Starting phenix.real_space_refine on Sun Dec 29 18:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydi_33748/12_2024/7ydi_33748.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1490 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6144 2.51 5 N 1602 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1530 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.89, per 1000 atoms: 0.71 Number of scatterers: 9675 At special positions: 0 Unit cell: (108.416, 160.512, 95.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1878 8.00 N 1602 7.00 C 6144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 53 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 35.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.802A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.726A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.750A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.975A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.535A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.800A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.902A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.582A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.667A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.852A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.039A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.512A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.206A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.736A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.676A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.594A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.717A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.091A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.571A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.177A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.476A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.511A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.520A pdb=" N GLU H 10 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.548A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS H 151 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.743A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 164 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN H 208 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 87 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN L 40 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 23 Processing sheet with id=AB5, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.176A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 141 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 179 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP L 143 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.646A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1071 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: 2.87 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3101 1.35 - 1.46: 2498 1.46 - 1.58: 4259 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9931 Sorted by residual: bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C GLU H 159 " pdb=" N PRO H 160 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CB GLN H 65 " pdb=" CG GLN H 65 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 9926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13284 2.32 - 4.65: 183 4.65 - 6.97: 36 6.97 - 9.29: 13 9.29 - 11.62: 3 Bond angle restraints: 13519 Sorted by residual: angle pdb=" CB MET A 557 " pdb=" CG MET A 557 " pdb=" SD MET A 557 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA GLU A 110 " pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET A 82 " pdb=" CB MET A 82 " pdb=" CG MET A 82 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET A 332 " pdb=" CG MET A 332 " pdb=" SD MET A 332 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB LYS E 458 " pdb=" CG LYS E 458 " pdb=" CD LYS E 458 " ideal model delta sigma weight residual 111.30 119.23 -7.93 2.30e+00 1.89e-01 1.19e+01 ... (remaining 13514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5333 17.87 - 35.74: 455 35.74 - 53.61: 126 53.61 - 71.47: 18 71.47 - 89.34: 9 Dihedral angle restraints: 5941 sinusoidal: 2365 harmonic: 3576 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 139.36 -46.36 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -47.98 -38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA ILE H 51 " pdb=" C ILE H 51 " pdb=" N ILE H 52 " pdb=" CA ILE H 52 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1310 0.073 - 0.145: 155 0.145 - 0.218: 3 0.218 - 0.290: 1 0.290 - 0.363: 1 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB THR A 334 " pdb=" CA THR A 334 " pdb=" OG1 THR A 334 " pdb=" CG2 THR A 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 1467 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" C GLY L 112 " -0.076 2.00e-02 2.50e+03 pdb=" O GLY L 112 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN L 113 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 159 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO H 160 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 110 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" CD GLU A 110 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 110 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 110 " 0.014 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 61 2.53 - 3.12: 6859 3.12 - 3.72: 15478 3.72 - 4.31: 20678 4.31 - 4.90: 34224 Nonbonded interactions: 77300 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.938 2.230 nonbonded pdb=" OE1 GLU H 6 " pdb=" N GLY H 117 " model vdw 2.086 3.120 nonbonded pdb=" O TYR A 515 " pdb=" OG1 THR A 519 " model vdw 2.288 3.040 nonbonded pdb=" O LYS A 114 " pdb=" OG1 THR A 118 " model vdw 2.310 3.040 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.316 3.040 ... (remaining 77295 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.010 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 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 0.044 9931 Z= 0.207 Angle : 0.698 11.618 13519 Z= 0.346 Chirality : 0.045 0.363 1470 Planarity : 0.005 0.057 1744 Dihedral : 14.601 89.344 3621 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 20.53 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.82 (0.23), residues: 1223 helix: 0.22 (0.25), residues: 403 sheet: -0.29 (0.38), residues: 186 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS A 34 PHE 0.014 0.001 PHE E 486 TYR 0.023 0.001 TYR H 32 ARG 0.012 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7813 (t80) cc_final: 0.7459 (t80) REVERT: A 45 LEU cc_start: 0.7501 (tp) cc_final: 0.7255 (mt) REVERT: A 49 ASN cc_start: 0.7790 (m-40) cc_final: 0.7235 (m-40) REVERT: A 90 ASN cc_start: 0.5282 (OUTLIER) cc_final: 0.4943 (t0) REVERT: A 121 ASN cc_start: 0.8153 (m-40) cc_final: 0.7820 (m-40) REVERT: A 150 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6658 (mm-30) REVERT: A 198 ASP cc_start: 0.7134 (p0) cc_final: 0.6916 (p0) REVERT: A 213 ASP cc_start: 0.7902 (p0) cc_final: 0.7584 (m-30) REVERT: A 245 ARG cc_start: 0.5956 (ttp-170) cc_final: 0.5477 (ttp80) REVERT: A 323 MET cc_start: 0.8302 (mmm) cc_final: 0.7988 (mmm) REVERT: A 328 TRP cc_start: 0.7696 (m100) cc_final: 0.6866 (m100) REVERT: A 330 ASN cc_start: 0.8204 (t0) cc_final: 0.7968 (t0) REVERT: A 355 ASP cc_start: 0.7684 (t0) cc_final: 0.6999 (t0) REVERT: A 390 PHE cc_start: 0.6364 (t80) cc_final: 0.6121 (t80) REVERT: A 434 THR cc_start: 0.4862 (p) cc_final: 0.4264 (t) REVERT: A 435 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5499 (pm20) REVERT: A 462 MET cc_start: 0.6783 (ptp) cc_final: 0.6506 (mpp) REVERT: A 471 ASP cc_start: 0.7606 (t0) cc_final: 0.6176 (p0) REVERT: A 472 GLN cc_start: 0.6912 (mt0) cc_final: 0.6485 (tm-30) REVERT: A 480 MET cc_start: 0.7141 (ptm) cc_final: 0.6507 (ptp) REVERT: A 534 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7536 (mmtt) REVERT: A 546 ASN cc_start: 0.5202 (m-40) cc_final: 0.4493 (t0) REVERT: A 582 ARG cc_start: 0.6646 (mmp80) cc_final: 0.5370 (tpm170) REVERT: E 338 PHE cc_start: 0.6314 (m-80) cc_final: 0.5383 (m-80) REVERT: E 406 GLU cc_start: 0.7264 (mp0) cc_final: 0.6814 (mp0) REVERT: E 424 LYS cc_start: 0.7421 (tttm) cc_final: 0.7190 (tttm) REVERT: E 428 ASP cc_start: 0.8414 (p0) cc_final: 0.8186 (p0) REVERT: E 467 ASP cc_start: 0.8139 (t0) cc_final: 0.7854 (t0) REVERT: H 59 ASN cc_start: 0.8435 (p0) cc_final: 0.8047 (p0) REVERT: H 60 TYR cc_start: 0.8523 (m-80) cc_final: 0.8129 (m-10) REVERT: H 65 GLN cc_start: 0.7363 (pm20) cc_final: 0.6688 (tp40) REVERT: H 90 ASP cc_start: 0.7019 (m-30) cc_final: 0.6707 (t0) REVERT: H 94 TYR cc_start: 0.7824 (m-80) cc_final: 0.7606 (m-80) REVERT: H 103 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.6940 (m) REVERT: L 37 TRP cc_start: 0.8188 (m100) cc_final: 0.7884 (m100) REVERT: L 64 PHE cc_start: 0.6393 (m-80) cc_final: 0.5993 (m-80) REVERT: L 87 ASP cc_start: 0.6840 (p0) cc_final: 0.6571 (p0) outliers start: 6 outliers final: 1 residues processed: 283 average time/residue: 0.2364 time to fit residues: 91.4721 Evaluate side-chains 178 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain H residue 103 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 70 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 506 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9931 Z= 0.192 Angle : 0.600 7.917 13519 Z= 0.303 Chirality : 0.044 0.188 1470 Planarity : 0.004 0.051 1744 Dihedral : 4.588 57.014 1418 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.80 % Allowed : 19.30 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.41 (0.24), residues: 1223 helix: 0.51 (0.26), residues: 415 sheet: 0.29 (0.36), residues: 199 loop : -0.99 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS A 493 PHE 0.015 0.002 PHE A 504 TYR 0.013 0.001 TYR A 510 ARG 0.008 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7523 (tp) cc_final: 0.7229 (mt) REVERT: A 49 ASN cc_start: 0.7732 (m-40) cc_final: 0.6878 (m-40) REVERT: A 75 GLU cc_start: 0.8629 (pt0) cc_final: 0.8414 (pp20) REVERT: A 90 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.5830 (t0) REVERT: A 121 ASN cc_start: 0.8092 (m-40) cc_final: 0.7710 (m110) REVERT: A 145 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 150 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6677 (mm-30) REVERT: A 213 ASP cc_start: 0.8097 (p0) cc_final: 0.7802 (m-30) REVERT: A 323 MET cc_start: 0.8601 (mmm) cc_final: 0.8346 (mmm) REVERT: A 328 TRP cc_start: 0.7514 (m100) cc_final: 0.6799 (m100) REVERT: A 329 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 330 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8074 (m-40) REVERT: A 355 ASP cc_start: 0.7990 (t0) cc_final: 0.7107 (t0) REVERT: A 359 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5683 (mm) REVERT: A 432 ASN cc_start: 0.7017 (m-40) cc_final: 0.6526 (p0) REVERT: A 434 THR cc_start: 0.4735 (p) cc_final: 0.3981 (t) REVERT: A 435 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6253 (pm20) REVERT: A 471 ASP cc_start: 0.6883 (t0) cc_final: 0.6046 (p0) REVERT: A 480 MET cc_start: 0.7314 (ptm) cc_final: 0.6850 (ptp) REVERT: A 546 ASN cc_start: 0.5561 (m-40) cc_final: 0.4635 (t0) REVERT: A 582 ARG cc_start: 0.6605 (mmp80) cc_final: 0.5431 (tpm170) REVERT: E 338 PHE cc_start: 0.6500 (m-80) cc_final: 0.5885 (m-80) REVERT: E 406 GLU cc_start: 0.7513 (mp0) cc_final: 0.6996 (mp0) REVERT: E 424 LYS cc_start: 0.7467 (tttm) cc_final: 0.7261 (tttm) REVERT: E 467 ASP cc_start: 0.8224 (t0) cc_final: 0.7890 (t0) REVERT: H 59 ASN cc_start: 0.8547 (p0) cc_final: 0.8166 (p0) REVERT: H 60 TYR cc_start: 0.8546 (m-80) cc_final: 0.8125 (m-10) REVERT: H 65 GLN cc_start: 0.7253 (pm20) cc_final: 0.7023 (tp40) REVERT: L 19 THR cc_start: 0.7526 (m) cc_final: 0.6754 (p) REVERT: L 64 PHE cc_start: 0.6486 (m-80) cc_final: 0.6174 (m-80) REVERT: L 94 ASP cc_start: 0.7142 (t0) cc_final: 0.6933 (t0) outliers start: 39 outliers final: 15 residues processed: 217 average time/residue: 0.2038 time to fit residues: 63.6463 Evaluate side-chains 171 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 182 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.0470 chunk 34 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9931 Z= 0.157 Angle : 0.577 13.746 13519 Z= 0.291 Chirality : 0.044 0.337 1470 Planarity : 0.004 0.047 1744 Dihedral : 4.391 57.287 1417 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.28 % Allowed : 21.10 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.34 (0.24), residues: 1223 helix: 0.68 (0.27), residues: 413 sheet: 0.35 (0.37), residues: 196 loop : -1.05 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 493 PHE 0.026 0.001 PHE H 64 TYR 0.015 0.001 TYR A 510 ARG 0.006 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7966 (mp0) cc_final: 0.7363 (pm20) REVERT: A 45 LEU cc_start: 0.7573 (tp) cc_final: 0.7227 (mt) REVERT: A 49 ASN cc_start: 0.7778 (m-40) cc_final: 0.6956 (m-40) REVERT: A 90 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.5896 (t0) REVERT: A 121 ASN cc_start: 0.8068 (m-40) cc_final: 0.7655 (m110) REVERT: A 145 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 150 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6682 (mm-30) REVERT: A 213 ASP cc_start: 0.8030 (p0) cc_final: 0.7701 (m-30) REVERT: A 323 MET cc_start: 0.8841 (mmm) cc_final: 0.8417 (mmm) REVERT: A 359 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5573 (mm) REVERT: A 361 CYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4076 (p) REVERT: A 366 MET cc_start: 0.6806 (tpp) cc_final: 0.6384 (mmm) REVERT: A 432 ASN cc_start: 0.7139 (m-40) cc_final: 0.6765 (p0) REVERT: A 434 THR cc_start: 0.4734 (p) cc_final: 0.4045 (t) REVERT: A 435 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6270 (pm20) REVERT: A 471 ASP cc_start: 0.6803 (t0) cc_final: 0.5979 (p0) REVERT: A 480 MET cc_start: 0.7429 (ptm) cc_final: 0.7028 (ptp) REVERT: A 546 ASN cc_start: 0.5775 (m-40) cc_final: 0.4619 (t0) REVERT: A 582 ARG cc_start: 0.6196 (mmp80) cc_final: 0.5308 (tpm170) REVERT: E 393 THR cc_start: 0.6764 (p) cc_final: 0.6220 (t) REVERT: E 406 GLU cc_start: 0.7470 (mp0) cc_final: 0.6861 (mp0) REVERT: E 424 LYS cc_start: 0.7389 (tttm) cc_final: 0.7085 (tppt) REVERT: E 493 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7424 (mm-40) REVERT: H 46 GLU cc_start: 0.8406 (pt0) cc_final: 0.8033 (pt0) REVERT: H 59 ASN cc_start: 0.8596 (p0) cc_final: 0.8204 (p0) REVERT: H 60 TYR cc_start: 0.8611 (m-80) cc_final: 0.8142 (m-10) REVERT: H 65 GLN cc_start: 0.7356 (pm20) cc_final: 0.7123 (tp40) REVERT: L 34 ASP cc_start: 0.8386 (m-30) cc_final: 0.7892 (m-30) REVERT: L 87 ASP cc_start: 0.6587 (p0) cc_final: 0.5622 (p0) REVERT: L 94 ASP cc_start: 0.7481 (t0) cc_final: 0.7041 (t0) outliers start: 23 outliers final: 12 residues processed: 178 average time/residue: 0.2066 time to fit residues: 53.2513 Evaluate side-chains 163 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN ** H 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9931 Z= 0.210 Angle : 0.586 8.952 13519 Z= 0.297 Chirality : 0.043 0.178 1470 Planarity : 0.004 0.045 1744 Dihedral : 4.524 55.426 1417 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 20.91 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.25 (0.24), residues: 1223 helix: 0.80 (0.27), residues: 408 sheet: 0.26 (0.36), residues: 195 loop : -0.95 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS A 417 PHE 0.025 0.002 PHE H 64 TYR 0.014 0.001 TYR A 237 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8053 (mp0) cc_final: 0.7655 (pm20) REVERT: A 82 MET cc_start: 0.8161 (tmm) cc_final: 0.7597 (tmm) REVERT: A 90 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6383 (t0) REVERT: A 121 ASN cc_start: 0.7820 (m-40) cc_final: 0.7247 (m110) REVERT: A 145 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 150 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6702 (mm-30) REVERT: A 279 TYR cc_start: 0.7814 (t80) cc_final: 0.7607 (t80) REVERT: A 323 MET cc_start: 0.8935 (mmm) cc_final: 0.8544 (mmt) REVERT: A 359 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5905 (mm) REVERT: A 366 MET cc_start: 0.6852 (tpp) cc_final: 0.6586 (tpp) REVERT: A 398 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4711 (tp30) REVERT: A 432 ASN cc_start: 0.7288 (m-40) cc_final: 0.6724 (p0) REVERT: A 434 THR cc_start: 0.5252 (p) cc_final: 0.4613 (t) REVERT: A 435 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6244 (pm20) REVERT: A 480 MET cc_start: 0.7652 (ptm) cc_final: 0.6962 (ptp) REVERT: A 582 ARG cc_start: 0.6392 (mmp80) cc_final: 0.5453 (tpm170) REVERT: E 393 THR cc_start: 0.6557 (p) cc_final: 0.6189 (t) REVERT: E 406 GLU cc_start: 0.7574 (mp0) cc_final: 0.7169 (mp0) REVERT: E 420 ASP cc_start: 0.7773 (t0) cc_final: 0.7492 (t0) REVERT: E 424 LYS cc_start: 0.7603 (tttm) cc_final: 0.7219 (tppt) REVERT: E 444 LYS cc_start: 0.8314 (pttm) cc_final: 0.8106 (ptpp) REVERT: E 493 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7432 (mm-40) REVERT: H 59 ASN cc_start: 0.8755 (p0) cc_final: 0.8303 (p0) REVERT: H 60 TYR cc_start: 0.8817 (m-80) cc_final: 0.8538 (m-10) REVERT: H 90 ASP cc_start: 0.7067 (t0) cc_final: 0.6866 (t0) REVERT: L 19 THR cc_start: 0.7719 (m) cc_final: 0.6941 (p) REVERT: L 87 ASP cc_start: 0.7297 (p0) cc_final: 0.6875 (p0) REVERT: L 94 ASP cc_start: 0.7828 (t0) cc_final: 0.7223 (t0) REVERT: L 107 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7441 (mtpp) outliers start: 34 outliers final: 22 residues processed: 186 average time/residue: 0.2111 time to fit residues: 56.1386 Evaluate side-chains 163 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 0.0040 chunk 80 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN H 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9931 Z= 0.166 Angle : 0.570 9.866 13519 Z= 0.287 Chirality : 0.043 0.293 1470 Planarity : 0.003 0.044 1744 Dihedral : 4.779 79.046 1417 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.80 % Allowed : 21.86 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.12 (0.24), residues: 1223 helix: 0.92 (0.27), residues: 409 sheet: 0.41 (0.36), residues: 200 loop : -0.93 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS A 505 PHE 0.031 0.002 PHE H 64 TYR 0.014 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7986 (tmm) cc_final: 0.7635 (tmm) REVERT: A 90 ASN cc_start: 0.6936 (OUTLIER) cc_final: 0.6434 (t0) REVERT: A 121 ASN cc_start: 0.7690 (m-40) cc_final: 0.7110 (m110) REVERT: A 145 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 150 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6703 (mm-30) REVERT: A 213 ASP cc_start: 0.7881 (p0) cc_final: 0.7552 (m-30) REVERT: A 279 TYR cc_start: 0.7811 (t80) cc_final: 0.7605 (t80) REVERT: A 310 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 398 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.4679 (tp30) REVERT: A 432 ASN cc_start: 0.7413 (m-40) cc_final: 0.6937 (p0) REVERT: A 434 THR cc_start: 0.5609 (p) cc_final: 0.5318 (t) REVERT: A 435 GLU cc_start: 0.6373 (mm-30) cc_final: 0.5907 (pm20) REVERT: A 442 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6798 (mm-40) REVERT: A 479 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: A 480 MET cc_start: 0.7281 (ptm) cc_final: 0.6863 (ptp) REVERT: A 582 ARG cc_start: 0.6373 (mmp80) cc_final: 0.5455 (tpm170) REVERT: E 406 GLU cc_start: 0.7650 (mp0) cc_final: 0.7174 (mp0) REVERT: E 420 ASP cc_start: 0.7781 (t0) cc_final: 0.7440 (t0) REVERT: E 424 LYS cc_start: 0.7593 (tttm) cc_final: 0.7118 (tppt) REVERT: E 493 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7373 (mm-40) REVERT: H 46 GLU cc_start: 0.8509 (pt0) cc_final: 0.7967 (pt0) REVERT: H 59 ASN cc_start: 0.8729 (p0) cc_final: 0.8315 (p0) REVERT: H 60 TYR cc_start: 0.8745 (m-80) cc_final: 0.8432 (m-10) REVERT: L 19 THR cc_start: 0.7730 (m) cc_final: 0.6980 (p) REVERT: L 87 ASP cc_start: 0.7031 (p0) cc_final: 0.6687 (p0) REVERT: L 94 ASP cc_start: 0.7794 (t0) cc_final: 0.7171 (t0) outliers start: 39 outliers final: 23 residues processed: 182 average time/residue: 0.2060 time to fit residues: 53.7985 Evaluate side-chains 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN E 370 ASN E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN H 166 ASN L 55 ASN L 189 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9931 Z= 0.175 Angle : 0.585 9.691 13519 Z= 0.293 Chirality : 0.043 0.212 1470 Planarity : 0.003 0.043 1744 Dihedral : 4.860 88.712 1417 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.61 % Allowed : 21.67 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.12 (0.24), residues: 1223 helix: 0.91 (0.26), residues: 410 sheet: 0.38 (0.35), residues: 200 loop : -0.90 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.008 0.001 HIS A 401 PHE 0.031 0.001 PHE H 64 TYR 0.014 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.183 Fit side-chains REVERT: A 75 GLU cc_start: 0.8655 (pt0) cc_final: 0.8277 (pp20) REVERT: A 82 MET cc_start: 0.7951 (tmm) cc_final: 0.7705 (tmm) REVERT: A 90 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6441 (t0) REVERT: A 121 ASN cc_start: 0.7589 (m-40) cc_final: 0.7022 (m110) REVERT: A 145 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 150 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6726 (mm-30) REVERT: A 213 ASP cc_start: 0.7921 (p0) cc_final: 0.7567 (m-30) REVERT: A 310 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 313 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5908 (ptpt) REVERT: A 325 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 366 MET cc_start: 0.6727 (tpp) cc_final: 0.6306 (mmm) REVERT: A 398 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.4780 (tp30) REVERT: A 432 ASN cc_start: 0.7435 (m-40) cc_final: 0.6830 (p0) REVERT: A 434 THR cc_start: 0.5595 (p) cc_final: 0.5256 (t) REVERT: A 435 GLU cc_start: 0.6409 (mm-30) cc_final: 0.5948 (pm20) REVERT: A 442 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6880 (mm-40) REVERT: A 479 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6452 (tm-30) REVERT: A 480 MET cc_start: 0.7324 (ptm) cc_final: 0.6855 (ptp) REVERT: A 582 ARG cc_start: 0.6467 (mmp80) cc_final: 0.5485 (tpm170) REVERT: E 357 ARG cc_start: 0.8494 (tpt-90) cc_final: 0.8213 (ttt90) REVERT: E 378 LYS cc_start: 0.8287 (ptpp) cc_final: 0.7072 (mmmt) REVERT: E 406 GLU cc_start: 0.7663 (mp0) cc_final: 0.7173 (mp0) REVERT: E 420 ASP cc_start: 0.7804 (t0) cc_final: 0.7535 (t0) REVERT: E 424 LYS cc_start: 0.7596 (tttm) cc_final: 0.7113 (tppt) REVERT: E 487 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.5834 (t0) REVERT: E 493 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7446 (mm-40) REVERT: H 43 GLN cc_start: 0.7033 (mp10) cc_final: 0.6831 (mp10) REVERT: H 46 GLU cc_start: 0.8457 (pt0) cc_final: 0.7999 (pt0) REVERT: H 59 ASN cc_start: 0.8730 (p0) cc_final: 0.8325 (p0) REVERT: H 60 TYR cc_start: 0.8753 (m-80) cc_final: 0.8441 (m-10) REVERT: H 87 ARG cc_start: 0.7003 (mpp80) cc_final: 0.6222 (mpp80) REVERT: L 19 THR cc_start: 0.7692 (m) cc_final: 0.6980 (p) REVERT: L 87 ASP cc_start: 0.7035 (p0) cc_final: 0.6681 (p0) REVERT: L 94 ASP cc_start: 0.7807 (t0) cc_final: 0.7152 (t0) outliers start: 37 outliers final: 23 residues processed: 175 average time/residue: 0.2143 time to fit residues: 53.6330 Evaluate side-chains 160 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9931 Z= 0.214 Angle : 0.606 7.957 13519 Z= 0.304 Chirality : 0.044 0.201 1470 Planarity : 0.004 0.104 1744 Dihedral : 4.877 77.670 1417 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 22.05 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.14 (0.24), residues: 1223 helix: 0.88 (0.26), residues: 409 sheet: 0.39 (0.36), residues: 193 loop : -0.91 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS A 401 PHE 0.032 0.002 PHE H 64 TYR 0.026 0.001 TYR A 279 ARG 0.005 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.046 Fit side-chains REVERT: A 75 GLU cc_start: 0.8556 (pt0) cc_final: 0.8248 (pp20) REVERT: A 82 MET cc_start: 0.7923 (tmm) cc_final: 0.7719 (tmm) REVERT: A 90 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6921 (t0) REVERT: A 117 ASN cc_start: 0.7973 (t0) cc_final: 0.7305 (t0) REVERT: A 121 ASN cc_start: 0.7531 (m-40) cc_final: 0.6997 (m110) REVERT: A 145 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 150 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6747 (mm-30) REVERT: A 213 ASP cc_start: 0.7988 (p0) cc_final: 0.7589 (m-30) REVERT: A 310 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 325 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 366 MET cc_start: 0.6839 (tpp) cc_final: 0.6410 (mmm) REVERT: A 398 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.4972 (tp30) REVERT: A 432 ASN cc_start: 0.7283 (m-40) cc_final: 0.6825 (p0) REVERT: A 434 THR cc_start: 0.6746 (p) cc_final: 0.6414 (t) REVERT: A 435 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5978 (pm20) REVERT: A 438 PHE cc_start: 0.7673 (t80) cc_final: 0.7459 (t80) REVERT: A 442 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7010 (mm-40) REVERT: A 462 MET cc_start: 0.6938 (mpp) cc_final: 0.6721 (mpp) REVERT: A 479 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: A 480 MET cc_start: 0.7462 (ptm) cc_final: 0.6780 (ptp) REVERT: A 582 ARG cc_start: 0.6506 (mmp80) cc_final: 0.5456 (tpm170) REVERT: E 378 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7087 (mmmt) REVERT: E 406 GLU cc_start: 0.7885 (mp0) cc_final: 0.7302 (mp0) REVERT: E 420 ASP cc_start: 0.7852 (t0) cc_final: 0.7601 (t0) REVERT: E 424 LYS cc_start: 0.7862 (tttm) cc_final: 0.7353 (tppt) REVERT: E 493 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7632 (mm-40) REVERT: H 59 ASN cc_start: 0.8777 (p0) cc_final: 0.8357 (p0) REVERT: H 60 TYR cc_start: 0.8780 (m-80) cc_final: 0.8519 (m-10) REVERT: L 19 THR cc_start: 0.8067 (m) cc_final: 0.7432 (p) REVERT: L 87 ASP cc_start: 0.7110 (p0) cc_final: 0.6839 (p0) REVERT: L 94 ASP cc_start: 0.7801 (t0) cc_final: 0.7139 (t0) REVERT: L 107 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7573 (mtpp) outliers start: 34 outliers final: 25 residues processed: 170 average time/residue: 0.2246 time to fit residues: 54.4320 Evaluate side-chains 156 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9931 Z= 0.196 Angle : 0.600 8.542 13519 Z= 0.300 Chirality : 0.044 0.179 1470 Planarity : 0.003 0.033 1744 Dihedral : 4.623 57.386 1417 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.04 % Allowed : 22.72 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.12 (0.24), residues: 1223 helix: 0.87 (0.26), residues: 409 sheet: 0.30 (0.36), residues: 194 loop : -0.83 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 401 PHE 0.039 0.002 PHE H 64 TYR 0.017 0.001 TYR A 510 ARG 0.008 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8379 (pt0) cc_final: 0.8149 (pp20) REVERT: A 90 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.6976 (t0) REVERT: A 117 ASN cc_start: 0.7938 (t0) cc_final: 0.7602 (t0) REVERT: A 121 ASN cc_start: 0.7553 (m-40) cc_final: 0.7228 (m110) REVERT: A 145 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 150 GLU cc_start: 0.7634 (tm-30) cc_final: 0.6806 (mm-30) REVERT: A 325 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 398 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5076 (tp30) REVERT: A 432 ASN cc_start: 0.7169 (m-40) cc_final: 0.6868 (p0) REVERT: A 435 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5979 (pm20) REVERT: A 438 PHE cc_start: 0.7726 (t80) cc_final: 0.7522 (t80) REVERT: A 442 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6880 (mm-40) REVERT: A 462 MET cc_start: 0.7089 (mpp) cc_final: 0.6784 (mpp) REVERT: A 479 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: A 480 MET cc_start: 0.7523 (ptm) cc_final: 0.6911 (ptp) REVERT: A 523 PHE cc_start: 0.6607 (m-80) cc_final: 0.6309 (m-80) REVERT: A 582 ARG cc_start: 0.6504 (mmp80) cc_final: 0.5507 (tpm170) REVERT: E 378 LYS cc_start: 0.8367 (ptpp) cc_final: 0.7052 (mmmt) REVERT: E 406 GLU cc_start: 0.7949 (mp0) cc_final: 0.7277 (mp0) REVERT: E 420 ASP cc_start: 0.7870 (t0) cc_final: 0.7577 (t0) REVERT: E 422 ASN cc_start: 0.8752 (m-40) cc_final: 0.8527 (m110) REVERT: E 424 LYS cc_start: 0.7899 (tttm) cc_final: 0.7460 (tppt) REVERT: E 493 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7604 (mm-40) REVERT: H 29 PHE cc_start: 0.7747 (t80) cc_final: 0.6815 (t80) REVERT: H 46 GLU cc_start: 0.8423 (pt0) cc_final: 0.7849 (pt0) REVERT: H 59 ASN cc_start: 0.8767 (p0) cc_final: 0.8374 (p0) REVERT: H 60 TYR cc_start: 0.8788 (m-80) cc_final: 0.8523 (m-10) REVERT: H 63 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8600 (ptmm) REVERT: H 65 GLN cc_start: 0.7408 (tp40) cc_final: 0.6881 (tp-100) REVERT: H 87 ARG cc_start: 0.7036 (mpp80) cc_final: 0.6351 (mpp80) REVERT: L 87 ASP cc_start: 0.7045 (p0) cc_final: 0.6681 (p0) REVERT: L 94 ASP cc_start: 0.7808 (t0) cc_final: 0.7163 (t0) REVERT: L 107 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7585 (mtpp) REVERT: L 111 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5459 (mt) outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 0.2021 time to fit residues: 48.8038 Evaluate side-chains 151 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.0010 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9931 Z= 0.181 Angle : 0.594 8.602 13519 Z= 0.296 Chirality : 0.044 0.180 1470 Planarity : 0.003 0.032 1744 Dihedral : 4.464 50.070 1417 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.47 % Allowed : 23.76 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.11 (0.24), residues: 1223 helix: 0.83 (0.26), residues: 414 sheet: 0.27 (0.36), residues: 192 loop : -0.78 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.006 0.001 HIS A 373 PHE 0.055 0.002 PHE H 64 TYR 0.012 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8423 (pt0) cc_final: 0.8186 (pp20) REVERT: A 90 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6770 (t0) REVERT: A 117 ASN cc_start: 0.8190 (t0) cc_final: 0.7806 (t0) REVERT: A 121 ASN cc_start: 0.7524 (m-40) cc_final: 0.7130 (m110) REVERT: A 150 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6822 (mm-30) REVERT: A 210 ASN cc_start: 0.8381 (m-40) cc_final: 0.8039 (t0) REVERT: A 310 GLU cc_start: 0.7007 (tm-30) cc_final: 0.5512 (mp0) REVERT: A 325 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 398 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5109 (tp30) REVERT: A 435 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5869 (pm20) REVERT: A 438 PHE cc_start: 0.7738 (t80) cc_final: 0.7532 (t80) REVERT: A 442 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6746 (mm-40) REVERT: A 462 MET cc_start: 0.7083 (mpp) cc_final: 0.6780 (mpp) REVERT: A 479 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: A 480 MET cc_start: 0.7554 (ptm) cc_final: 0.6935 (ptp) REVERT: A 523 PHE cc_start: 0.6604 (m-80) cc_final: 0.6333 (m-80) REVERT: A 582 ARG cc_start: 0.6488 (mmp80) cc_final: 0.5502 (tpm170) REVERT: E 378 LYS cc_start: 0.8297 (ptpp) cc_final: 0.6982 (mmmt) REVERT: E 406 GLU cc_start: 0.7896 (mp0) cc_final: 0.7271 (mp0) REVERT: E 420 ASP cc_start: 0.7836 (t0) cc_final: 0.7546 (t0) REVERT: E 422 ASN cc_start: 0.8728 (m-40) cc_final: 0.8503 (m110) REVERT: E 424 LYS cc_start: 0.7829 (tttm) cc_final: 0.7374 (tppt) REVERT: E 493 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7606 (mm-40) REVERT: H 29 PHE cc_start: 0.7321 (t80) cc_final: 0.6488 (t80) REVERT: H 59 ASN cc_start: 0.8703 (p0) cc_final: 0.8251 (p0) REVERT: H 60 TYR cc_start: 0.8792 (m-80) cc_final: 0.8418 (m-10) REVERT: H 63 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8463 (ptpt) REVERT: H 65 GLN cc_start: 0.7677 (tp40) cc_final: 0.6521 (tp-100) REVERT: L 64 PHE cc_start: 0.7530 (m-80) cc_final: 0.7193 (m-80) REVERT: L 87 ASP cc_start: 0.6975 (p0) cc_final: 0.6650 (p0) REVERT: L 94 ASP cc_start: 0.7806 (t0) cc_final: 0.7170 (t0) outliers start: 25 outliers final: 20 residues processed: 159 average time/residue: 0.2141 time to fit residues: 48.9599 Evaluate side-chains 154 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9931 Z= 0.219 Angle : 0.625 8.694 13519 Z= 0.313 Chirality : 0.044 0.179 1470 Planarity : 0.004 0.043 1744 Dihedral : 4.499 48.771 1417 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.95 % Allowed : 24.05 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.16 (0.24), residues: 1223 helix: 0.84 (0.26), residues: 406 sheet: 0.14 (0.36), residues: 194 loop : -0.79 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.006 0.001 HIS A 373 PHE 0.050 0.002 PHE H 64 TYR 0.020 0.001 TYR A 510 ARG 0.007 0.001 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8465 (pt0) cc_final: 0.8198 (pp20) REVERT: A 90 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.6797 (t0) REVERT: A 117 ASN cc_start: 0.8197 (t0) cc_final: 0.7808 (t0) REVERT: A 121 ASN cc_start: 0.7528 (m-40) cc_final: 0.7137 (m110) REVERT: A 145 GLU cc_start: 0.8308 (mp0) cc_final: 0.7978 (tm-30) REVERT: A 150 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6779 (mm-30) REVERT: A 210 ASN cc_start: 0.8391 (m-40) cc_final: 0.7348 (t0) REVERT: A 398 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5318 (tp30) REVERT: A 435 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6156 (pm20) REVERT: A 442 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6821 (mm-40) REVERT: A 462 MET cc_start: 0.7149 (mpp) cc_final: 0.6820 (mpp) REVERT: A 479 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: A 480 MET cc_start: 0.7604 (ptm) cc_final: 0.6958 (ptp) REVERT: A 582 ARG cc_start: 0.6679 (mmp80) cc_final: 0.5622 (tpm170) REVERT: E 378 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7181 (tptp) REVERT: E 406 GLU cc_start: 0.7901 (mp0) cc_final: 0.7291 (mp0) REVERT: E 420 ASP cc_start: 0.7868 (t0) cc_final: 0.7611 (t0) REVERT: E 422 ASN cc_start: 0.8790 (m-40) cc_final: 0.8584 (m110) REVERT: E 424 LYS cc_start: 0.7869 (tttm) cc_final: 0.7394 (tppt) REVERT: H 29 PHE cc_start: 0.7373 (t80) cc_final: 0.6508 (t80) REVERT: H 59 ASN cc_start: 0.8751 (p0) cc_final: 0.8294 (p0) REVERT: H 60 TYR cc_start: 0.8845 (m-80) cc_final: 0.8453 (m-10) REVERT: H 63 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8395 (ptmm) REVERT: H 65 GLN cc_start: 0.7669 (tp40) cc_final: 0.6523 (tp-100) REVERT: H 87 ARG cc_start: 0.6880 (mtm180) cc_final: 0.6629 (mpp80) REVERT: L 64 PHE cc_start: 0.7478 (m-80) cc_final: 0.7069 (m-80) REVERT: L 87 ASP cc_start: 0.7082 (p0) cc_final: 0.6693 (p0) REVERT: L 94 ASP cc_start: 0.7820 (t0) cc_final: 0.7181 (t0) REVERT: L 107 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7587 (mtpp) REVERT: L 111 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5494 (mt) outliers start: 30 outliers final: 25 residues processed: 152 average time/residue: 0.2245 time to fit residues: 48.9835 Evaluate side-chains 152 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 182 TYR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 40 optimal weight: 0.0070 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 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 = 0.3992 r_free = 0.3992 target = 0.169771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162888 restraints weight = 21278.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153233 restraints weight = 37797.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149327 restraints weight = 30022.014| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 9931 Z= 0.289 Angle : 0.913 59.105 13519 Z= 0.531 Chirality : 0.045 0.362 1470 Planarity : 0.004 0.049 1744 Dihedral : 4.645 48.716 1417 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 2.95 % Allowed : 24.24 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.16 (0.24), residues: 1223 helix: 0.84 (0.26), residues: 406 sheet: 0.14 (0.36), residues: 194 loop : -0.79 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.006 0.001 HIS A 373 PHE 0.045 0.002 PHE H 64 TYR 0.019 0.001 TYR A 510 ARG 0.007 0.001 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.80 seconds wall clock time: 42 minutes 32.44 seconds (2552.44 seconds total)