Starting phenix.real_space_refine on Thu Sep 26 11:47:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwf_26831/09_2024/7uwf_26831.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.274 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 94 5.16 5 C 8394 2.51 5 N 2306 2.21 5 O 2380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2725 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved chain links: 3 Chain breaks: 1 Unresolved chain link angles: 9 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3862 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 32, 'TRANS': 486} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2725 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved chain links: 3 Chain breaks: 1 Unresolved chain link angles: 9 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3862 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 32, 'TRANS': 486} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 7.89, per 1000 atoms: 0.60 Number of scatterers: 13174 At special positions: 0 Unit cell: (93.984, 108.768, 107.712, 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 94 16.00 O 2380 8.00 N 2306 7.00 C 8394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 52.4% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.521A pdb=" N LEU A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 101 removed outlier: 3.605A pdb=" N SER C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 120 through 140 removed outlier: 3.506A pdb=" N GLN C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 165 through 186 removed outlier: 3.606A pdb=" N ARG C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.268A pdb=" N SER C 212 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.930A pdb=" N SER C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 249 through 279 removed outlier: 5.338A pdb=" N LYS C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 327 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.579A pdb=" N ILE C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 388 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 389 through 393 removed outlier: 4.335A pdb=" N ARG C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 409 Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 424 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.229A pdb=" N GLY C 455 " --> pdb=" O GLY C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 537 Processing helix chain 'C' and resid 541 through 561 Proline residue: C 554 - end of helix removed outlier: 4.065A pdb=" N GLN C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 561 " --> pdb=" O MET C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 571 Processing helix chain 'C' and resid 572 through 589 Processing helix chain 'C' and resid 597 through 609 Processing helix chain 'C' and resid 613 through 632 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.522A pdb=" N LEU B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.605A pdb=" N SER D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 120 through 140 removed outlier: 3.507A pdb=" N GLN D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 163 Processing helix chain 'D' and resid 165 through 186 removed outlier: 3.606A pdb=" N ARG D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.269A pdb=" N SER D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 226 removed outlier: 3.931A pdb=" N SER D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 249 through 279 removed outlier: 5.337A pdb=" N LYS D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS D 256 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 327 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.580A pdb=" N ILE D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 388 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 389 through 393 removed outlier: 4.335A pdb=" N ARG D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 Proline residue: D 403 - end of helix Processing helix chain 'D' and resid 424 through 443 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 451 through 467 removed outlier: 4.229A pdb=" N GLY D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 537 Processing helix chain 'D' and resid 541 through 561 Proline residue: D 554 - end of helix removed outlier: 4.065A pdb=" N GLN D 560 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 Processing helix chain 'D' and resid 572 through 589 Processing helix chain 'D' and resid 597 through 609 Processing helix chain 'D' and resid 613 through 632 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.952A pdb=" N ASN A 30 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU A 24 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 47 removed outlier: 5.844A pdb=" N ALA A 55 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ARG A 42 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N LEU A 53 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N LEU A 44 " --> pdb=" O TYR A 51 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N TYR A 51 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 61 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.609A pdb=" N VAL A 115 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU A 107 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 113 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 180 removed outlier: 3.557A pdb=" N ASP A 177 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU A 202 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 208 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 223 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.909A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 293 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 306 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 295 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 302 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.951A pdb=" N ASN B 30 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 24 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 47 removed outlier: 5.844A pdb=" N ALA B 55 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ARG B 42 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N LEU B 53 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU B 44 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N TYR B 51 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR B 61 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.611A pdb=" N VAL B 115 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B 107 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 113 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 180 removed outlier: 3.556A pdb=" N ASP B 177 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 202 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 208 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 223 Processing sheet with id=AB6, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.909A pdb=" N THR B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 293 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 306 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 295 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 302 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 398 782 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 3.72 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: 4330 1.34 - 1.46: 2720 1.46 - 1.58: 6254 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 13430 Sorted by residual: bond pdb=" SD MET D 70 " pdb=" CE MET D 70 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" SD MET C 70 " pdb=" CE MET C 70 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.89e+00 bond pdb=" CB VAL A 283 " pdb=" CG1 VAL A 283 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL B 283 " pdb=" CG1 VAL B 283 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG LEU B 412 " pdb=" CD1 LEU B 412 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 13425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 17639 1.49 - 2.97: 486 2.97 - 4.46: 95 4.46 - 5.94: 28 5.94 - 7.43: 4 Bond angle restraints: 18252 Sorted by residual: angle pdb=" C LEU A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta sigma weight residual 121.14 116.41 4.73 1.75e+00 3.27e-01 7.30e+00 angle pdb=" C LEU B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta sigma weight residual 121.14 116.42 4.72 1.75e+00 3.27e-01 7.29e+00 angle pdb=" C LEU C 534 " pdb=" N MET C 535 " pdb=" CA MET C 535 " ideal model delta sigma weight residual 121.92 117.87 4.05 1.73e+00 3.34e-01 5.47e+00 angle pdb=" C LEU D 534 " pdb=" N MET D 535 " pdb=" CA MET D 535 " ideal model delta sigma weight residual 121.92 117.90 4.02 1.73e+00 3.34e-01 5.41e+00 angle pdb=" N ARG B 413 " pdb=" CA ARG B 413 " pdb=" CB ARG B 413 " ideal model delta sigma weight residual 110.40 114.03 -3.63 1.63e+00 3.76e-01 4.97e+00 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 7446 16.24 - 32.47: 522 32.47 - 48.71: 88 48.71 - 64.94: 18 64.94 - 81.18: 14 Dihedral angle restraints: 8088 sinusoidal: 3070 harmonic: 5018 Sorted by residual: dihedral pdb=" CA TRP A 65 " pdb=" C TRP A 65 " pdb=" N GLU A 66 " pdb=" CA GLU A 66 " ideal model delta harmonic sigma weight residual 180.00 164.37 15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA TRP B 65 " pdb=" C TRP B 65 " pdb=" N GLU B 66 " pdb=" CA GLU B 66 " ideal model delta harmonic sigma weight residual 180.00 164.40 15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" CA SER D 519 " pdb=" C SER D 519 " pdb=" N ASP D 520 " pdb=" CA ASP D 520 " ideal model delta harmonic sigma weight residual 180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.65e+00 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1617 0.041 - 0.082: 389 0.082 - 0.122: 154 0.122 - 0.163: 19 0.163 - 0.204: 3 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CG LEU D 37 " pdb=" CB LEU D 37 " pdb=" CD1 LEU D 37 " pdb=" CD2 LEU D 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU C 37 " pdb=" CB LEU C 37 " pdb=" CD1 LEU C 37 " pdb=" CD2 LEU C 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ARG B 413 " pdb=" N ARG B 413 " pdb=" C ARG B 413 " pdb=" CB ARG B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2179 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 165 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 166 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 165 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO C 166 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 173 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C SER D 173 " 0.034 2.00e-02 2.50e+03 pdb=" O SER D 173 " -0.013 2.00e-02 2.50e+03 pdb=" N MET D 174 " -0.012 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 160 2.68 - 3.24: 12733 3.24 - 3.79: 21540 3.79 - 4.35: 29247 4.35 - 4.90: 48540 Nonbonded interactions: 112220 Sorted by model distance: nonbonded pdb=" OH TYR D 432 " pdb=" OD2 ASP D 465 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR C 432 " pdb=" OD2 ASP C 465 " model vdw 2.127 3.040 nonbonded pdb=" O LEU D 115 " pdb=" OG SER D 119 " model vdw 2.145 3.040 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.145 3.040 nonbonded pdb=" O LEU D 38 " pdb=" OG SER D 42 " model vdw 2.277 3.040 ... (remaining 112215 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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 individual isotropic 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.037 13430 Z= 0.233 Angle : 0.617 7.430 18252 Z= 0.310 Chirality : 0.043 0.204 2182 Planarity : 0.005 0.064 2310 Dihedral : 12.055 81.179 4832 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1708 helix: 2.14 (0.18), residues: 816 sheet: 0.32 (0.30), residues: 278 loop : -0.27 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 201 HIS 0.005 0.001 HIS D 373 PHE 0.026 0.002 PHE D 619 TYR 0.017 0.002 TYR D 240 ARG 0.012 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.439 Fit side-chains REVERT: C 520 ASP cc_start: 0.6601 (t0) cc_final: 0.6285 (t0) REVERT: C 535 MET cc_start: 0.8255 (mmm) cc_final: 0.7904 (mmm) REVERT: B 310 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7984 (mptt) REVERT: B 325 MET cc_start: 0.8491 (mtt) cc_final: 0.8254 (mtt) REVERT: D 70 MET cc_start: 0.7211 (mmm) cc_final: 0.6946 (tpt) REVERT: D 240 TYR cc_start: 0.8259 (t80) cc_final: 0.8058 (t80) REVERT: D 308 LEU cc_start: 0.8375 (mt) cc_final: 0.8164 (tp) REVERT: D 535 MET cc_start: 0.8216 (mmm) cc_final: 0.7901 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 1.4752 time to fit residues: 389.2828 Evaluate side-chains 197 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13430 Z= 0.194 Angle : 0.573 9.281 18252 Z= 0.291 Chirality : 0.041 0.175 2182 Planarity : 0.005 0.048 2310 Dihedral : 4.088 15.472 1856 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 7.91 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1708 helix: 2.70 (0.18), residues: 818 sheet: 0.61 (0.31), residues: 278 loop : -0.40 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 201 HIS 0.004 0.001 HIS A 120 PHE 0.018 0.002 PHE B 136 TYR 0.012 0.001 TYR A 121 ARG 0.007 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 1.542 Fit side-chains REVERT: A 413 ARG cc_start: 0.6369 (mpp-170) cc_final: 0.5422 (mtm-85) REVERT: C 188 ARG cc_start: 0.6883 (mtm-85) cc_final: 0.6520 (mtm-85) REVERT: C 436 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: C 593 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7161 (ptt-90) REVERT: B 72 GLN cc_start: 0.5356 (tp40) cc_final: 0.4881 (tp40) REVERT: B 282 SER cc_start: 0.8464 (p) cc_final: 0.8191 (p) REVERT: B 305 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6995 (ttp80) REVERT: B 310 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7992 (mptt) REVERT: B 325 MET cc_start: 0.8509 (mtt) cc_final: 0.8290 (mtt) REVERT: D 197 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: D 262 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: D 520 ASP cc_start: 0.6658 (t0) cc_final: 0.6380 (t0) REVERT: D 535 MET cc_start: 0.8242 (mmm) cc_final: 0.8010 (mmm) REVERT: D 577 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7531 (ttp80) outliers start: 28 outliers final: 6 residues processed: 228 average time/residue: 1.4997 time to fit residues: 367.5101 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN C 193 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13430 Z= 0.173 Angle : 0.543 7.720 18252 Z= 0.273 Chirality : 0.040 0.188 2182 Planarity : 0.005 0.042 2310 Dihedral : 3.959 14.902 1856 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.73 % Allowed : 11.23 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.21), residues: 1708 helix: 2.88 (0.18), residues: 820 sheet: 0.75 (0.31), residues: 278 loop : -0.42 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 201 HIS 0.004 0.001 HIS B 120 PHE 0.017 0.002 PHE B 136 TYR 0.016 0.001 TYR B 61 ARG 0.005 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.715 Fit side-chains REVERT: A 72 GLN cc_start: 0.5037 (tp40) cc_final: 0.4707 (tp40) REVERT: C 174 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5855 (mpp) REVERT: C 188 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6628 (mtm-85) REVERT: C 436 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: C 593 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7058 (ptt-90) REVERT: B 72 GLN cc_start: 0.5253 (tp40) cc_final: 0.4943 (tp40) REVERT: B 282 SER cc_start: 0.8485 (p) cc_final: 0.8236 (p) REVERT: B 310 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7970 (mptt) REVERT: B 325 MET cc_start: 0.8527 (mtt) cc_final: 0.8262 (mtt) REVERT: D 197 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 262 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: D 577 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7565 (ttp80) outliers start: 25 outliers final: 7 residues processed: 226 average time/residue: 1.5390 time to fit residues: 374.0422 Evaluate side-chains 219 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.5980 chunk 119 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 158 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 140 optimal weight: 5.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN C 373 HIS B 299 GLN D 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13430 Z= 0.152 Angle : 0.522 7.081 18252 Z= 0.261 Chirality : 0.040 0.170 2182 Planarity : 0.005 0.074 2310 Dihedral : 3.849 15.013 1856 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.60 % Allowed : 12.21 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.21), residues: 1708 helix: 3.01 (0.18), residues: 822 sheet: 0.80 (0.32), residues: 266 loop : -0.43 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 201 HIS 0.003 0.001 HIS A 120 PHE 0.015 0.001 PHE B 136 TYR 0.016 0.001 TYR B 61 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.410 Fit side-chains REVERT: A 72 GLN cc_start: 0.5109 (tp40) cc_final: 0.4836 (tp40) REVERT: A 207 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: C 70 MET cc_start: 0.7043 (mmm) cc_final: 0.6828 (mmm) REVERT: C 188 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6600 (mtm-85) REVERT: C 262 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: C 436 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: C 593 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7070 (ptt-90) REVERT: B 72 GLN cc_start: 0.5375 (tp40) cc_final: 0.4920 (tp40) REVERT: B 207 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: B 282 SER cc_start: 0.8480 (p) cc_final: 0.8217 (p) REVERT: B 295 LEU cc_start: 0.9056 (mm) cc_final: 0.8677 (mm) REVERT: B 310 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7987 (mptt) REVERT: B 325 MET cc_start: 0.8611 (mtt) cc_final: 0.8354 (mtt) REVERT: D 197 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: D 262 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: D 577 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7534 (ttp80) outliers start: 23 outliers final: 5 residues processed: 216 average time/residue: 1.6105 time to fit residues: 372.5328 Evaluate side-chains 208 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 234 GLN D 373 HIS D 560 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13430 Z= 0.212 Angle : 0.566 7.624 18252 Z= 0.282 Chirality : 0.041 0.136 2182 Planarity : 0.005 0.043 2310 Dihedral : 3.979 15.631 1856 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.87 % Allowed : 13.80 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.21), residues: 1708 helix: 2.96 (0.18), residues: 822 sheet: 0.80 (0.32), residues: 278 loop : -0.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 201 HIS 0.004 0.001 HIS C 373 PHE 0.019 0.002 PHE B 136 TYR 0.016 0.002 TYR B 61 ARG 0.005 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.601 Fit side-chains REVERT: A 72 GLN cc_start: 0.5250 (tp40) cc_final: 0.5010 (tp40) REVERT: C 188 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6624 (mtm-85) REVERT: C 262 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: C 436 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: C 593 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7118 (ptt-90) REVERT: B 72 GLN cc_start: 0.5417 (tp40) cc_final: 0.4993 (tp40) REVERT: B 282 SER cc_start: 0.8537 (p) cc_final: 0.8326 (p) REVERT: B 325 MET cc_start: 0.8611 (mtt) cc_final: 0.8313 (mtt) REVERT: D 197 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: D 262 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: D 577 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7615 (ttp80) outliers start: 27 outliers final: 9 residues processed: 212 average time/residue: 1.5466 time to fit residues: 352.2253 Evaluate side-chains 214 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 164 GLN D 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13430 Z= 0.251 Angle : 0.595 8.482 18252 Z= 0.296 Chirality : 0.042 0.147 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.119 16.426 1856 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 14.70 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1708 helix: 2.82 (0.18), residues: 820 sheet: 0.69 (0.31), residues: 280 loop : -0.44 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 201 HIS 0.005 0.001 HIS C 373 PHE 0.020 0.002 PHE A 136 TYR 0.016 0.002 TYR B 61 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.480 Fit side-chains REVERT: A 72 GLN cc_start: 0.5258 (tp40) cc_final: 0.4990 (tp40) REVERT: C 188 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6648 (mtm-85) REVERT: C 262 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: C 436 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: C 593 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7006 (ptt-90) REVERT: B 72 GLN cc_start: 0.5397 (tp40) cc_final: 0.4926 (tp40) REVERT: B 325 MET cc_start: 0.8601 (mtt) cc_final: 0.8308 (mtt) REVERT: D 73 LEU cc_start: 0.8097 (tp) cc_final: 0.7867 (mt) REVERT: D 197 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: D 262 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: D 436 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: D 577 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7628 (ttp80) outliers start: 27 outliers final: 10 residues processed: 216 average time/residue: 1.4983 time to fit residues: 348.5550 Evaluate side-chains 216 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13430 Z= 0.170 Angle : 0.547 8.290 18252 Z= 0.274 Chirality : 0.040 0.219 2182 Planarity : 0.004 0.042 2310 Dihedral : 3.953 16.886 1856 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 15.67 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1708 helix: 2.92 (0.18), residues: 820 sheet: 0.82 (0.31), residues: 278 loop : -0.43 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 201 HIS 0.004 0.001 HIS B 120 PHE 0.017 0.002 PHE D 169 TYR 0.016 0.001 TYR A 61 ARG 0.007 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.441 Fit side-chains REVERT: A 72 GLN cc_start: 0.5300 (tp40) cc_final: 0.5070 (tp40) REVERT: C 188 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6611 (mtm-85) REVERT: C 262 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: C 436 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: C 593 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6980 (ptt-90) REVERT: B 325 MET cc_start: 0.8597 (mtt) cc_final: 0.8311 (mtt) REVERT: D 197 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: D 262 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: D 436 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: D 560 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6568 (mt0) REVERT: D 577 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7618 (ttp80) outliers start: 21 outliers final: 7 residues processed: 216 average time/residue: 1.5154 time to fit residues: 351.5626 Evaluate side-chains 213 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13430 Z= 0.177 Angle : 0.558 8.247 18252 Z= 0.277 Chirality : 0.040 0.176 2182 Planarity : 0.004 0.042 2310 Dihedral : 3.945 16.576 1856 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.25 % Allowed : 16.16 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.21), residues: 1708 helix: 2.90 (0.18), residues: 820 sheet: 0.75 (0.32), residues: 268 loop : -0.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 201 HIS 0.004 0.001 HIS B 120 PHE 0.017 0.002 PHE D 169 TYR 0.016 0.001 TYR A 61 ARG 0.008 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 1.447 Fit side-chains REVERT: A 207 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 188 ARG cc_start: 0.6897 (mtm-85) cc_final: 0.6613 (mtm-85) REVERT: C 262 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: C 436 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 593 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6969 (ptt-90) REVERT: B 69 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6539 (ttm-80) REVERT: B 325 MET cc_start: 0.8609 (mtt) cc_final: 0.8351 (mtt) REVERT: D 197 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: D 262 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: D 560 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6567 (mt0) REVERT: D 577 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7630 (ttp80) outliers start: 18 outliers final: 8 residues processed: 207 average time/residue: 1.5371 time to fit residues: 342.7812 Evaluate side-chains 213 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13430 Z= 0.172 Angle : 0.554 8.227 18252 Z= 0.276 Chirality : 0.040 0.157 2182 Planarity : 0.004 0.042 2310 Dihedral : 3.903 16.797 1856 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.46 % Allowed : 16.23 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.21), residues: 1708 helix: 2.92 (0.18), residues: 820 sheet: 0.87 (0.32), residues: 278 loop : -0.39 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 201 HIS 0.003 0.001 HIS B 120 PHE 0.019 0.002 PHE D 169 TYR 0.017 0.001 TYR A 61 ARG 0.009 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.614 Fit side-chains REVERT: A 207 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 70 MET cc_start: 0.6518 (mmm) cc_final: 0.6240 (tpt) REVERT: C 188 ARG cc_start: 0.6886 (mtm-85) cc_final: 0.6619 (mtm-85) REVERT: C 262 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: C 436 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 593 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6945 (ptt-90) REVERT: B 69 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6520 (ttm-80) REVERT: B 325 MET cc_start: 0.8613 (mtt) cc_final: 0.8350 (mtt) REVERT: D 70 MET cc_start: 0.6879 (mmm) cc_final: 0.6583 (tpt) REVERT: D 197 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: D 262 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: D 560 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6551 (mt0) REVERT: D 577 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7625 (ttp80) outliers start: 21 outliers final: 10 residues processed: 210 average time/residue: 1.5796 time to fit residues: 356.7595 Evaluate side-chains 215 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13430 Z= 0.265 Angle : 0.624 8.780 18252 Z= 0.309 Chirality : 0.043 0.171 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.177 16.430 1856 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.32 % Allowed : 16.23 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1708 helix: 2.73 (0.18), residues: 820 sheet: 0.74 (0.31), residues: 280 loop : -0.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 201 HIS 0.005 0.001 HIS C 373 PHE 0.020 0.002 PHE B 136 TYR 0.017 0.002 TYR A 61 ARG 0.008 0.000 ARG C 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.407 Fit side-chains REVERT: C 188 ARG cc_start: 0.6869 (mtm-85) cc_final: 0.6575 (mtm-85) REVERT: C 262 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: C 436 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: C 593 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7028 (ptt-90) REVERT: B 69 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6672 (ttm-80) REVERT: B 325 MET cc_start: 0.8579 (mtt) cc_final: 0.8349 (mtt) REVERT: D 197 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: D 262 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 520 ASP cc_start: 0.8527 (m-30) cc_final: 0.8303 (m-30) REVERT: D 560 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6534 (mt0) REVERT: D 577 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7654 (ttp80) outliers start: 19 outliers final: 9 residues processed: 213 average time/residue: 1.5287 time to fit residues: 349.5571 Evaluate side-chains 214 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 0.0270 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132263 restraints weight = 13296.690| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.30 r_work: 0.3244 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13430 Z= 0.187 Angle : 0.580 9.126 18252 Z= 0.288 Chirality : 0.041 0.167 2182 Planarity : 0.005 0.042 2310 Dihedral : 4.039 16.660 1856 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.46 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.21), residues: 1708 helix: 2.83 (0.18), residues: 820 sheet: 0.82 (0.31), residues: 278 loop : -0.42 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 201 HIS 0.004 0.001 HIS B 120 PHE 0.020 0.002 PHE D 169 TYR 0.017 0.002 TYR A 61 ARG 0.008 0.000 ARG C 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5602.80 seconds wall clock time: 98 minutes 23.53 seconds (5903.53 seconds total)