Starting phenix.real_space_refine on Fri Mar 15 08:52:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydi_33748/03_2024/7ydi_33748.pdb" } 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 Residue "A GLU 110": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ASP 112": "OD1" <-> "OD2" Residue "L ASP 84": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.44, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 3.96 Conformation dependent library (CDL) restraints added in 2.1 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: 1.05 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: 2.93 Time building geometry restraints manager: 4.31 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: 99.17 - 106.16: 283 106.16 - 113.16: 5195 113.16 - 120.15: 3510 120.15 - 127.15: 4394 127.15 - 134.14: 137 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 2.520 nonbonded pdb=" O TYR A 515 " pdb=" OG1 THR A 519 " model vdw 2.288 2.440 nonbonded pdb=" O LYS A 114 " pdb=" OG1 THR A 118 " model vdw 2.310 2.440 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.316 2.440 ... (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 ========== 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: 1.420 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: 6.530 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 32.030 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9931 Z= 0.207 Angle : 0.698 11.618 13519 Z= 0.346 Chirality : 0.045 0.363 1470 Planarity : 0.005 0.057 1744 Dihedral : 14.601 89.344 3621 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 20.53 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1223 helix: 0.22 (0.25), residues: 403 sheet: -0.29 (0.38), residues: 186 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS A 34 PHE 0.014 0.001 PHE E 486 TYR 0.023 0.001 TYR H 32 ARG 0.012 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.056 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: 0.2186 time to fit residues: 84.4599 Evaluate side-chains 178 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain H residue 103 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 81 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 330 ASN E 394 ASN E 409 GLN E 437 ASN E 506 GLN H 39 GLN L 39 GLN L 40 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9931 Z= 0.204 Angle : 0.590 7.426 13519 Z= 0.297 Chirality : 0.043 0.177 1470 Planarity : 0.004 0.051 1744 Dihedral : 4.697 57.174 1418 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.18 % Allowed : 19.39 % Favored : 76.43 % 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: 0.56 (0.27), residues: 411 sheet: 0.23 (0.36), residues: 201 loop : -1.01 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS A 401 PHE 0.021 0.002 PHE E 392 TYR 0.016 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7801 (t80) cc_final: 0.7497 (t80) REVERT: A 45 LEU cc_start: 0.7444 (tp) cc_final: 0.7083 (mt) REVERT: A 49 ASN cc_start: 0.7690 (m-40) cc_final: 0.6912 (m-40) REVERT: A 90 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.5937 (t0) REVERT: A 117 ASN cc_start: 0.7318 (p0) cc_final: 0.7068 (p0) REVERT: A 121 ASN cc_start: 0.8081 (m-40) cc_final: 0.7718 (m110) REVERT: A 145 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 150 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6690 (mm-30) REVERT: A 213 ASP cc_start: 0.8102 (p0) cc_final: 0.7819 (m-30) REVERT: A 245 ARG cc_start: 0.6292 (ttp-170) cc_final: 0.5905 (ttp80) REVERT: A 323 MET cc_start: 0.8909 (mmm) cc_final: 0.8602 (mmt) REVERT: A 328 TRP cc_start: 0.7738 (m100) cc_final: 0.6741 (m100) REVERT: A 330 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: A 355 ASP cc_start: 0.8034 (t0) cc_final: 0.7269 (t0) REVERT: A 359 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5707 (mm) REVERT: A 434 THR cc_start: 0.4566 (p) cc_final: 0.3934 (t) REVERT: A 435 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6134 (pm20) REVERT: A 471 ASP cc_start: 0.6978 (t0) cc_final: 0.6109 (p0) REVERT: A 480 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7120 (ptp) REVERT: A 546 ASN cc_start: 0.5423 (m-40) cc_final: 0.4399 (t0) REVERT: A 582 ARG cc_start: 0.6791 (mmp80) cc_final: 0.5650 (tpm170) REVERT: E 406 GLU cc_start: 0.7626 (mp0) cc_final: 0.6985 (mp0) REVERT: E 418 ILE cc_start: 0.6371 (mt) cc_final: 0.5723 (mt) REVERT: E 424 LYS cc_start: 0.7466 (tttm) cc_final: 0.7186 (tppt) REVERT: H 46 GLU cc_start: 0.8349 (pm20) cc_final: 0.7983 (pt0) REVERT: H 59 ASN cc_start: 0.8622 (p0) cc_final: 0.8250 (p0) REVERT: H 60 TYR cc_start: 0.8432 (m-80) cc_final: 0.8171 (m-10) REVERT: H 94 TYR cc_start: 0.8260 (m-80) cc_final: 0.8020 (m-80) REVERT: L 87 ASP cc_start: 0.6997 (p0) cc_final: 0.6722 (p0) REVERT: L 94 ASP cc_start: 0.6773 (t0) cc_final: 0.6530 (t0) outliers start: 43 outliers final: 15 residues processed: 214 average time/residue: 0.2124 time to fit residues: 64.9597 Evaluate side-chains 170 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 182 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9931 Z= 0.190 Angle : 0.550 6.417 13519 Z= 0.277 Chirality : 0.042 0.189 1470 Planarity : 0.004 0.048 1744 Dihedral : 4.430 56.897 1417 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.85 % Allowed : 22.34 % Favored : 74.81 % 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: 0.81 (0.27), residues: 406 sheet: 0.55 (0.38), residues: 185 loop : -1.05 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 417 PHE 0.028 0.002 PHE H 64 TYR 0.015 0.001 TYR A 510 ARG 0.007 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8047 (mp0) cc_final: 0.7682 (pm20) REVERT: A 82 MET cc_start: 0.8278 (tmm) cc_final: 0.7793 (tmm) REVERT: A 90 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.5982 (t0) REVERT: A 120 LEU cc_start: 0.8495 (tt) cc_final: 0.8183 (mm) REVERT: A 121 ASN cc_start: 0.8066 (m-40) cc_final: 0.7518 (m110) REVERT: A 145 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7437 (tm-30) REVERT: A 150 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6698 (mm-30) REVERT: A 213 ASP cc_start: 0.8232 (p0) cc_final: 0.7950 (m-30) REVERT: A 245 ARG cc_start: 0.6679 (ttp-170) cc_final: 0.5902 (ttp80) REVERT: A 323 MET cc_start: 0.8963 (mmm) cc_final: 0.8593 (mmm) REVERT: A 355 ASP cc_start: 0.7748 (t0) cc_final: 0.6937 (t0) REVERT: A 359 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5667 (mm) REVERT: A 361 CYS cc_start: 0.4191 (OUTLIER) cc_final: 0.3152 (p) REVERT: A 366 MET cc_start: 0.6929 (tpp) cc_final: 0.6702 (tpp) REVERT: A 432 ASN cc_start: 0.7156 (m-40) cc_final: 0.6776 (p0) REVERT: A 434 THR cc_start: 0.4851 (p) cc_final: 0.4264 (t) REVERT: A 435 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6212 (pm20) REVERT: A 471 ASP cc_start: 0.7233 (t0) cc_final: 0.6299 (p0) REVERT: A 480 MET cc_start: 0.7783 (ptm) cc_final: 0.7449 (ptp) REVERT: A 582 ARG cc_start: 0.6687 (mmp80) cc_final: 0.5567 (tpm170) REVERT: E 406 GLU cc_start: 0.7696 (mp0) cc_final: 0.7151 (mp0) REVERT: E 424 LYS cc_start: 0.7574 (tttm) cc_final: 0.7207 (tppt) REVERT: E 493 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7481 (mm-40) REVERT: H 59 ASN cc_start: 0.8736 (p0) cc_final: 0.8301 (p0) REVERT: H 60 TYR cc_start: 0.8555 (m-80) cc_final: 0.8196 (m-10) REVERT: L 87 ASP cc_start: 0.7051 (p0) cc_final: 0.6438 (p0) REVERT: L 94 ASP cc_start: 0.7308 (t0) cc_final: 0.6810 (t0) outliers start: 29 outliers final: 19 residues processed: 184 average time/residue: 0.2212 time to fit residues: 57.9994 Evaluate side-chains 167 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 427 ASP 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 H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 2 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 97 optimal weight: 0.0050 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 101 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN H 166 ASN ** H 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9931 Z= 0.267 Angle : 0.635 7.754 13519 Z= 0.324 Chirality : 0.045 0.293 1470 Planarity : 0.004 0.047 1744 Dihedral : 4.752 54.091 1417 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.85 % Allowed : 21.29 % Favored : 73.86 % 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: -0.41 (0.24), residues: 1223 helix: 0.63 (0.26), residues: 409 sheet: 0.08 (0.34), residues: 204 loop : -0.99 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 165 HIS 0.004 0.001 HIS A 417 PHE 0.020 0.002 PHE E 497 TYR 0.023 0.002 TYR E 380 ARG 0.008 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8126 (mp0) cc_final: 0.7912 (mp0) REVERT: A 82 MET cc_start: 0.7988 (tmm) cc_final: 0.7720 (tmm) REVERT: A 90 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 117 ASN cc_start: 0.7893 (t0) cc_final: 0.7313 (t0) REVERT: A 121 ASN cc_start: 0.7691 (m-40) cc_final: 0.7217 (m-40) REVERT: A 145 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 150 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6712 (mm-30) REVERT: A 213 ASP cc_start: 0.8021 (p0) cc_final: 0.7732 (m-30) REVERT: A 323 MET cc_start: 0.9124 (mmm) cc_final: 0.8893 (mmm) REVERT: A 329 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8063 (pp20) REVERT: A 359 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6316 (mm) REVERT: A 366 MET cc_start: 0.7113 (tpp) cc_final: 0.6896 (tpp) REVERT: A 398 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.4829 (tp30) REVERT: A 432 ASN cc_start: 0.7028 (m-40) cc_final: 0.6439 (p0) REVERT: A 434 THR cc_start: 0.6533 (p) cc_final: 0.6124 (t) REVERT: A 435 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6104 (pm20) REVERT: A 442 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6973 (mm-40) REVERT: A 462 MET cc_start: 0.6917 (ptp) cc_final: 0.6624 (mpp) REVERT: A 479 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: A 480 MET cc_start: 0.8152 (ptm) cc_final: 0.7132 (ptp) REVERT: A 582 ARG cc_start: 0.6842 (mmp80) cc_final: 0.5754 (tpm170) REVERT: E 406 GLU cc_start: 0.7811 (mp0) cc_final: 0.7404 (mp0) REVERT: E 420 ASP cc_start: 0.8180 (t0) cc_final: 0.7832 (t0) REVERT: E 487 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6171 (t0) REVERT: H 46 GLU cc_start: 0.8657 (pt0) cc_final: 0.8387 (pt0) REVERT: H 90 ASP cc_start: 0.6447 (t0) cc_final: 0.6135 (t0) REVERT: L 64 PHE cc_start: 0.7230 (m-80) cc_final: 0.6894 (m-80) REVERT: L 87 ASP cc_start: 0.7233 (p0) cc_final: 0.6729 (p0) REVERT: L 94 ASP cc_start: 0.7490 (t0) cc_final: 0.6811 (t0) REVERT: L 107 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7600 (mtpp) outliers start: 50 outliers final: 31 residues processed: 195 average time/residue: 0.2030 time to fit residues: 56.2911 Evaluate side-chains 158 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 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 394 ASN Chi-restraints excluded: chain E residue 427 ASP 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 500 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 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 2 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 80 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN ** H 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9931 Z= 0.171 Angle : 0.557 7.067 13519 Z= 0.280 Chirality : 0.043 0.188 1470 Planarity : 0.003 0.045 1744 Dihedral : 4.461 54.812 1417 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.90 % Allowed : 22.91 % Favored : 73.19 % 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: -0.26 (0.24), residues: 1223 helix: 0.84 (0.27), residues: 408 sheet: -0.06 (0.34), residues: 209 loop : -0.89 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 401 PHE 0.014 0.001 PHE A 555 TYR 0.013 0.001 TYR H 60 ARG 0.007 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7860 (mm-40) REVERT: A 90 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.6667 (t0) REVERT: A 145 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 150 GLU cc_start: 0.7557 (tm-30) cc_final: 0.6746 (mm-30) REVERT: A 213 ASP cc_start: 0.8031 (p0) cc_final: 0.7738 (m-30) REVERT: A 309 LYS cc_start: 0.7195 (mmmt) cc_final: 0.6765 (mtmt) REVERT: A 310 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 329 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7890 (pp20) REVERT: A 398 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.4957 (tp30) REVERT: A 432 ASN cc_start: 0.7157 (m-40) cc_final: 0.6524 (p0) REVERT: A 434 THR cc_start: 0.6502 (p) cc_final: 0.6073 (t) REVERT: A 435 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6038 (pm20) REVERT: A 442 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6945 (mm-40) REVERT: A 479 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6449 (tm-30) REVERT: A 480 MET cc_start: 0.7768 (ptm) cc_final: 0.7258 (ptp) REVERT: A 582 ARG cc_start: 0.6786 (mmp80) cc_final: 0.5694 (tpm170) REVERT: E 406 GLU cc_start: 0.7775 (mp0) cc_final: 0.7380 (mp0) REVERT: E 420 ASP cc_start: 0.8118 (t0) cc_final: 0.7762 (t0) REVERT: H 90 ASP cc_start: 0.6395 (t0) cc_final: 0.6100 (t0) REVERT: L 87 ASP cc_start: 0.7017 (p0) cc_final: 0.6524 (p0) REVERT: L 94 ASP cc_start: 0.7580 (t0) cc_final: 0.6934 (t0) outliers start: 40 outliers final: 25 residues processed: 171 average time/residue: 0.1877 time to fit residues: 46.7664 Evaluate side-chains 151 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 2 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 0.0000 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS E 409 GLN H 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9931 Z= 0.149 Angle : 0.559 9.353 13519 Z= 0.273 Chirality : 0.042 0.179 1470 Planarity : 0.003 0.043 1744 Dihedral : 4.311 54.555 1417 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.61 % Allowed : 23.86 % Favored : 72.53 % 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: -0.13 (0.24), residues: 1223 helix: 0.92 (0.26), residues: 410 sheet: 0.20 (0.36), residues: 196 loop : -0.85 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS A 401 PHE 0.015 0.001 PHE A 555 TYR 0.012 0.001 TYR A 510 ARG 0.007 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7829 (mm-40) REVERT: A 90 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.6606 (t0) REVERT: A 145 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 150 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6762 (mm-30) REVERT: A 213 ASP cc_start: 0.8037 (p0) cc_final: 0.7742 (m-30) REVERT: A 261 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6853 (p) REVERT: A 309 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6768 (mtmt) REVERT: A 329 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8032 (pp20) REVERT: A 398 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.4851 (tp30) REVERT: A 432 ASN cc_start: 0.7123 (m-40) cc_final: 0.6620 (p0) REVERT: A 434 THR cc_start: 0.6382 (p) cc_final: 0.6155 (t) REVERT: A 435 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5889 (pm20) REVERT: A 438 PHE cc_start: 0.7726 (t80) cc_final: 0.7489 (t80) REVERT: A 442 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6847 (mm-40) REVERT: A 479 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: A 480 MET cc_start: 0.7913 (ptm) cc_final: 0.7084 (ptp) REVERT: A 582 ARG cc_start: 0.6811 (mmp80) cc_final: 0.5702 (tpm170) REVERT: E 378 LYS cc_start: 0.8347 (ptpp) cc_final: 0.7057 (mmmt) REVERT: E 406 GLU cc_start: 0.7787 (mp0) cc_final: 0.7421 (mp0) REVERT: E 420 ASP cc_start: 0.8000 (t0) cc_final: 0.7692 (t0) REVERT: H 90 ASP cc_start: 0.6378 (t0) cc_final: 0.6064 (t0) REVERT: L 87 ASP cc_start: 0.6850 (p0) cc_final: 0.6367 (p0) REVERT: L 94 ASP cc_start: 0.7595 (t0) cc_final: 0.6989 (t0) outliers start: 37 outliers final: 28 residues processed: 166 average time/residue: 0.1940 time to fit residues: 46.6478 Evaluate side-chains 155 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 427 ASP 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 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 136 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9931 Z= 0.201 Angle : 0.600 10.740 13519 Z= 0.296 Chirality : 0.043 0.197 1470 Planarity : 0.003 0.035 1744 Dihedral : 4.400 52.517 1417 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.28 % Allowed : 23.57 % 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: -0.12 (0.24), residues: 1223 helix: 0.94 (0.27), residues: 408 sheet: 0.12 (0.36), residues: 196 loop : -0.81 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 PHE 0.019 0.002 PHE H 64 TYR 0.013 0.001 TYR H 205 ARG 0.010 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.6850 (t0) REVERT: A 145 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 150 GLU cc_start: 0.7592 (tm-30) cc_final: 0.6788 (mm-30) REVERT: A 213 ASP cc_start: 0.8095 (p0) cc_final: 0.7769 (m-30) REVERT: A 249 MET cc_start: 0.5145 (ppp) cc_final: 0.4767 (ppp) REVERT: A 309 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6817 (mtmt) REVERT: A 329 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7735 (pp20) REVERT: A 366 MET cc_start: 0.7312 (tpp) cc_final: 0.6811 (mmm) REVERT: A 398 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5015 (tp30) REVERT: A 432 ASN cc_start: 0.7228 (m-40) cc_final: 0.6568 (p0) REVERT: A 434 THR cc_start: 0.7007 (p) cc_final: 0.6557 (p) REVERT: A 435 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5943 (pm20) REVERT: A 438 PHE cc_start: 0.7779 (t80) cc_final: 0.7543 (t80) REVERT: A 442 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6995 (mm-40) REVERT: A 479 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6427 (tm-30) REVERT: A 480 MET cc_start: 0.7749 (ptm) cc_final: 0.7426 (ptp) REVERT: A 526 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7408 (tp40) REVERT: A 582 ARG cc_start: 0.6847 (mmp80) cc_final: 0.5798 (tpm170) REVERT: E 357 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8094 (tpt-90) REVERT: E 378 LYS cc_start: 0.8412 (ptpp) cc_final: 0.7098 (mmmt) REVERT: E 420 ASP cc_start: 0.7871 (t0) cc_final: 0.7523 (t0) REVERT: H 87 ARG cc_start: 0.7178 (mpp80) cc_final: 0.6769 (mtt90) REVERT: H 90 ASP cc_start: 0.6481 (t0) cc_final: 0.6119 (t0) REVERT: L 81 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: L 87 ASP cc_start: 0.7079 (p0) cc_final: 0.6517 (p0) REVERT: L 94 ASP cc_start: 0.7613 (t0) cc_final: 0.6978 (t0) outliers start: 44 outliers final: 35 residues processed: 163 average time/residue: 0.1978 time to fit residues: 46.4776 Evaluate side-chains 167 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 427 ASP 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 500 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 2 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9931 Z= 0.168 Angle : 0.567 7.393 13519 Z= 0.279 Chirality : 0.042 0.178 1470 Planarity : 0.003 0.046 1744 Dihedral : 4.315 51.860 1417 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.09 % Allowed : 23.38 % Favored : 72.53 % 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: -0.06 (0.24), residues: 1223 helix: 1.03 (0.27), residues: 407 sheet: 0.10 (0.36), residues: 196 loop : -0.79 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 PHE 0.021 0.001 PHE H 64 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.6692 (t0) REVERT: A 145 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 150 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6729 (mm-30) REVERT: A 210 ASN cc_start: 0.8579 (m-40) cc_final: 0.7417 (t0) REVERT: A 213 ASP cc_start: 0.8180 (p0) cc_final: 0.7814 (m-30) REVERT: A 249 MET cc_start: 0.5237 (ppp) cc_final: 0.4968 (ppp) REVERT: A 329 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7680 (pp20) REVERT: A 366 MET cc_start: 0.7338 (tpp) cc_final: 0.6899 (mmm) REVERT: A 398 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.4970 (tp30) REVERT: A 434 THR cc_start: 0.7118 (p) cc_final: 0.6585 (p) REVERT: A 435 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5764 (pm20) REVERT: A 438 PHE cc_start: 0.7753 (t80) cc_final: 0.7514 (t80) REVERT: A 442 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6969 (mm-40) REVERT: A 479 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: A 480 MET cc_start: 0.7478 (ptm) cc_final: 0.7170 (ptp) REVERT: A 582 ARG cc_start: 0.6829 (mmp80) cc_final: 0.5782 (tpm170) REVERT: E 357 ARG cc_start: 0.8418 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: E 378 LYS cc_start: 0.8325 (ptpp) cc_final: 0.7026 (mmmt) REVERT: E 420 ASP cc_start: 0.7852 (t0) cc_final: 0.7499 (t0) REVERT: H 87 ARG cc_start: 0.7127 (mpp80) cc_final: 0.6710 (mtt90) REVERT: H 90 ASP cc_start: 0.6497 (t0) cc_final: 0.6098 (t0) REVERT: L 81 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: L 87 ASP cc_start: 0.6970 (p0) cc_final: 0.6397 (p0) REVERT: L 94 ASP cc_start: 0.7633 (t0) cc_final: 0.6927 (t0) outliers start: 42 outliers final: 34 residues processed: 167 average time/residue: 0.1923 time to fit residues: 46.9089 Evaluate side-chains 162 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain E residue 500 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 81 GLN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS E 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9931 Z= 0.167 Angle : 0.567 6.970 13519 Z= 0.278 Chirality : 0.042 0.176 1470 Planarity : 0.003 0.032 1744 Dihedral : 4.377 51.077 1417 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.37 % Allowed : 23.29 % Favored : 72.34 % 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: 0.01 (0.24), residues: 1223 helix: 1.10 (0.27), residues: 407 sheet: 0.16 (0.36), residues: 196 loop : -0.75 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 373 PHE 0.018 0.001 PHE H 64 TYR 0.010 0.001 TYR A 41 ARG 0.006 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.6716 (t0) REVERT: A 121 ASN cc_start: 0.7518 (m-40) cc_final: 0.7145 (m110) REVERT: A 150 GLU cc_start: 0.7653 (tm-30) cc_final: 0.6698 (mm-30) REVERT: A 210 ASN cc_start: 0.8608 (m-40) cc_final: 0.7464 (t0) REVERT: A 213 ASP cc_start: 0.8194 (p0) cc_final: 0.7832 (m-30) REVERT: A 325 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7483 (tp40) REVERT: A 329 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7566 (pp20) REVERT: A 398 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.4903 (tp30) REVERT: A 434 THR cc_start: 0.7224 (p) cc_final: 0.6737 (p) REVERT: A 435 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5775 (pm20) REVERT: A 438 PHE cc_start: 0.7752 (t80) cc_final: 0.7521 (t80) REVERT: A 442 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6914 (mm-40) REVERT: A 462 MET cc_start: 0.6892 (mpp) cc_final: 0.6632 (mpp) REVERT: A 479 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: A 480 MET cc_start: 0.7534 (ptm) cc_final: 0.7243 (ptp) REVERT: A 582 ARG cc_start: 0.6940 (mmp80) cc_final: 0.5843 (tpm170) REVERT: E 357 ARG cc_start: 0.8505 (tpt-90) cc_final: 0.8113 (tpt-90) REVERT: E 378 LYS cc_start: 0.8308 (ptpp) cc_final: 0.6948 (mmmt) REVERT: E 406 GLU cc_start: 0.7690 (mp0) cc_final: 0.6939 (mm-30) REVERT: E 409 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7165 (tp40) REVERT: E 420 ASP cc_start: 0.7857 (t0) cc_final: 0.7510 (t0) REVERT: H 87 ARG cc_start: 0.7183 (mpp80) cc_final: 0.6548 (mtt90) REVERT: H 90 ASP cc_start: 0.6559 (t0) cc_final: 0.6202 (t0) REVERT: L 81 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: L 87 ASP cc_start: 0.6934 (p0) cc_final: 0.6374 (p0) REVERT: L 94 ASP cc_start: 0.7568 (t0) cc_final: 0.6904 (t0) outliers start: 45 outliers final: 38 residues processed: 164 average time/residue: 0.1955 time to fit residues: 46.8456 Evaluate side-chains 168 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 51 ILE 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 2 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 0.0060 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9931 Z= 0.190 Angle : 0.862 59.200 13519 Z= 0.486 Chirality : 0.044 0.395 1470 Planarity : 0.003 0.032 1744 Dihedral : 4.382 51.036 1417 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.18 % Allowed : 23.67 % 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: 0.01 (0.24), residues: 1223 helix: 1.09 (0.27), residues: 407 sheet: 0.17 (0.36), residues: 196 loop : -0.75 (0.26), residues: 620 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 0.019 0.001 PHE H 64 TYR 0.010 0.001 TYR A 41 ARG 0.006 0.000 ARG E 357 ********************** 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 167 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.6720 (t0) REVERT: A 121 ASN cc_start: 0.7498 (m-40) cc_final: 0.7144 (m110) REVERT: A 150 GLU cc_start: 0.7653 (tm-30) cc_final: 0.6698 (mm-30) REVERT: A 210 ASN cc_start: 0.8610 (m-40) cc_final: 0.7466 (t0) REVERT: A 213 ASP cc_start: 0.8196 (p0) cc_final: 0.7832 (m-30) REVERT: A 325 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7484 (tp40) REVERT: A 329 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7567 (pp20) REVERT: A 398 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.4906 (tp30) REVERT: A 434 THR cc_start: 0.7191 (p) cc_final: 0.6737 (p) REVERT: A 435 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5775 (pm20) REVERT: A 438 PHE cc_start: 0.7751 (t80) cc_final: 0.7521 (t80) REVERT: A 442 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6916 (mm-40) REVERT: A 462 MET cc_start: 0.6884 (mpp) cc_final: 0.6627 (mpp) REVERT: A 479 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: A 480 MET cc_start: 0.7547 (ptm) cc_final: 0.7236 (ptp) REVERT: A 582 ARG cc_start: 0.6942 (mmp80) cc_final: 0.5844 (tpm170) REVERT: E 357 ARG cc_start: 0.8492 (tpt-90) cc_final: 0.8116 (tpt-90) REVERT: E 378 LYS cc_start: 0.8309 (ptpp) cc_final: 0.6948 (mmmt) REVERT: E 406 GLU cc_start: 0.7693 (mp0) cc_final: 0.6943 (mm-30) REVERT: E 409 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: E 420 ASP cc_start: 0.7857 (t0) cc_final: 0.7510 (t0) REVERT: H 87 ARG cc_start: 0.7186 (mpp80) cc_final: 0.6553 (mtt90) REVERT: H 90 ASP cc_start: 0.6581 (t0) cc_final: 0.6203 (t0) REVERT: L 81 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: L 87 ASP cc_start: 0.6933 (p0) cc_final: 0.6374 (p0) REVERT: L 94 ASP cc_start: 0.7571 (t0) cc_final: 0.6902 (t0) outliers start: 43 outliers final: 38 residues processed: 157 average time/residue: 0.1973 time to fit residues: 45.0810 Evaluate side-chains 167 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 51 ILE 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 81 GLN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 186 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 88 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151714 restraints weight = 21293.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150862 restraints weight = 28696.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150756 restraints weight = 28401.612| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9931 Z= 0.190 Angle : 0.862 59.200 13519 Z= 0.486 Chirality : 0.044 0.395 1470 Planarity : 0.003 0.032 1744 Dihedral : 4.382 51.036 1417 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.18 % Allowed : 23.67 % 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: 0.01 (0.24), residues: 1223 helix: 1.09 (0.27), residues: 407 sheet: 0.17 (0.36), residues: 196 loop : -0.75 (0.26), residues: 620 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 0.019 0.001 PHE H 64 TYR 0.010 0.001 TYR A 41 ARG 0.006 0.000 ARG E 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2199.69 seconds wall clock time: 40 minutes 32.53 seconds (2432.53 seconds total)