Starting phenix.real_space_refine on Thu Jun 4 19:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.map" model { file = "/net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1v_53516/06_2026/9r1v_53516.cif" } resolution = 3.53 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= 0.003 sd= 0.065 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 9552 2.51 5 N 2448 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3666 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3666 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3666 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "D" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3666 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 91 Time building chain proxies: 3.20, per 1000 atoms: 0.22 Number of scatterers: 14664 At special positions: 0 Unit cell: (117.45, 117.45, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2552 8.00 N 2448 7.00 C 9552 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: 1.03 Conformation dependent library (CDL) restraints added in 598.2 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 71.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.635A pdb=" N THR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 195 removed outlier: 4.025A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.274A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 472 removed outlier: 5.960A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.821A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.516A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.635A pdb=" N THR B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 195 removed outlier: 4.025A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.274A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 472 removed outlier: 5.959A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.822A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Proline residue: B 481 - end of helix Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.516A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.632A pdb=" N THR C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 195 removed outlier: 3.993A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.273A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 472 removed outlier: 5.959A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 491 removed outlier: 3.819A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.509A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.635A pdb=" N THR D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 195 removed outlier: 4.025A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.274A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 Processing helix chain 'D' and resid 424 through 437 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 472 removed outlier: 5.959A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 491 removed outlier: 3.821A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Proline residue: D 481 - end of helix Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.516A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.626A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 564 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.477A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.626A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 564 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.476A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 564 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.477A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.626A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 564 " --> pdb=" O MET D 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.476A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 3003 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: 2.04 Time building geometry restraints manager: 1.37 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: 4620 1.34 - 1.46: 3627 1.46 - 1.58: 6597 1.58 - 1.70: 0 1.70 - 1.81: 196 Bond restraints: 15040 Sorted by residual: bond pdb=" CA ASP D 480 " pdb=" CB ASP D 480 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.58e-02 4.01e+03 1.84e+00 bond pdb=" CA ASP A 480 " pdb=" CB ASP A 480 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.58e-02 4.01e+03 1.77e+00 bond pdb=" CA ASP C 480 " pdb=" CB ASP C 480 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.58e-02 4.01e+03 1.74e+00 bond pdb=" CA ASP B 480 " pdb=" CB ASP B 480 " ideal model delta sigma weight residual 1.530 1.550 -0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" C ASP A 480 " pdb=" N PRO A 481 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.36e-02 5.41e+03 1.51e+00 ... (remaining 15035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20093 2.04 - 4.08: 247 4.08 - 6.12: 73 6.12 - 8.15: 7 8.15 - 10.19: 4 Bond angle restraints: 20424 Sorted by residual: angle pdb=" C ALA B 479 " pdb=" N ASP B 480 " pdb=" CA ASP B 480 " ideal model delta sigma weight residual 121.80 131.99 -10.19 2.44e+00 1.68e-01 1.75e+01 angle pdb=" C ALA A 479 " pdb=" N ASP A 480 " pdb=" CA ASP A 480 " ideal model delta sigma weight residual 121.80 131.91 -10.11 2.44e+00 1.68e-01 1.72e+01 angle pdb=" C ALA C 479 " pdb=" N ASP C 480 " pdb=" CA ASP C 480 " ideal model delta sigma weight residual 121.80 131.90 -10.10 2.44e+00 1.68e-01 1.71e+01 angle pdb=" C ALA D 479 " pdb=" N ASP D 480 " pdb=" CA ASP D 480 " ideal model delta sigma weight residual 121.80 131.87 -10.07 2.44e+00 1.68e-01 1.70e+01 angle pdb=" C ILE A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta sigma weight residual 122.54 116.14 6.40 1.65e+00 3.67e-01 1.51e+01 ... (remaining 20419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 7879 17.05 - 34.10: 735 34.10 - 51.16: 170 51.16 - 68.21: 20 68.21 - 85.26: 12 Dihedral angle restraints: 8816 sinusoidal: 3264 harmonic: 5552 Sorted by residual: dihedral pdb=" CA PHE B 444 " pdb=" C PHE B 444 " pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA PHE A 444 " pdb=" C PHE A 444 " pdb=" N ASP A 445 " pdb=" CA ASP A 445 " ideal model delta harmonic sigma weight residual 180.00 148.08 31.92 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA PHE D 444 " pdb=" C PHE D 444 " pdb=" N ASP D 445 " pdb=" CA ASP D 445 " ideal model delta harmonic sigma weight residual 180.00 148.09 31.91 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 8813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1673 0.042 - 0.084: 478 0.084 - 0.125: 109 0.125 - 0.167: 8 0.167 - 0.209: 4 Chirality restraints: 2272 Sorted by residual: chirality pdb=" CB VAL C 484 " pdb=" CA VAL C 484 " pdb=" CG1 VAL C 484 " pdb=" CG2 VAL C 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL A 484 " pdb=" CA VAL A 484 " pdb=" CG1 VAL A 484 " pdb=" CG2 VAL A 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL B 484 " pdb=" CA VAL B 484 " pdb=" CG1 VAL B 484 " pdb=" CG2 VAL B 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2269 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 479 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ALA D 479 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA D 479 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP D 480 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 479 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C ALA B 479 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA B 479 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP B 480 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 479 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ALA A 479 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 479 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 480 " -0.011 2.00e-02 2.50e+03 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 68 2.46 - 3.07: 10304 3.07 - 3.68: 23898 3.68 - 4.29: 33380 4.29 - 4.90: 55555 Nonbonded interactions: 123205 Sorted by model distance: nonbonded pdb=" OE2 GLU C 282 " pdb=" ND2 ASN C 300 " model vdw 1.845 3.120 nonbonded pdb=" OE2 GLU A 282 " pdb=" ND2 ASN A 300 " model vdw 1.846 3.120 nonbonded pdb=" OE2 GLU B 282 " pdb=" ND2 ASN B 300 " model vdw 1.846 3.120 nonbonded pdb=" OE2 GLU D 282 " pdb=" ND2 ASN D 300 " model vdw 1.847 3.120 nonbonded pdb=" OG SER D 565 " pdb=" OD1 ASP D 567 " model vdw 2.180 3.040 ... (remaining 123200 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 0.035 15040 Z= 0.147 Angle : 0.630 10.193 20424 Z= 0.328 Chirality : 0.041 0.209 2272 Planarity : 0.004 0.032 2576 Dihedral : 14.092 85.259 5232 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1872 helix: 1.17 (0.15), residues: 1284 sheet: 0.23 (0.39), residues: 108 loop : -1.85 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 404 TYR 0.016 0.001 TYR A 411 PHE 0.017 0.001 PHE D 569 TRP 0.011 0.001 TRP D 221 HIS 0.002 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (15040) covalent geometry : angle 0.62960 / 0.33 (20424) hydrogen bonds : bond 0.11760 / 7.88 ( 1021) hydrogen bonds : angle 5.67299 / 4.29 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.561 Fit side-chains REVERT: A 146 ASP cc_start: 0.8012 (t0) cc_final: 0.7722 (t70) REVERT: A 189 ASP cc_start: 0.7308 (t70) cc_final: 0.7106 (t0) REVERT: A 410 LYS cc_start: 0.8281 (ttmt) cc_final: 0.8063 (ttmt) REVERT: B 146 ASP cc_start: 0.8014 (t0) cc_final: 0.7719 (t70) REVERT: B 410 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8071 (ttmt) REVERT: C 146 ASP cc_start: 0.8018 (t0) cc_final: 0.7732 (t70) REVERT: C 410 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8077 (ttmt) REVERT: D 146 ASP cc_start: 0.7999 (t0) cc_final: 0.7725 (t70) REVERT: D 189 ASP cc_start: 0.7304 (t70) cc_final: 0.7096 (t0) REVERT: D 410 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8081 (ttmt) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1037 time to fit residues: 62.4422 Evaluate side-chains 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 GLN C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.196848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163896 restraints weight = 16891.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.168155 restraints weight = 10240.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171024 restraints weight = 7540.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172781 restraints weight = 6235.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173666 restraints weight = 5568.119| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15040 Z= 0.201 Angle : 0.619 6.541 20424 Z= 0.329 Chirality : 0.042 0.145 2272 Planarity : 0.004 0.034 2576 Dihedral : 4.780 31.504 2052 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.73 % Allowed : 9.22 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1872 helix: 1.25 (0.14), residues: 1292 sheet: -0.35 (0.42), residues: 84 loop : -1.72 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 404 TYR 0.018 0.001 TYR A 411 PHE 0.026 0.002 PHE D 464 TRP 0.013 0.002 TRP C 373 HIS 0.006 0.001 HIS C 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (15040) covalent geometry : angle 0.61915 / 0.33 (20424) hydrogen bonds : bond 0.04829 / 3.30 ( 1021) hydrogen bonds : angle 4.98761 / 3.74 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.517 Fit side-chains REVERT: A 146 ASP cc_start: 0.8250 (t0) cc_final: 0.7664 (t70) REVERT: A 226 PHE cc_start: 0.8466 (t80) cc_final: 0.8144 (t80) REVERT: A 379 MET cc_start: 0.7481 (ttp) cc_final: 0.7093 (ttp) REVERT: A 410 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8130 (ttmt) REVERT: B 146 ASP cc_start: 0.8230 (t0) cc_final: 0.7662 (t70) REVERT: B 226 PHE cc_start: 0.8424 (t80) cc_final: 0.8119 (t80) REVERT: B 379 MET cc_start: 0.7483 (ttp) cc_final: 0.7087 (ttp) REVERT: B 410 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8134 (ttmt) REVERT: C 146 ASP cc_start: 0.8270 (t0) cc_final: 0.7677 (t70) REVERT: C 225 ASP cc_start: 0.7783 (m-30) cc_final: 0.7576 (m-30) REVERT: C 226 PHE cc_start: 0.8475 (t80) cc_final: 0.8160 (t80) REVERT: C 353 MET cc_start: 0.7075 (mmm) cc_final: 0.6677 (mmm) REVERT: C 379 MET cc_start: 0.7481 (ttp) cc_final: 0.7099 (ttp) REVERT: C 410 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8142 (ttmt) REVERT: D 146 ASP cc_start: 0.8237 (t0) cc_final: 0.7642 (t70) REVERT: D 226 PHE cc_start: 0.8449 (t80) cc_final: 0.8120 (t80) REVERT: D 379 MET cc_start: 0.7456 (ttp) cc_final: 0.7134 (ttp) REVERT: D 410 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8147 (ttmt) outliers start: 40 outliers final: 25 residues processed: 348 average time/residue: 0.0875 time to fit residues: 49.2097 Evaluate side-chains 350 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 523 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.197450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165044 restraints weight = 16991.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169129 restraints weight = 10560.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171815 restraints weight = 7868.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172979 restraints weight = 6577.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.174320 restraints weight = 6003.660| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15040 Z= 0.156 Angle : 0.584 8.374 20424 Z= 0.307 Chirality : 0.041 0.146 2272 Planarity : 0.004 0.033 2576 Dihedral : 4.678 29.064 2052 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.66 % Allowed : 11.48 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1872 helix: 1.31 (0.14), residues: 1292 sheet: -0.24 (0.41), residues: 84 loop : -1.72 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 112 TYR 0.018 0.001 TYR A 411 PHE 0.018 0.002 PHE A 464 TRP 0.011 0.001 TRP C 373 HIS 0.011 0.002 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (15040) covalent geometry : angle 0.58387 / 0.31 (20424) hydrogen bonds : bond 0.04482 / 3.05 ( 1021) hydrogen bonds : angle 4.77803 / 3.59 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 0.544 Fit side-chains REVERT: A 146 ASP cc_start: 0.8301 (t0) cc_final: 0.7666 (t70) REVERT: A 226 PHE cc_start: 0.8457 (t80) cc_final: 0.8122 (t80) REVERT: A 267 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6719 (ttm170) REVERT: A 353 MET cc_start: 0.7060 (mmm) cc_final: 0.6662 (mmm) REVERT: A 379 MET cc_start: 0.7443 (ttp) cc_final: 0.7052 (ttp) REVERT: B 146 ASP cc_start: 0.8225 (t0) cc_final: 0.7832 (t70) REVERT: B 226 PHE cc_start: 0.8427 (t80) cc_final: 0.8104 (t80) REVERT: B 267 ARG cc_start: 0.7169 (ttm110) cc_final: 0.6649 (ttm170) REVERT: B 379 MET cc_start: 0.7456 (ttp) cc_final: 0.7081 (ttp) REVERT: C 146 ASP cc_start: 0.8306 (t0) cc_final: 0.7740 (t70) REVERT: C 225 ASP cc_start: 0.7752 (m-30) cc_final: 0.7517 (m-30) REVERT: C 226 PHE cc_start: 0.8483 (t80) cc_final: 0.8152 (t80) REVERT: C 356 MET cc_start: 0.6857 (ttm) cc_final: 0.6592 (ttt) REVERT: C 410 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8116 (ttmt) REVERT: D 146 ASP cc_start: 0.8287 (t0) cc_final: 0.7658 (t70) REVERT: D 226 PHE cc_start: 0.8440 (t80) cc_final: 0.8107 (t80) REVERT: D 267 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6625 (ttm170) REVERT: D 353 MET cc_start: 0.7064 (mmm) cc_final: 0.6656 (mmm) REVERT: D 410 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7858 (ttmm) outliers start: 39 outliers final: 33 residues processed: 367 average time/residue: 0.0921 time to fit residues: 53.2367 Evaluate side-chains 365 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166036 restraints weight = 17076.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.170079 restraints weight = 10492.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172838 restraints weight = 7765.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.174067 restraints weight = 6484.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.175435 restraints weight = 5900.332| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15040 Z= 0.148 Angle : 0.583 8.529 20424 Z= 0.302 Chirality : 0.041 0.148 2272 Planarity : 0.004 0.035 2576 Dihedral : 4.621 28.040 2052 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.60 % Allowed : 15.37 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1872 helix: 1.42 (0.14), residues: 1288 sheet: -0.04 (0.41), residues: 84 loop : -1.73 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 270 TYR 0.018 0.001 TYR B 558 PHE 0.017 0.001 PHE D 464 TRP 0.010 0.001 TRP D 373 HIS 0.009 0.002 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15040) covalent geometry : angle 0.58266 / 0.30 (20424) hydrogen bonds : bond 0.04274 / 2.91 ( 1021) hydrogen bonds : angle 4.69841 / 3.54 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 0.536 Fit side-chains REVERT: A 146 ASP cc_start: 0.8273 (t0) cc_final: 0.7848 (t70) REVERT: A 443 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7379 (ttt) REVERT: A 513 TYR cc_start: 0.7648 (m-80) cc_final: 0.7439 (m-80) REVERT: B 146 ASP cc_start: 0.8308 (t0) cc_final: 0.7836 (t70) REVERT: B 513 TYR cc_start: 0.7674 (m-80) cc_final: 0.7454 (m-80) REVERT: C 146 ASP cc_start: 0.8309 (t0) cc_final: 0.7944 (t70) REVERT: C 225 ASP cc_start: 0.7790 (m-30) cc_final: 0.7571 (m-30) REVERT: C 513 TYR cc_start: 0.7663 (m-80) cc_final: 0.7423 (m-80) REVERT: D 146 ASP cc_start: 0.8288 (t0) cc_final: 0.7846 (t70) REVERT: D 513 TYR cc_start: 0.7669 (m-80) cc_final: 0.7454 (m-80) outliers start: 38 outliers final: 30 residues processed: 356 average time/residue: 0.0890 time to fit residues: 50.7932 Evaluate side-chains 351 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 149 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 300 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.197351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164308 restraints weight = 16989.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.168286 restraints weight = 10629.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170962 restraints weight = 7916.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172595 restraints weight = 6644.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.173320 restraints weight = 5991.845| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15040 Z= 0.171 Angle : 0.603 8.982 20424 Z= 0.311 Chirality : 0.041 0.150 2272 Planarity : 0.004 0.036 2576 Dihedral : 4.623 27.432 2052 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.28 % Allowed : 14.82 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1872 helix: 1.35 (0.14), residues: 1296 sheet: 0.07 (0.41), residues: 84 loop : -1.86 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.019 0.002 TYR B 558 PHE 0.017 0.002 PHE A 464 TRP 0.010 0.001 TRP C 373 HIS 0.008 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15040) covalent geometry : angle 0.60322 / 0.31 (20424) hydrogen bonds : bond 0.04332 / 2.95 ( 1021) hydrogen bonds : angle 4.66837 / 3.51 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 0.531 Fit side-chains REVERT: A 146 ASP cc_start: 0.8305 (t0) cc_final: 0.7937 (t70) REVERT: B 146 ASP cc_start: 0.8309 (t0) cc_final: 0.7831 (t70) REVERT: C 146 ASP cc_start: 0.8356 (t0) cc_final: 0.7991 (t70) REVERT: C 225 ASP cc_start: 0.7870 (m-30) cc_final: 0.7602 (m-30) REVERT: D 146 ASP cc_start: 0.8310 (t0) cc_final: 0.7929 (t70) outliers start: 48 outliers final: 34 residues processed: 337 average time/residue: 0.0867 time to fit residues: 47.7326 Evaluate side-chains 352 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 0.0050 chunk 185 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.198994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.166621 restraints weight = 16880.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170691 restraints weight = 10428.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173413 restraints weight = 7709.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.175060 restraints weight = 6444.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175376 restraints weight = 5792.729| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15040 Z= 0.138 Angle : 0.591 8.376 20424 Z= 0.303 Chirality : 0.040 0.155 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.595 26.435 2052 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.14 % Allowed : 16.33 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1872 helix: 1.45 (0.14), residues: 1288 sheet: 0.19 (0.42), residues: 84 loop : -1.82 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.020 0.002 TYR A 558 PHE 0.016 0.002 PHE D 464 TRP 0.009 0.001 TRP D 373 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15040) covalent geometry : angle 0.59105 / 0.30 (20424) hydrogen bonds : bond 0.04133 / 2.81 ( 1021) hydrogen bonds : angle 4.61989 / 3.48 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.479 Fit side-chains REVERT: A 146 ASP cc_start: 0.8286 (t0) cc_final: 0.7916 (t70) REVERT: A 226 PHE cc_start: 0.8327 (t80) cc_final: 0.8057 (t80) REVERT: B 146 ASP cc_start: 0.8321 (t0) cc_final: 0.8005 (t70) REVERT: C 146 ASP cc_start: 0.8343 (t0) cc_final: 0.7999 (t70) REVERT: C 226 PHE cc_start: 0.8377 (t80) cc_final: 0.8130 (t80) REVERT: D 146 ASP cc_start: 0.8281 (t0) cc_final: 0.7904 (t70) REVERT: D 226 PHE cc_start: 0.8329 (t80) cc_final: 0.8055 (t80) outliers start: 46 outliers final: 34 residues processed: 338 average time/residue: 0.0847 time to fit residues: 46.9784 Evaluate side-chains 342 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.0010 chunk 107 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 162 optimal weight: 0.0570 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.200571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.168513 restraints weight = 16860.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172686 restraints weight = 10342.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.175443 restraints weight = 7649.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.177131 restraints weight = 6382.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177826 restraints weight = 5722.735| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15040 Z= 0.128 Angle : 0.580 9.386 20424 Z= 0.296 Chirality : 0.040 0.152 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.548 25.057 2052 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.42 % Allowed : 16.46 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1872 helix: 1.47 (0.14), residues: 1292 sheet: 0.36 (0.43), residues: 84 loop : -1.90 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.023 0.001 TYR B 217 PHE 0.015 0.001 PHE C 464 TRP 0.013 0.001 TRP B 145 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (15040) covalent geometry : angle 0.58008 / 0.30 (20424) hydrogen bonds : bond 0.04025 / 2.74 ( 1021) hydrogen bonds : angle 4.56508 / 3.44 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 0.545 Fit side-chains REVERT: A 146 ASP cc_start: 0.8342 (t0) cc_final: 0.7977 (t70) REVERT: A 226 PHE cc_start: 0.8427 (t80) cc_final: 0.8163 (t80) REVERT: B 146 ASP cc_start: 0.8378 (t0) cc_final: 0.7988 (t70) REVERT: C 146 ASP cc_start: 0.8416 (t0) cc_final: 0.8031 (t70) REVERT: C 225 ASP cc_start: 0.7855 (m-30) cc_final: 0.7624 (m-30) REVERT: C 226 PHE cc_start: 0.8390 (t80) cc_final: 0.8106 (t80) REVERT: D 146 ASP cc_start: 0.8343 (t0) cc_final: 0.7977 (t70) REVERT: D 226 PHE cc_start: 0.8428 (t80) cc_final: 0.8163 (t80) outliers start: 50 outliers final: 36 residues processed: 337 average time/residue: 0.0859 time to fit residues: 47.4023 Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 128 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 138 optimal weight: 0.2980 chunk 144 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.197699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.164868 restraints weight = 17186.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169012 restraints weight = 10618.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171766 restraints weight = 7890.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173398 restraints weight = 6598.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.174197 restraints weight = 5945.312| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15040 Z= 0.168 Angle : 0.598 9.392 20424 Z= 0.307 Chirality : 0.041 0.153 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.560 25.544 2052 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.69 % Allowed : 17.35 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1872 helix: 1.37 (0.14), residues: 1296 sheet: 0.37 (0.44), residues: 84 loop : -1.86 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.018 0.002 TYR B 411 PHE 0.016 0.002 PHE D 464 TRP 0.014 0.001 TRP C 145 HIS 0.007 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (15040) covalent geometry : angle 0.59805 / 0.31 (20424) hydrogen bonds : bond 0.04181 / 2.83 ( 1021) hydrogen bonds : angle 4.59544 / 3.46 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.488 Fit side-chains REVERT: A 146 ASP cc_start: 0.8346 (t0) cc_final: 0.7953 (t70) REVERT: B 146 ASP cc_start: 0.8417 (t0) cc_final: 0.7975 (t70) REVERT: C 146 ASP cc_start: 0.8423 (t0) cc_final: 0.8036 (t70) REVERT: C 225 ASP cc_start: 0.7862 (m-30) cc_final: 0.7595 (m-30) REVERT: D 146 ASP cc_start: 0.8337 (t0) cc_final: 0.7929 (t70) outliers start: 54 outliers final: 50 residues processed: 333 average time/residue: 0.0861 time to fit residues: 46.8769 Evaluate side-chains 351 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 15 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN A 437 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN D 437 HIS ** D 465 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 = 0.4177 r_free = 0.4177 target = 0.199262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.166870 restraints weight = 17048.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.170909 restraints weight = 10567.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173660 restraints weight = 7807.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175243 restraints weight = 6533.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.175972 restraints weight = 5882.844| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15040 Z= 0.138 Angle : 0.622 9.953 20424 Z= 0.312 Chirality : 0.041 0.164 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.587 24.962 2052 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.42 % Allowed : 18.78 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1872 helix: 1.43 (0.14), residues: 1292 sheet: 0.45 (0.44), residues: 84 loop : -1.95 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.016 0.001 TYR B 411 PHE 0.019 0.002 PHE B 186 TRP 0.018 0.001 TRP B 145 HIS 0.006 0.001 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15040) covalent geometry : angle 0.62210 / 0.31 (20424) hydrogen bonds : bond 0.04057 / 2.75 ( 1021) hydrogen bonds : angle 4.59406 / 3.46 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 0.468 Fit side-chains REVERT: C 146 ASP cc_start: 0.8412 (t0) cc_final: 0.8047 (t70) REVERT: C 225 ASP cc_start: 0.7900 (m-30) cc_final: 0.7614 (m-30) outliers start: 50 outliers final: 41 residues processed: 332 average time/residue: 0.0819 time to fit residues: 44.3900 Evaluate side-chains 342 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 137 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 166 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.200343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167322 restraints weight = 16951.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171769 restraints weight = 10082.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174741 restraints weight = 7260.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.176309 restraints weight = 5979.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177567 restraints weight = 5363.935| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15040 Z= 0.132 Angle : 0.597 10.134 20424 Z= 0.303 Chirality : 0.040 0.156 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.544 24.333 2052 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.21 % Allowed : 18.92 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1872 helix: 1.44 (0.14), residues: 1296 sheet: 0.42 (0.44), residues: 84 loop : -1.87 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 270 TYR 0.029 0.001 TYR A 558 PHE 0.020 0.001 PHE C 186 TRP 0.015 0.001 TRP B 145 HIS 0.006 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15040) covalent geometry : angle 0.59692 / 0.30 (20424) hydrogen bonds : bond 0.04025 / 2.72 ( 1021) hydrogen bonds : angle 4.57900 / 3.44 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.606 Fit side-chains REVERT: A 299 PHE cc_start: 0.8136 (m-80) cc_final: 0.7929 (m-80) REVERT: C 146 ASP cc_start: 0.8519 (t0) cc_final: 0.8051 (t70) REVERT: C 225 ASP cc_start: 0.7897 (m-30) cc_final: 0.7623 (m-30) REVERT: C 226 PHE cc_start: 0.8380 (t80) cc_final: 0.8092 (t80) REVERT: D 299 PHE cc_start: 0.8143 (m-80) cc_final: 0.7940 (m-80) outliers start: 47 outliers final: 31 residues processed: 326 average time/residue: 0.0848 time to fit residues: 45.1024 Evaluate side-chains 327 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 109 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.199315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165947 restraints weight = 16991.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170453 restraints weight = 10122.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173387 restraints weight = 7351.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174903 restraints weight = 6068.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.176215 restraints weight = 5449.989| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15040 Z= 0.148 Angle : 0.637 10.169 20424 Z= 0.319 Chirality : 0.041 0.169 2272 Planarity : 0.004 0.037 2576 Dihedral : 4.556 24.438 2052 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.73 % Allowed : 19.54 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1872 helix: 1.42 (0.14), residues: 1300 sheet: 0.39 (0.45), residues: 84 loop : -1.86 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.024 0.001 TYR B 558 PHE 0.018 0.002 PHE D 226 TRP 0.013 0.001 TRP B 145 HIS 0.006 0.001 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (15040) covalent geometry : angle 0.63734 / 0.32 (20424) hydrogen bonds : bond 0.04083 / 2.75 ( 1021) hydrogen bonds : angle 4.57986 / 3.44 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.70 seconds wall clock time: 42 minutes 32.66 seconds (2552.66 seconds total)