Starting phenix.real_space_refine on Tue Jul 29 06:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydi_33748/07_2025/7ydi_33748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydi_33748/07_2025/7ydi_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_33748/07_2025/7ydi_33748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2025/7ydi_33748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2025/7ydi_33748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydi_33748/07_2025/7ydi_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.96, per 1000 atoms: 0.72 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 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: 1.23 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: 2.81 Time building geometry restraints manager: 3.24 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: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.130 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- 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 9949 Z= 0.154 Angle : 0.701 11.618 13555 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 2.19484 ( 12) hydrogen bonds : bond 0.17796 ( 378) hydrogen bonds : angle 7.02040 ( 1071) metal coordination : bond 0.00064 ( 2) SS BOND : bond 0.00094 ( 12) SS BOND : angle 0.56956 ( 24) covalent geometry : bond 0.00318 ( 9931) covalent geometry : angle 0.69839 (13519) *********************** 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 : 1.254 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: 0.2363 time to fit residues: 91.8863 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 : 1.226 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.176511 restraints weight = 31753.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176492 restraints weight = 47571.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.176733 restraints weight = 34139.294| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 9949 Z= 0.136 Angle : 0.603 7.917 13555 Z= 0.304 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 4) link_NAG-ASN : angle 1.82462 ( 12) hydrogen bonds : bond 0.04035 ( 378) hydrogen bonds : angle 4.98398 ( 1071) metal coordination : bond 0.00325 ( 2) SS BOND : bond 0.00257 ( 12) SS BOND : angle 1.08638 ( 24) covalent geometry : bond 0.00297 ( 9931) covalent geometry : angle 0.59989 (13519) *********************** 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 : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.7431 (m-40) cc_final: 0.6841 (m-40) REVERT: A 328 TRP cc_start: 0.7978 (m100) cc_final: 0.7109 (m100) REVERT: A 329 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6328 (tm-30) REVERT: A 355 ASP cc_start: 0.7972 (t0) cc_final: 0.7437 (t0) REVERT: A 359 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7104 (mm) REVERT: A 434 THR cc_start: 0.5688 (p) cc_final: 0.5400 (t) REVERT: A 480 MET cc_start: 0.7671 (ptm) cc_final: 0.7368 (ptp) REVERT: A 520 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8237 (mt) REVERT: A 582 ARG cc_start: 0.6682 (mmp80) cc_final: 0.6278 (tpm170) REVERT: E 338 PHE cc_start: 0.7078 (m-80) cc_final: 0.6764 (m-80) REVERT: E 406 GLU cc_start: 0.7772 (mp0) cc_final: 0.7104 (mp0) REVERT: E 425 LEU cc_start: 0.6809 (mt) cc_final: 0.6561 (mt) REVERT: E 467 ASP cc_start: 0.8870 (t0) cc_final: 0.7970 (t0) REVERT: H 59 ASN cc_start: 0.8955 (p0) cc_final: 0.8491 (p0) REVERT: H 60 TYR cc_start: 0.8645 (m-80) cc_final: 0.8312 (m-10) REVERT: L 19 THR cc_start: 0.7076 (m) cc_final: 0.6226 (p) outliers start: 39 outliers final: 15 residues processed: 217 average time/residue: 0.1930 time to fit residues: 60.0380 Evaluate side-chains 166 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 91 LEU 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 A residue 520 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 34 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 34 HIS A 51 ASN A 101 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165038 restraints weight = 32983.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166550 restraints weight = 48252.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166288 restraints weight = 32435.983| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9949 Z= 0.172 Angle : 0.705 24.363 13555 Z= 0.345 Chirality : 0.055 1.047 1470 Planarity : 0.004 0.048 1744 Dihedral : 4.601 50.791 1415 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.57 % Allowed : 21.58 % Favored : 75.86 % 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: -0.48 (0.24), residues: 1223 helix: 0.54 (0.26), residues: 409 sheet: 0.26 (0.37), residues: 192 loop : -1.08 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS A 417 PHE 0.028 0.002 PHE H 64 TYR 0.016 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01959 ( 4) link_NAG-ASN : angle 8.36421 ( 12) hydrogen bonds : bond 0.04065 ( 378) hydrogen bonds : angle 4.62584 ( 1071) metal coordination : bond 0.00180 ( 2) SS BOND : bond 0.00822 ( 12) SS BOND : angle 2.50367 ( 24) covalent geometry : bond 0.00380 ( 9931) covalent geometry : angle 0.65220 (13519) *********************** 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 188 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7505 (tmm) cc_final: 0.6779 (tmm) REVERT: A 328 TRP cc_start: 0.8066 (m100) cc_final: 0.7459 (m100) REVERT: A 329 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 330 ASN cc_start: 0.7705 (m-40) cc_final: 0.7374 (m110) REVERT: A 434 THR cc_start: 0.5854 (p) cc_final: 0.5533 (t) REVERT: A 435 GLU cc_start: 0.7171 (pm20) cc_final: 0.6818 (pm20) REVERT: E 360 ASN cc_start: 0.6356 (p0) cc_final: 0.6101 (p0) REVERT: E 406 GLU cc_start: 0.8260 (mp0) cc_final: 0.7278 (mp0) REVERT: E 423 TYR cc_start: 0.8476 (t80) cc_final: 0.8142 (t80) REVERT: H 59 ASN cc_start: 0.9158 (p0) cc_final: 0.8699 (p0) REVERT: H 60 TYR cc_start: 0.8948 (m-80) cc_final: 0.8663 (m-10) REVERT: L 19 THR cc_start: 0.7369 (m) cc_final: 0.6626 (p) REVERT: L 107 LYS cc_start: 0.8584 (ttmm) cc_final: 0.7953 (mtpp) outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 0.1987 time to fit residues: 52.8135 Evaluate side-chains 157 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP 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 394 ASN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN E 409 GLN E 487 ASN H 175 HIS L 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.184325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164887 restraints weight = 26948.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164787 restraints weight = 31013.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165094 restraints weight = 24828.009| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9949 Z= 0.115 Angle : 0.595 11.120 13555 Z= 0.296 Chirality : 0.043 0.230 1470 Planarity : 0.003 0.046 1744 Dihedral : 4.283 53.241 1415 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.42 % Allowed : 22.05 % Favored : 74.52 % 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: 0.73 (0.27), residues: 408 sheet: 0.11 (0.34), residues: 213 loop : -1.00 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.000 HIS A 493 PHE 0.017 0.001 PHE H 64 TYR 0.012 0.001 TYR A 510 ARG 0.007 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 4) link_NAG-ASN : angle 3.54308 ( 12) hydrogen bonds : bond 0.03450 ( 378) hydrogen bonds : angle 4.42116 ( 1071) metal coordination : bond 0.00047 ( 2) SS BOND : bond 0.00932 ( 12) SS BOND : angle 2.55636 ( 24) covalent geometry : bond 0.00253 ( 9931) covalent geometry : angle 0.57649 (13519) *********************** 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 180 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7402 (tmm) cc_final: 0.6893 (tmm) REVERT: A 310 GLU cc_start: 0.7290 (pp20) cc_final: 0.7004 (tm-30) REVERT: A 330 ASN cc_start: 0.7574 (m-40) cc_final: 0.6999 (m-40) REVERT: A 434 THR cc_start: 0.6280 (p) cc_final: 0.6022 (t) REVERT: A 435 GLU cc_start: 0.7419 (pm20) cc_final: 0.7109 (pm20) REVERT: E 406 GLU cc_start: 0.8301 (mp0) cc_final: 0.7395 (mp0) REVERT: E 467 ASP cc_start: 0.8497 (t0) cc_final: 0.7990 (t0) REVERT: H 59 ASN cc_start: 0.9078 (p0) cc_final: 0.8636 (p0) REVERT: H 60 TYR cc_start: 0.8862 (m-80) cc_final: 0.8584 (m-10) REVERT: L 19 THR cc_start: 0.7355 (m) cc_final: 0.6542 (p) REVERT: L 94 ASP cc_start: 0.8462 (t70) cc_final: 0.7927 (p0) REVERT: L 107 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7954 (mtpp) outliers start: 35 outliers final: 20 residues processed: 173 average time/residue: 0.1832 time to fit residues: 45.8203 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR 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 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain E residue 500 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 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 120 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173430 restraints weight = 19786.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160793 restraints weight = 34788.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158015 restraints weight = 29650.165| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9949 Z= 0.141 Angle : 0.623 11.488 13555 Z= 0.313 Chirality : 0.044 0.222 1470 Planarity : 0.004 0.043 1744 Dihedral : 4.607 71.008 1415 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.80 % Allowed : 22.15 % Favored : 74.05 % 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: -0.29 (0.24), residues: 1223 helix: 0.73 (0.26), residues: 409 sheet: 0.36 (0.36), residues: 198 loop : -1.00 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 417 PHE 0.019 0.002 PHE A 555 TYR 0.021 0.001 TYR A 279 ARG 0.008 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 2.91159 ( 12) hydrogen bonds : bond 0.03594 ( 378) hydrogen bonds : angle 4.41545 ( 1071) metal coordination : bond 0.00094 ( 2) SS BOND : bond 0.00529 ( 12) SS BOND : angle 2.33128 ( 24) covalent geometry : bond 0.00316 ( 9931) covalent geometry : angle 0.60971 (13519) *********************** 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 180 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7424 (tmm) cc_final: 0.7037 (tmm) REVERT: A 435 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: A 479 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: E 406 GLU cc_start: 0.8577 (mp0) cc_final: 0.7639 (mp0) REVERT: E 467 ASP cc_start: 0.8494 (t0) cc_final: 0.7976 (t0) REVERT: H 59 ASN cc_start: 0.9159 (p0) cc_final: 0.8728 (p0) REVERT: H 60 TYR cc_start: 0.8934 (m-80) cc_final: 0.8577 (m-10) REVERT: L 19 THR cc_start: 0.7434 (m) cc_final: 0.6799 (p) REVERT: L 107 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8214 (mtpp) outliers start: 39 outliers final: 25 residues processed: 175 average time/residue: 0.2177 time to fit residues: 54.6189 Evaluate side-chains 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 435 GLU 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 A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR 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 500 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 511 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 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 108 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN L 55 ASN L 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159046 restraints weight = 25597.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159364 restraints weight = 32450.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159517 restraints weight = 25562.135| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9949 Z= 0.128 Angle : 0.609 8.216 13555 Z= 0.305 Chirality : 0.044 0.168 1470 Planarity : 0.003 0.036 1744 Dihedral : 4.831 89.170 1415 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.61 % Allowed : 22.81 % Favored : 73.57 % 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: 0.77 (0.26), residues: 407 sheet: 0.24 (0.36), residues: 199 loop : -0.92 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 417 PHE 0.014 0.001 PHE E 392 TYR 0.009 0.001 TYR E 423 ARG 0.006 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 4) link_NAG-ASN : angle 2.65391 ( 12) hydrogen bonds : bond 0.03575 ( 378) hydrogen bonds : angle 4.40761 ( 1071) metal coordination : bond 0.00083 ( 2) SS BOND : bond 0.00555 ( 12) SS BOND : angle 2.03357 ( 24) covalent geometry : bond 0.00284 ( 9931) covalent geometry : angle 0.59895 (13519) *********************** 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 176 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 435 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: A 479 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: A 497 TYR cc_start: 0.5699 (m-80) cc_final: 0.5482 (m-80) REVERT: E 406 GLU cc_start: 0.8573 (mp0) cc_final: 0.7551 (mp0) REVERT: E 467 ASP cc_start: 0.8483 (t0) cc_final: 0.7831 (t0) REVERT: H 59 ASN cc_start: 0.9152 (p0) cc_final: 0.8775 (p0) REVERT: H 60 TYR cc_start: 0.8907 (m-80) cc_final: 0.8615 (m-10) REVERT: H 87 ARG cc_start: 0.7035 (mpp80) cc_final: 0.6174 (mtt90) REVERT: L 19 THR cc_start: 0.7597 (m) cc_final: 0.6903 (p) REVERT: L 107 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8167 (mtpp) outliers start: 37 outliers final: 23 residues processed: 171 average time/residue: 0.2141 time to fit residues: 51.8419 Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 435 GLU 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 393 THR 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 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 H residue 204 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 373 HIS ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN L 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.173082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151293 restraints weight = 25887.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151614 restraints weight = 36885.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151602 restraints weight = 33561.199| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9949 Z= 0.131 Angle : 0.613 9.849 13555 Z= 0.305 Chirality : 0.044 0.164 1470 Planarity : 0.003 0.030 1744 Dihedral : 4.673 75.235 1415 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.14 % Allowed : 23.29 % Favored : 73.57 % 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: -0.21 (0.24), residues: 1223 helix: 0.78 (0.26), residues: 408 sheet: 0.32 (0.37), residues: 193 loop : -0.89 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 401 PHE 0.016 0.002 PHE A 555 TYR 0.010 0.001 TYR H 205 ARG 0.005 0.001 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 4) link_NAG-ASN : angle 2.62445 ( 12) hydrogen bonds : bond 0.03649 ( 378) hydrogen bonds : angle 4.44119 ( 1071) metal coordination : bond 0.00075 ( 2) SS BOND : bond 0.00378 ( 12) SS BOND : angle 1.75461 ( 24) covalent geometry : bond 0.00297 ( 9931) covalent geometry : angle 0.60449 (13519) *********************** 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 155 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 479 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: E 357 ARG cc_start: 0.8306 (tpt-90) cc_final: 0.8069 (ttt90) REVERT: E 406 GLU cc_start: 0.8656 (mp0) cc_final: 0.7614 (mp0) REVERT: H 59 ASN cc_start: 0.9160 (p0) cc_final: 0.8785 (p0) REVERT: H 60 TYR cc_start: 0.8945 (m-80) cc_final: 0.8651 (m-10) REVERT: H 204 THR cc_start: 0.4824 (OUTLIER) cc_final: 0.3923 (m) REVERT: L 107 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8134 (mtpp) outliers start: 32 outliers final: 22 residues processed: 151 average time/residue: 0.2032 time to fit residues: 44.5957 Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 393 THR 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 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 53 ASN 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 34 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 108 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165513 restraints weight = 17542.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154784 restraints weight = 35536.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152924 restraints weight = 30838.332| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9949 Z= 0.126 Angle : 0.627 13.714 13555 Z= 0.310 Chirality : 0.044 0.226 1470 Planarity : 0.003 0.027 1744 Dihedral : 4.461 61.021 1415 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.85 % Allowed : 24.14 % 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: -0.24 (0.24), residues: 1223 helix: 0.70 (0.26), residues: 408 sheet: 0.27 (0.36), residues: 193 loop : -0.85 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 373 PHE 0.019 0.002 PHE H 64 TYR 0.018 0.001 TYR A 279 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 4) link_NAG-ASN : angle 2.57319 ( 12) hydrogen bonds : bond 0.03592 ( 378) hydrogen bonds : angle 4.46560 ( 1071) metal coordination : bond 0.00046 ( 2) SS BOND : bond 0.00333 ( 12) SS BOND : angle 1.60588 ( 24) covalent geometry : bond 0.00283 ( 9931) covalent geometry : angle 0.61916 (13519) *********************** 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 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASP cc_start: 0.7080 (t0) cc_final: 0.6828 (t70) REVERT: A 435 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: A 479 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: E 406 GLU cc_start: 0.8570 (mp0) cc_final: 0.7522 (mp0) REVERT: H 59 ASN cc_start: 0.9170 (p0) cc_final: 0.8797 (p0) REVERT: H 60 TYR cc_start: 0.8964 (m-80) cc_final: 0.8687 (m-10) REVERT: L 107 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8126 (mtpp) outliers start: 29 outliers final: 25 residues processed: 152 average time/residue: 0.1980 time to fit residues: 43.5038 Evaluate side-chains 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 329 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 380 TYR 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 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 L residue 53 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.171775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165251 restraints weight = 19917.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154066 restraints weight = 42767.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152066 restraints weight = 38306.486| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9949 Z= 0.124 Angle : 0.615 8.560 13555 Z= 0.305 Chirality : 0.044 0.169 1470 Planarity : 0.003 0.027 1744 Dihedral : 4.301 48.651 1415 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.04 % Allowed : 24.71 % Favored : 72.24 % 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: -0.21 (0.24), residues: 1223 helix: 0.69 (0.26), residues: 414 sheet: 0.44 (0.38), residues: 181 loop : -0.86 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS A 373 PHE 0.020 0.001 PHE H 64 TYR 0.010 0.001 TYR H 205 ARG 0.005 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 2.51311 ( 12) hydrogen bonds : bond 0.03597 ( 378) hydrogen bonds : angle 4.44223 ( 1071) metal coordination : bond 0.00116 ( 2) SS BOND : bond 0.00327 ( 12) SS BOND : angle 1.43521 ( 24) covalent geometry : bond 0.00281 ( 9931) covalent geometry : angle 0.60862 (13519) *********************** 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 154 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7518 (m-40) cc_final: 0.6904 (t0) REVERT: A 350 ASP cc_start: 0.7171 (t0) cc_final: 0.6906 (t70) REVERT: A 435 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: A 479 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: A 582 ARG cc_start: 0.7595 (tpm170) cc_final: 0.7314 (tpm170) REVERT: E 406 GLU cc_start: 0.8503 (mp0) cc_final: 0.7532 (mp0) REVERT: H 29 PHE cc_start: 0.7142 (t80) cc_final: 0.6778 (t80) REVERT: H 59 ASN cc_start: 0.9166 (p0) cc_final: 0.8826 (p0) REVERT: H 60 TYR cc_start: 0.8949 (m-80) cc_final: 0.8669 (m-10) REVERT: L 107 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8031 (mtpp) outliers start: 31 outliers final: 28 residues processed: 149 average time/residue: 0.2254 time to fit residues: 49.5186 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 361 CYS Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR 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 487 ASN 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 53 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 109 optimal weight: 0.0030 chunk 71 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150589 restraints weight = 25595.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150395 restraints weight = 33721.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150699 restraints weight = 33317.582| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9949 Z= 0.122 Angle : 0.617 8.562 13555 Z= 0.306 Chirality : 0.044 0.169 1470 Planarity : 0.003 0.030 1744 Dihedral : 4.243 48.454 1415 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.76 % Allowed : 25.00 % Favored : 72.24 % 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: -0.22 (0.24), residues: 1223 helix: 0.68 (0.26), residues: 415 sheet: 0.43 (0.38), residues: 182 loop : -0.86 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.005 0.001 HIS A 373 PHE 0.027 0.001 PHE H 64 TYR 0.021 0.001 TYR A 279 ARG 0.005 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 4) link_NAG-ASN : angle 2.43579 ( 12) hydrogen bonds : bond 0.03586 ( 378) hydrogen bonds : angle 4.41777 ( 1071) metal coordination : bond 0.00054 ( 2) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.42019 ( 24) covalent geometry : bond 0.00274 ( 9931) covalent geometry : angle 0.61018 (13519) ********************** 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 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7582 (m-40) cc_final: 0.6998 (t0) REVERT: A 350 ASP cc_start: 0.7116 (t0) cc_final: 0.6845 (t70) REVERT: A 435 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: A 479 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: A 610 TRP cc_start: 0.5578 (t60) cc_final: 0.5283 (t-100) REVERT: E 357 ARG cc_start: 0.7882 (tpt-90) cc_final: 0.7607 (tpt170) REVERT: E 406 GLU cc_start: 0.8496 (mp0) cc_final: 0.7535 (mp0) REVERT: H 29 PHE cc_start: 0.7146 (t80) cc_final: 0.6764 (t80) REVERT: H 59 ASN cc_start: 0.9163 (p0) cc_final: 0.8816 (p0) REVERT: H 60 TYR cc_start: 0.8940 (m-80) cc_final: 0.8670 (m-10) REVERT: L 64 PHE cc_start: 0.7785 (m-80) cc_final: 0.7480 (m-80) REVERT: L 107 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8085 (mtpp) outliers start: 28 outliers final: 25 residues processed: 143 average time/residue: 0.2158 time to fit residues: 44.7255 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 329 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 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 76 THR Chi-restraints excluded: chain H residue 87 ARG 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 53 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 115 optimal weight: 0.0170 chunk 46 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.172120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149159 restraints weight = 23746.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148256 restraints weight = 29334.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149065 restraints weight = 33981.896| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9949 Z= 0.133 Angle : 0.633 8.434 13555 Z= 0.314 Chirality : 0.044 0.172 1470 Planarity : 0.003 0.033 1744 Dihedral : 4.212 47.469 1415 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.14 % Allowed : 24.71 % Favored : 72.15 % 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: -0.17 (0.24), residues: 1223 helix: 0.72 (0.26), residues: 415 sheet: 0.44 (0.38), residues: 186 loop : -0.84 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 373 PHE 0.018 0.002 PHE H 64 TYR 0.011 0.001 TYR H 205 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 2.39174 ( 12) hydrogen bonds : bond 0.03691 ( 378) hydrogen bonds : angle 4.47497 ( 1071) metal coordination : bond 0.00046 ( 2) SS BOND : bond 0.00314 ( 12) SS BOND : angle 1.47858 ( 24) covalent geometry : bond 0.00305 ( 9931) covalent geometry : angle 0.62701 (13519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.46 seconds wall clock time: 60 minutes 58.10 seconds (3658.10 seconds total)