pp20) cc_final: 0.7272 (pp20) REVERT: D 175 TRP cc_start: 0.7201 (m100) cc_final: 0.6773 (m-90) REVERT: D 401 ASP cc_start: 0.8386 (p0) cc_final: 0.7952 (p0) REVERT: D 405 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8431 (ttp-110) REVERT: D 429 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7522 (tm-30) REVERT: D 473 MET cc_start: 0.8033 (tpp) cc_final: 0.7727 (ttm) REVERT: D 529 GLU cc_start: 0.7528 (pp20) cc_final: 0.7296 (pp20) REVERT: C 175 TRP cc_start: 0.7300 (m100) cc_final: 0.6852 (m-90) REVERT: C 401 ASP cc_start: 0.8361 (p0) cc_final: 0.7933 (p0) REVERT: C 429 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 473 MET cc_start: 0.8076 (tpp) cc_final: 0.7723 (ttm) REVERT: C 529 GLU cc_start: 0.7466 (pp20) cc_final: 0.7252 (pp20) REVERT: B 175 TRP cc_start: 0.7310 (m100) cc_final: 0.6915 (m-90) REVERT: B 301 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 330 TRP cc_start: 0.7638 (p-90) cc_final: 0.7318 (p90) REVERT: B 351 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8244 (mttp) REVERT: B 356 MET cc_start: 0.8700 (tmm) cc_final: 0.8390 (tmm) REVERT: B 416 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8652 (tm-30) REVERT: B 429 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 473 MET cc_start: 0.8069 (tpp) cc_final: 0.7725 (ttm) outliers start: 83 outliers final: 67 residues processed: 316 average time/residue: 0.0987 time to fit residues: 47.9083 Evaluate side-chains 330 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 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 519 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR 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 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 433 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 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 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 572 VAL Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 138 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 43 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 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 465 ASN B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103507 restraints weight = 23592.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106656 restraints weight = 13818.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108782 restraints weight = 9877.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110375 restraints weight = 7998.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111107 restraints weight = 6973.201| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13616 Z= 0.136 Angle : 0.588 8.619 18680 Z= 0.305 Chirality : 0.039 0.275 2196 Planarity : 0.003 0.031 2452 Dihedral : 11.956 164.110 2156 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.67 % Allowed : 33.11 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.20), residues: 1972 helix: 3.06 (0.13), residues: 1456 sheet: -0.04 (0.52), residues: 112 loop : -2.88 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 405 TYR 0.014 0.001 TYR B 411 PHE 0.018 0.001 PHE B 166 TRP 0.015 0.001 TRP A 330 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00299 (13616) covalent geometry : angle 0.58770 (18680) hydrogen bonds : bond 0.02969 ( 1153) hydrogen bonds : angle 3.50340 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 0.504 Fit side-chains REVERT: A 175 TRP cc_start: 0.7319 (m100) cc_final: 0.6895 (m-90) REVERT: A 301 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8106 (mm) REVERT: A 351 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8257 (mttp) REVERT: A 379 MET cc_start: 0.8993 (mtm) cc_final: 0.8773 (mtm) REVERT: A 401 ASP cc_start: 0.8245 (p0) cc_final: 0.8013 (p0) REVERT: A 405 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8392 (ttp-110) REVERT: A 406 GLN cc_start: 0.8644 (mt0) cc_final: 0.8427 (mt0) REVERT: A 429 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 460 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 473 MET cc_start: 0.8021 (tpp) cc_final: 0.7577 (ttp) REVERT: D 175 TRP cc_start: 0.7165 (m100) cc_final: 0.6760 (m-90) REVERT: D 401 ASP cc_start: 0.8255 (p0) cc_final: 0.8025 (p0) REVERT: D 405 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8423 (ttp-110) REVERT: D 429 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7376 (tm-30) REVERT: D 460 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 473 MET cc_start: 0.8029 (tpp) cc_final: 0.7580 (ttp) REVERT: C 175 TRP cc_start: 0.7291 (m100) cc_final: 0.6870 (m-90) REVERT: C 429 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7374 (tm-30) REVERT: C 473 MET cc_start: 0.8019 (tpp) cc_final: 0.7569 (ttp) REVERT: B 175 TRP cc_start: 0.7319 (m100) cc_final: 0.6908 (m-90) REVERT: B 301 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 351 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8232 (mttp) REVERT: B 406 GLN cc_start: 0.8666 (mt0) cc_final: 0.8456 (mt0) REVERT: B 416 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 429 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 473 MET cc_start: 0.8013 (tpp) cc_final: 0.7580 (ttp) outliers start: 60 outliers final: 44 residues processed: 306 average time/residue: 0.1016 time to fit residues: 47.4393 Evaluate side-chains 310 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 448 ASN Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 517 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 50 optimal weight: 50.0000 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100275 restraints weight = 23467.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103422 restraints weight = 13957.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.105528 restraints weight = 10032.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106790 restraints weight = 8114.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107914 restraints weight = 7106.538| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3024 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= 0.226 Angle : 0.640 8.294 18680 Z= 0.337 Chirality : 0.041 0.266 2196 Planarity : 0.004 0.033 2452 Dihedral : 11.866 162.657 2156 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 7.89 % Allowed : 32.44 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.20), residues: 1972 helix: 2.98 (0.13), residues: 1456 sheet: -0.07 (0.50), residues: 112 loop : -2.86 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 405 TYR 0.016 0.001 TYR B 411 PHE 0.016 0.002 PHE B 166 TRP 0.019 0.001 TRP B 330 HIS 0.006 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00514 (13616) covalent geometry : angle 0.64020 (18680) hydrogen bonds : bond 0.03292 ( 1153) hydrogen bonds : angle 3.63004 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 0.519 Fit side-chains REVERT: A 175 TRP cc_start: 0.7339 (m100) cc_final: 0.6906 (m-90) REVERT: A 301 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 351 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8325 (mttp) REVERT: A 379 MET cc_start: 0.9086 (mtm) cc_final: 0.8856 (mtm) REVERT: A 401 ASP cc_start: 0.8332 (p0) cc_final: 0.8111 (p0) REVERT: A 405 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8422 (ttp-110) REVERT: A 406 GLN cc_start: 0.8696 (mt0) cc_final: 0.8473 (mt0) REVERT: A 429 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 473 MET cc_start: 0.8063 (tpp) cc_final: 0.7721 (ttp) REVERT: D 175 TRP cc_start: 0.7176 (m100) cc_final: 0.6755 (m-90) REVERT: D 401 ASP cc_start: 0.8352 (p0) cc_final: 0.8128 (p0) REVERT: D 405 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8427 (ttp-110) REVERT: D 429 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7419 (tm-30) REVERT: D 473 MET cc_start: 0.8082 (tpp) cc_final: 0.7724 (ttp) REVERT: C 175 TRP cc_start: 0.7306 (m100) cc_final: 0.6860 (m-90) REVERT: C 406 GLN cc_start: 0.8728 (mt0) cc_final: 0.8483 (mt0) REVERT: C 429 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 473 MET cc_start: 0.8067 (tpp) cc_final: 0.7716 (ttp) REVERT: B 175 TRP cc_start: 0.7320 (m100) cc_final: 0.6889 (m-90) REVERT: B 299 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 301 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 351 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8331 (mttp) REVERT: B 406 GLN cc_start: 0.8726 (mt0) cc_final: 0.8500 (mt0) REVERT: B 429 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 473 MET cc_start: 0.8062 (tpp) cc_final: 0.7717 (ttp) outliers start: 71 outliers final: 57 residues processed: 307 average time/residue: 0.1006 time to fit residues: 47.1625 Evaluate side-chains 326 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 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 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 572 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 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 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 544 LEU Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 394 THR 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 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 161 optimal weight: 0.0050 chunk 166 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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** A 517 HIS D 465 ASN D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN C 465 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** B 517 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.160955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103995 restraints weight = 23484.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107260 restraints weight = 13854.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109484 restraints weight = 9886.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110819 restraints weight = 7988.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111298 restraints weight = 6978.760| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13616 Z= 0.131 Angle : 0.616 11.409 18680 Z= 0.318 Chirality : 0.039 0.331 2196 Planarity : 0.003 0.039 2452 Dihedral : 11.964 164.231 2156 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.89 % Allowed : 35.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.20), residues: 1972 helix: 3.06 (0.13), residues: 1456 sheet: 0.05 (0.50), residues: 112 loop : -2.82 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 405 TYR 0.014 0.001 TYR B 411 PHE 0.017 0.001 PHE B 166 TRP 0.019 0.001 TRP A 330 HIS 0.011 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00286 (13616) covalent geometry : angle 0.61596 (18680) hydrogen bonds : bond 0.02903 ( 1153) hydrogen bonds : angle 3.50058 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.519 Fit side-chains REVERT: A 175 TRP cc_start: 0.7311 (m100) cc_final: 0.6883 (m-90) REVERT: A 299 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 301 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 351 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8298 (mttp) REVERT: A 379 MET cc_start: 0.8988 (mtm) cc_final: 0.8761 (mtm) REVERT: A 401 ASP cc_start: 0.8260 (p0) cc_final: 0.8007 (p0) REVERT: A 405 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8414 (ttp-110) REVERT: A 429 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 473 MET cc_start: 0.8018 (tpp) cc_final: 0.7554 (ttp) REVERT: D 175 TRP cc_start: 0.7158 (m100) cc_final: 0.6745 (m-90) REVERT: D 405 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8432 (ttp-110) REVERT: D 429 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7415 (tm-30) REVERT: D 473 MET cc_start: 0.8025 (tpp) cc_final: 0.7554 (ttp) REVERT: C 175 TRP cc_start: 0.7296 (m100) cc_final: 0.6874 (m-90) REVERT: C 406 GLN cc_start: 0.8744 (mt0) cc_final: 0.8514 (mt0) REVERT: C 429 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 473 MET cc_start: 0.8055 (tpp) cc_final: 0.7598 (ttp) REVERT: B 175 TRP cc_start: 0.7296 (m100) cc_final: 0.6877 (m-90) REVERT: B 299 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7688 (t80) REVERT: B 301 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8114 (mm) REVERT: B 351 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: B 406 GLN cc_start: 0.8686 (mt0) cc_final: 0.8460 (mt0) REVERT: B 429 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 473 MET cc_start: 0.8023 (tpp) cc_final: 0.7562 (ttp) outliers start: 53 outliers final: 44 residues processed: 293 average time/residue: 0.0992 time to fit residues: 44.9760 Evaluate side-chains 307 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 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 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 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 421 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 465 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 594 ILE Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 448 ASN 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 524 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 158 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 143 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 40.0000 chunk 147 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- 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** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS D 465 ASN D 478 ASN ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 478 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 478 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.160700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103695 restraints weight = 23385.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106924 restraints weight = 13764.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109007 restraints weight = 9817.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110640 restraints weight = 7916.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111443 restraints weight = 6905.832| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.003 0.038 13616 Z= 0.143 Angle : 0.608 12.262 18680 Z= 0.316 Chirality : 0.040 0.335 2196 Planarity : 0.003 0.035 2452 Dihedral : 11.898 163.826 2156 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.22 % Allowed : 35.00 % Favored : 58.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.20), residues: 1972 helix: 3.11 (0.13), residues: 1456 sheet: 0.06 (0.50), residues: 112 loop : -2.79 (0.25), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 405 TYR 0.013 0.001 TYR B 411 PHE 0.017 0.001 PHE B 166 TRP 0.020 0.001 TRP A 330 HIS 0.016 0.002 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00317 (13616) covalent geometry : angle 0.60789 (18680) hydrogen bonds : bond 0.02889 ( 1153) hydrogen bonds : angle 3.46445 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.96 seconds wall clock time: 50 minutes 41.55 seconds (3041.55 seconds total)