Starting phenix.real_space_refine on Sat Aug 23 13:44:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.map" model { file = "/net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gqd_34200/08_2025/8gqd_34200.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 96 5.16 5 C 7872 2.51 5 N 2232 2.21 5 O 2440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12644 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2701 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 326} Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2701 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 326} Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2701 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 326} Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2701 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 326} Chain: "E" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "F" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "G" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "H" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10830 SG CYS E 87 19.277 39.468 21.751 1.00 84.72 S ATOM 10963 SG CYS E 105 21.399 35.641 22.429 1.00 75.82 S ATOM 10982 SG CYS E 108 22.330 39.951 23.617 1.00 79.30 S ATOM 11289 SG CYS F 87 77.550 48.442 21.873 1.00 84.92 S ATOM 11308 SG CYS F 90 77.357 50.831 25.730 1.00 80.35 S ATOM 11422 SG CYS F 105 75.406 52.254 22.568 1.00 74.57 S ATOM 11441 SG CYS F 108 74.505 47.934 23.745 1.00 77.89 S ATOM 11748 SG CYS G 87 19.231 38.815 128.892 1.00 85.15 S ATOM 11767 SG CYS G 90 18.651 41.141 125.036 1.00 79.15 S ATOM 11881 SG CYS G 105 20.060 43.108 128.194 1.00 71.69 S ATOM 12207 SG CYS H 87 77.539 49.235 129.301 1.00 87.92 S ATOM 12226 SG CYS H 90 78.170 46.901 125.457 1.00 83.39 S ATOM 12340 SG CYS H 105 76.706 44.944 128.597 1.00 73.73 S Time building chain proxies: 2.85, per 1000 atoms: 0.23 Number of scatterers: 12644 At special positions: 0 Unit cell: (97.9, 89.1, 152.9, 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 4 29.99 S 96 16.00 O 2440 8.00 N 2232 7.00 C 7872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 679.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 108 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 105 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 105 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 108 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 105 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 87 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 87 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 105 " Number of angles added : 6 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 52.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 45 through 59 removed outlier: 3.653A pdb=" N LEU D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.814A pdb=" N ILE D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 143 removed outlier: 4.405A pdb=" N LEU D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 223 through 252 removed outlier: 3.530A pdb=" N ILE D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 removed outlier: 3.639A pdb=" N GLN D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 291 removed outlier: 3.713A pdb=" N ALA D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 309 through 313 Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.868A pdb=" N GLU D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.548A pdb=" N ASP A 7 " --> pdb=" O HIS A 3 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 8' Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.654A pdb=" N LEU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.814A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 4.405A pdb=" N LEU A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 223 through 252 removed outlier: 3.671A pdb=" N ILE A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.640A pdb=" N GLN A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.714A pdb=" N ALA A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.142A pdb=" N ASN A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.869A pdb=" N GLU A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.653A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.815A pdb=" N ILE B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 removed outlier: 4.404A pdb=" N LEU B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 223 through 252 removed outlier: 3.679A pdb=" N ILE B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.640A pdb=" N GLN B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.713A pdb=" N ALA B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.543A pdb=" N VAL B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.865A pdb=" N ASP B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.790A pdb=" N LYS B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.653A pdb=" N LEU C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.815A pdb=" N ILE C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 143 removed outlier: 4.405A pdb=" N LEU C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 223 through 252 removed outlier: 3.578A pdb=" N ILE C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.640A pdb=" N GLN C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 291 removed outlier: 3.714A pdb=" N ALA C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.868A pdb=" N GLU C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 105 through 124 removed outlier: 7.069A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 105 through 124 removed outlier: 7.068A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 removed outlier: 3.533A pdb=" N LYS F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 101 Processing helix chain 'G' and resid 105 through 124 removed outlier: 7.068A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP G 115 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 143 removed outlier: 3.562A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 101 Processing helix chain 'H' and resid 105 through 124 removed outlier: 7.068A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 143 removed outlier: 3.650A pdb=" N LYS H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.962A pdb=" N GLU D 63 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 120 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER D 25 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET D 170 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER D 25 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER D 168 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 27 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG D 166 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.961A pdb=" N GLU A 63 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 120 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 25 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET A 170 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A 25 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 168 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 27 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 166 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.962A pdb=" N GLU B 63 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 120 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER B 25 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N MET B 170 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 25 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 168 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 27 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG B 166 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.962A pdb=" N GLU C 63 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 120 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 25 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET C 170 " --> pdb=" O MET C 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C 25 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 168 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 27 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG C 166 " --> pdb=" O ILE C 27 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1713 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: 2.08 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2463 1.32 - 1.45: 2904 1.45 - 1.57: 7289 1.57 - 1.70: 4 1.70 - 1.82: 168 Bond restraints: 12828 Sorted by residual: bond pdb=" N VAL B 306 " pdb=" CA VAL B 306 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.22e-02 6.72e+03 1.16e+01 bond pdb=" N ILE D 237 " pdb=" CA ILE D 237 " ideal model delta sigma weight residual 1.460 1.500 -0.041 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N LEU B 313 " pdb=" CA LEU B 313 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N LEU A 296 " pdb=" CA LEU A 296 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N ILE D 244 " pdb=" CA ILE D 244 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.17e-02 7.31e+03 1.08e+01 ... (remaining 12823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 14713 1.38 - 2.77: 1895 2.77 - 4.15: 521 4.15 - 5.53: 127 5.53 - 6.92: 28 Bond angle restraints: 17284 Sorted by residual: angle pdb=" CA SER H 138 " pdb=" C SER H 138 " pdb=" O SER H 138 " ideal model delta sigma weight residual 121.00 114.65 6.35 1.05e+00 9.07e-01 3.66e+01 angle pdb=" N LYS H 140 " pdb=" CA LYS H 140 " pdb=" C LYS H 140 " ideal model delta sigma weight residual 111.71 105.11 6.60 1.15e+00 7.56e-01 3.29e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 110.62 105.01 5.61 1.02e+00 9.61e-01 3.02e+01 angle pdb=" CA ILE A 5 " pdb=" C ILE A 5 " pdb=" O ILE A 5 " ideal model delta sigma weight residual 120.78 113.91 6.87 1.25e+00 6.40e-01 3.02e+01 angle pdb=" N LEU A 291 " pdb=" CA LEU A 291 " pdb=" C LEU A 291 " ideal model delta sigma weight residual 113.21 107.06 6.15 1.15e+00 7.56e-01 2.86e+01 ... (remaining 17279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6815 17.92 - 35.84: 800 35.84 - 53.75: 236 53.75 - 71.67: 53 71.67 - 89.59: 32 Dihedral angle restraints: 7936 sinusoidal: 3320 harmonic: 4616 Sorted by residual: dihedral pdb=" CA GLY D 198 " pdb=" C GLY D 198 " pdb=" N ILE D 199 " pdb=" CA ILE D 199 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY B 198 " pdb=" C GLY B 198 " pdb=" N ILE B 199 " pdb=" CA ILE B 199 " ideal model delta harmonic sigma weight residual 180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY C 198 " pdb=" C GLY C 198 " pdb=" N ILE C 199 " pdb=" CA ILE C 199 " ideal model delta harmonic sigma weight residual 180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 7933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1502 0.062 - 0.124: 358 0.124 - 0.186: 80 0.186 - 0.248: 17 0.248 - 0.311: 3 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ASN D 298 " pdb=" N ASN D 298 " pdb=" C ASN D 298 " pdb=" CB ASN D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA TYR C 293 " pdb=" N TYR C 293 " pdb=" C TYR C 293 " pdb=" CB TYR C 293 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA PHE C 299 " pdb=" N PHE C 299 " pdb=" C PHE C 299 " pdb=" CB PHE C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1957 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 235 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN D 235 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN D 235 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN D 236 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 138 " -0.015 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C SER H 138 " 0.057 2.00e-02 2.50e+03 pdb=" O SER H 138 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS H 139 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 298 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASN A 298 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN A 298 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 299 " -0.020 2.00e-02 2.50e+03 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 601 2.71 - 3.26: 12794 3.26 - 3.81: 18917 3.81 - 4.35: 23507 4.35 - 4.90: 39367 Nonbonded interactions: 95186 Sorted by model distance: nonbonded pdb=" NH1 ARG A 26 " pdb=" OE1 GLN A 212 " model vdw 2.168 3.120 nonbonded pdb=" NH1 ARG B 26 " pdb=" OE1 GLN B 212 " model vdw 2.168 3.120 nonbonded pdb=" NH1 ARG C 26 " pdb=" OE1 GLN C 212 " model vdw 2.168 3.120 nonbonded pdb=" NH1 ARG D 26 " pdb=" OE1 GLN D 212 " model vdw 2.169 3.120 nonbonded pdb=" O TRP D 12 " pdb=" ND2 ASN D 16 " model vdw 2.181 3.120 ... (remaining 95181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.840 Find NCS groups from input model: 0.220 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 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 : 0.014 0.637 12841 Z= 0.586 Angle : 1.134 24.461 17290 Z= 0.700 Chirality : 0.060 0.311 1960 Planarity : 0.005 0.037 2252 Dihedral : 18.050 89.591 4936 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 5.20 % Allowed : 5.20 % Favored : 89.61 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.17), residues: 1560 helix: -2.58 (0.14), residues: 768 sheet: -2.01 (0.49), residues: 88 loop : -4.32 (0.19), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 331 TYR 0.019 0.002 TYR C 200 PHE 0.020 0.002 PHE A 301 TRP 0.009 0.003 TRP C 12 HIS 0.010 0.002 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00780 (12828) covalent geometry : angle 1.10315 (17284) hydrogen bonds : bond 0.20252 ( 593) hydrogen bonds : angle 6.98279 ( 1713) metal coordination : bond 0.36133 ( 13) metal coordination : angle 14.16017 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 333 HIS cc_start: 0.5246 (m90) cc_final: 0.4973 (m90) REVERT: A 109 ASN cc_start: 0.7937 (t0) cc_final: 0.7710 (t0) REVERT: A 301 PHE cc_start: 0.3421 (m-80) cc_final: 0.3205 (m-80) REVERT: B 236 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: B 300 LYS cc_start: 0.4571 (OUTLIER) cc_final: 0.3465 (mttt) REVERT: B 305 MET cc_start: 0.3647 (mtt) cc_final: 0.3422 (mtt) REVERT: B 326 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6534 (ttp-110) REVERT: C 97 LEU cc_start: 0.7845 (tp) cc_final: 0.7564 (tp) REVERT: C 109 ASN cc_start: 0.7993 (t0) cc_final: 0.7712 (t0) REVERT: C 294 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6158 (mt) REVERT: C 301 PHE cc_start: 0.3937 (m-80) cc_final: 0.3265 (m-80) outliers start: 74 outliers final: 12 residues processed: 336 average time/residue: 0.0905 time to fit residues: 44.3512 Evaluate side-chains 205 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 300 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 ASN D 46 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 53 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN C 46 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN C 298 ASN E 130 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.233669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.200662 restraints weight = 13187.872| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 1.70 r_work: 0.4267 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12841 Z= 0.145 Angle : 0.707 10.348 17290 Z= 0.366 Chirality : 0.044 0.258 1960 Planarity : 0.004 0.031 2252 Dihedral : 7.292 88.538 1743 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.95 % Allowed : 14.04 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.19), residues: 1560 helix: -1.05 (0.17), residues: 788 sheet: -1.84 (0.45), residues: 120 loop : -3.97 (0.19), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 26 TYR 0.018 0.002 TYR E 109 PHE 0.021 0.001 PHE B 299 TRP 0.012 0.003 TRP C 12 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 (12828) covalent geometry : angle 0.69289 (17284) hydrogen bonds : bond 0.05559 ( 593) hydrogen bonds : angle 5.39808 ( 1713) metal coordination : bond 0.00925 ( 13) metal coordination : angle 7.59054 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6953 (ttp) REVERT: D 115 ARG cc_start: 0.6985 (ttm170) cc_final: 0.6697 (ttm170) REVERT: D 135 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7151 (tp) REVERT: A 297 GLN cc_start: 0.0309 (OUTLIER) cc_final: -0.0203 (mm-40) REVERT: A 301 PHE cc_start: 0.3892 (m-80) cc_final: 0.3523 (t80) REVERT: B 23 MET cc_start: 0.7304 (mtm) cc_final: 0.7046 (mtp) REVERT: B 79 VAL cc_start: 0.7480 (t) cc_final: 0.7263 (t) REVERT: B 115 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6766 (ttm170) REVERT: B 300 LYS cc_start: 0.4330 (OUTLIER) cc_final: 0.2962 (mttt) REVERT: B 301 PHE cc_start: 0.4673 (m-80) cc_final: 0.3449 (m-80) REVERT: B 305 MET cc_start: 0.4672 (mtt) cc_final: 0.3822 (mtt) REVERT: C 49 PHE cc_start: 0.6286 (m-80) cc_final: 0.5974 (m-10) REVERT: C 97 LEU cc_start: 0.7754 (tp) cc_final: 0.7454 (tp) REVERT: C 109 ASN cc_start: 0.8484 (t0) cc_final: 0.8254 (t0) outliers start: 42 outliers final: 18 residues processed: 254 average time/residue: 0.0856 time to fit residues: 32.5068 Evaluate side-chains 221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 130 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 172 HIS ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 172 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN C 8 ASN C 172 HIS ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 130 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.234231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.198590 restraints weight = 13575.702| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.97 r_work: 0.4197 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12841 Z= 0.122 Angle : 0.634 9.848 17290 Z= 0.326 Chirality : 0.041 0.155 1960 Planarity : 0.004 0.031 2252 Dihedral : 5.546 51.644 1722 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 3.58 % Allowed : 15.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.20), residues: 1560 helix: -0.38 (0.18), residues: 784 sheet: -1.75 (0.45), residues: 124 loop : -3.67 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 115 TYR 0.020 0.001 TYR C 129 PHE 0.023 0.001 PHE B 299 TRP 0.012 0.003 TRP A 12 HIS 0.017 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00257 (12828) covalent geometry : angle 0.61867 (17284) hydrogen bonds : bond 0.04662 ( 593) hydrogen bonds : angle 4.90970 ( 1713) metal coordination : bond 0.00628 ( 13) metal coordination : angle 7.50284 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.5438 (m-10) REVERT: D 170 MET cc_start: 0.6726 (tpt) cc_final: 0.6392 (ttm) REVERT: D 272 MET cc_start: 0.7133 (ttm) cc_final: 0.6283 (tmm) REVERT: A 65 MET cc_start: 0.7929 (mmm) cc_final: 0.7691 (mmp) REVERT: A 297 GLN cc_start: 0.0771 (OUTLIER) cc_final: 0.0503 (mm-40) REVERT: A 301 PHE cc_start: 0.3992 (m-80) cc_final: 0.3615 (m-80) REVERT: B 23 MET cc_start: 0.7179 (mtm) cc_final: 0.6967 (mtp) REVERT: B 42 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5862 (m-80) REVERT: B 115 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7138 (ttm170) REVERT: B 185 ILE cc_start: 0.7787 (pt) cc_final: 0.7511 (mt) REVERT: B 272 MET cc_start: 0.7292 (ttm) cc_final: 0.6388 (tmm) REVERT: B 300 LYS cc_start: 0.4317 (OUTLIER) cc_final: 0.3154 (mttt) REVERT: B 301 PHE cc_start: 0.4807 (m-80) cc_final: 0.3470 (m-80) REVERT: B 305 MET cc_start: 0.4987 (mtt) cc_final: 0.3998 (mtt) REVERT: C 49 PHE cc_start: 0.6433 (m-80) cc_final: 0.6165 (m-10) REVERT: C 64 LEU cc_start: 0.8395 (tt) cc_final: 0.8158 (tt) REVERT: C 65 MET cc_start: 0.7908 (mmm) cc_final: 0.7448 (mmt) REVERT: C 109 ASN cc_start: 0.8532 (t0) cc_final: 0.8287 (t0) REVERT: E 130 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5578 (m-70) REVERT: F 109 TYR cc_start: 0.6452 (t80) cc_final: 0.6191 (t80) outliers start: 51 outliers final: 29 residues processed: 249 average time/residue: 0.0940 time to fit residues: 35.4669 Evaluate side-chains 233 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 53 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.227641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.193945 restraints weight = 13373.564| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.10 r_work: 0.4128 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12841 Z= 0.158 Angle : 0.676 9.346 17290 Z= 0.347 Chirality : 0.042 0.145 1960 Planarity : 0.004 0.038 2252 Dihedral : 5.631 51.999 1722 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.28 % Allowed : 17.49 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.20), residues: 1560 helix: -0.39 (0.18), residues: 792 sheet: -0.91 (0.51), residues: 96 loop : -3.64 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 115 TYR 0.018 0.002 TYR E 109 PHE 0.023 0.002 PHE C 301 TRP 0.012 0.003 TRP A 12 HIS 0.006 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00361 (12828) covalent geometry : angle 0.66674 (17284) hydrogen bonds : bond 0.05751 ( 593) hydrogen bonds : angle 4.90376 ( 1713) metal coordination : bond 0.00580 ( 13) metal coordination : angle 6.13650 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7194 (ttp) REVERT: D 115 ARG cc_start: 0.7309 (ttm170) cc_final: 0.7078 (ttm170) REVERT: D 182 MET cc_start: 0.7298 (tpp) cc_final: 0.7084 (mmt) REVERT: D 272 MET cc_start: 0.7402 (ttm) cc_final: 0.6540 (tmm) REVERT: D 305 MET cc_start: 0.6543 (tpt) cc_final: 0.6108 (tpt) REVERT: A 23 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.5079 (mtp) REVERT: A 65 MET cc_start: 0.7947 (mmm) cc_final: 0.7582 (mmt) REVERT: A 109 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 297 GLN cc_start: 0.0337 (OUTLIER) cc_final: -0.0128 (mm-40) REVERT: A 301 PHE cc_start: 0.4373 (m-80) cc_final: 0.3686 (t80) REVERT: B 41 MET cc_start: 0.7168 (mmp) cc_final: 0.6760 (mmm) REVERT: B 42 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: B 115 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7160 (ttm170) REVERT: B 170 MET cc_start: 0.6744 (tpt) cc_final: 0.6504 (ttm) REVERT: B 185 ILE cc_start: 0.7574 (pt) cc_final: 0.7297 (mt) REVERT: B 272 MET cc_start: 0.7615 (ttm) cc_final: 0.6618 (tmm) REVERT: B 275 MET cc_start: 0.6405 (tpp) cc_final: 0.6131 (tpp) REVERT: B 300 LYS cc_start: 0.4492 (OUTLIER) cc_final: 0.3359 (mttt) REVERT: B 301 PHE cc_start: 0.4770 (m-80) cc_final: 0.3452 (m-80) REVERT: B 305 MET cc_start: 0.4991 (mtt) cc_final: 0.4005 (mtt) REVERT: B 309 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: B 324 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7315 (tt0) REVERT: C 23 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.4793 (mtp) REVERT: C 49 PHE cc_start: 0.6416 (m-80) cc_final: 0.6142 (m-10) REVERT: C 65 MET cc_start: 0.7992 (mmm) cc_final: 0.7476 (mmp) REVERT: C 294 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.6571 (mt) REVERT: F 92 MET cc_start: 0.7407 (ppp) cc_final: 0.7095 (ppp) outliers start: 61 outliers final: 36 residues processed: 248 average time/residue: 0.0859 time to fit residues: 32.1292 Evaluate side-chains 240 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN G 124 GLN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.223894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.189742 restraints weight = 13450.296| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 2.14 r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12841 Z= 0.174 Angle : 0.693 9.421 17290 Z= 0.357 Chirality : 0.043 0.199 1960 Planarity : 0.004 0.032 2252 Dihedral : 5.722 43.292 1722 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 4.78 % Allowed : 19.87 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.20), residues: 1560 helix: -0.33 (0.18), residues: 788 sheet: -0.94 (0.51), residues: 96 loop : -3.66 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 197 TYR 0.029 0.002 TYR D 42 PHE 0.022 0.002 PHE C 301 TRP 0.012 0.003 TRP A 12 HIS 0.007 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00405 (12828) covalent geometry : angle 0.68631 (17284) hydrogen bonds : bond 0.05931 ( 593) hydrogen bonds : angle 4.92496 ( 1713) metal coordination : bond 0.00569 ( 13) metal coordination : angle 5.29748 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6695 (ttp) REVERT: D 182 MET cc_start: 0.6997 (tpp) cc_final: 0.6621 (mmt) REVERT: D 272 MET cc_start: 0.6640 (ttm) cc_final: 0.6208 (tmm) REVERT: D 275 MET cc_start: 0.6330 (tpp) cc_final: 0.5812 (tpt) REVERT: D 309 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6200 (mp10) REVERT: D 317 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2732 (mm-30) REVERT: A 23 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.5204 (mtp) REVERT: A 109 ASN cc_start: 0.7694 (t0) cc_final: 0.7462 (t0) REVERT: B 272 MET cc_start: 0.6723 (ttm) cc_final: 0.6220 (tmm) REVERT: B 275 MET cc_start: 0.6226 (tpp) cc_final: 0.5958 (tpp) REVERT: B 300 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.3437 (mttt) REVERT: B 305 MET cc_start: 0.3653 (mtt) cc_final: 0.3115 (mtt) REVERT: B 309 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: B 324 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6825 (tt0) REVERT: C 23 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.4989 (mtp) REVERT: C 65 MET cc_start: 0.7761 (mmm) cc_final: 0.7382 (mmp) REVERT: C 294 ILE cc_start: 0.7100 (mt) cc_final: 0.6472 (mt) REVERT: F 92 MET cc_start: 0.6217 (ppp) cc_final: 0.5424 (ppp) REVERT: G 103 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4760 (m-80) outliers start: 68 outliers final: 42 residues processed: 250 average time/residue: 0.0773 time to fit residues: 29.5557 Evaluate side-chains 248 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.226577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.193691 restraints weight = 13261.054| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 2.00 r_work: 0.4116 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12841 Z= 0.129 Angle : 0.641 10.185 17290 Z= 0.328 Chirality : 0.041 0.247 1960 Planarity : 0.004 0.033 2252 Dihedral : 5.315 44.358 1720 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.35 % Allowed : 21.63 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.20), residues: 1560 helix: 0.12 (0.18), residues: 780 sheet: -0.70 (0.52), residues: 96 loop : -3.57 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 141 TYR 0.028 0.002 TYR B 42 PHE 0.032 0.002 PHE A 301 TRP 0.011 0.002 TRP A 12 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00284 (12828) covalent geometry : angle 0.63511 (17284) hydrogen bonds : bond 0.04831 ( 593) hydrogen bonds : angle 4.61403 ( 1713) metal coordination : bond 0.00462 ( 13) metal coordination : angle 4.83444 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 VAL cc_start: 0.7597 (t) cc_final: 0.7331 (t) REVERT: D 115 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7104 (ttm170) REVERT: D 272 MET cc_start: 0.7406 (ttm) cc_final: 0.6430 (tmm) REVERT: D 275 MET cc_start: 0.6513 (tpp) cc_final: 0.6154 (tpt) REVERT: D 305 MET cc_start: 0.6484 (tpt) cc_final: 0.6278 (tpt) REVERT: D 309 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: B 115 ARG cc_start: 0.7396 (ttm170) cc_final: 0.7089 (ttm170) REVERT: B 272 MET cc_start: 0.7496 (ttm) cc_final: 0.6479 (tmm) REVERT: B 275 MET cc_start: 0.6307 (tpp) cc_final: 0.6004 (tpp) REVERT: B 300 LYS cc_start: 0.4528 (OUTLIER) cc_final: 0.3343 (mttt) REVERT: B 301 PHE cc_start: 0.4535 (m-80) cc_final: 0.3066 (m-80) REVERT: B 305 MET cc_start: 0.4700 (mtt) cc_final: 0.3743 (mtt) REVERT: B 309 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: B 324 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7338 (tt0) REVERT: C 23 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.4282 (mtp) REVERT: C 65 MET cc_start: 0.7959 (mmm) cc_final: 0.7301 (mmp) REVERT: C 236 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.6275 (tt0) REVERT: F 92 MET cc_start: 0.7061 (ppp) cc_final: 0.6574 (ppp) outliers start: 62 outliers final: 35 residues processed: 249 average time/residue: 0.0798 time to fit residues: 30.2067 Evaluate side-chains 235 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 ASN D 6 HIS D 109 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.225839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.191640 restraints weight = 13287.897| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.20 r_work: 0.4122 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12841 Z= 0.140 Angle : 0.652 9.688 17290 Z= 0.334 Chirality : 0.042 0.207 1960 Planarity : 0.004 0.049 2252 Dihedral : 5.286 45.900 1720 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 4.35 % Allowed : 21.49 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.20), residues: 1560 helix: 0.27 (0.19), residues: 772 sheet: -0.62 (0.52), residues: 96 loop : -3.55 (0.19), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 115 TYR 0.022 0.002 TYR B 42 PHE 0.022 0.001 PHE A 301 TRP 0.012 0.002 TRP A 12 HIS 0.006 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00313 (12828) covalent geometry : angle 0.64573 (17284) hydrogen bonds : bond 0.05056 ( 593) hydrogen bonds : angle 4.58474 ( 1713) metal coordination : bond 0.00394 ( 13) metal coordination : angle 4.69147 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7428 (ttm) cc_final: 0.6485 (tmm) REVERT: D 275 MET cc_start: 0.6412 (tpp) cc_final: 0.6072 (tpt) REVERT: D 305 MET cc_start: 0.6730 (tpt) cc_final: 0.6348 (tpt) REVERT: D 309 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6565 (mp10) REVERT: A 23 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.4889 (mtp) REVERT: B 185 ILE cc_start: 0.7175 (mt) cc_final: 0.6936 (mt) REVERT: B 272 MET cc_start: 0.7542 (ttm) cc_final: 0.6571 (tmm) REVERT: B 275 MET cc_start: 0.6312 (tpp) cc_final: 0.6070 (tpp) REVERT: B 300 LYS cc_start: 0.4549 (OUTLIER) cc_final: 0.3362 (mttt) REVERT: B 301 PHE cc_start: 0.4499 (m-80) cc_final: 0.3026 (m-80) REVERT: B 305 MET cc_start: 0.4724 (mtt) cc_final: 0.3883 (mtt) REVERT: B 309 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: B 324 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7362 (tt0) REVERT: C 23 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.4323 (mtp) REVERT: C 65 MET cc_start: 0.8031 (mmm) cc_final: 0.7446 (mmp) REVERT: C 236 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: F 92 MET cc_start: 0.6960 (ppp) cc_final: 0.6576 (ppp) outliers start: 62 outliers final: 41 residues processed: 245 average time/residue: 0.0847 time to fit residues: 31.7172 Evaluate side-chains 248 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN B 4 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.227402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.192915 restraints weight = 13273.416| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.39 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12841 Z= 0.146 Angle : 0.660 9.326 17290 Z= 0.340 Chirality : 0.042 0.278 1960 Planarity : 0.004 0.042 2252 Dihedral : 5.303 46.098 1720 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.14 % Allowed : 22.54 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.20), residues: 1560 helix: 0.21 (0.18), residues: 780 sheet: -0.59 (0.52), residues: 96 loop : -3.49 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.024 0.002 TYR B 42 PHE 0.020 0.002 PHE A 301 TRP 0.012 0.002 TRP A 12 HIS 0.007 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00330 (12828) covalent geometry : angle 0.65425 (17284) hydrogen bonds : bond 0.05201 ( 593) hydrogen bonds : angle 4.62945 ( 1713) metal coordination : bond 0.00417 ( 13) metal coordination : angle 4.59077 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.6780 (ttm) cc_final: 0.6295 (tmm) REVERT: D 275 MET cc_start: 0.6311 (tpp) cc_final: 0.5965 (tpt) REVERT: D 305 MET cc_start: 0.6710 (tpt) cc_final: 0.6353 (tpt) REVERT: D 309 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6176 (mp10) REVERT: A 23 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.5020 (mtp) REVERT: B 185 ILE cc_start: 0.7357 (mt) cc_final: 0.7123 (mt) REVERT: B 272 MET cc_start: 0.6672 (ttm) cc_final: 0.6186 (tmm) REVERT: B 275 MET cc_start: 0.6172 (tpp) cc_final: 0.5870 (tpp) REVERT: B 300 LYS cc_start: 0.4474 (OUTLIER) cc_final: 0.3292 (mttt) REVERT: B 305 MET cc_start: 0.3438 (mtt) cc_final: 0.3007 (mtt) REVERT: B 309 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.6087 (mp10) REVERT: C 23 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.4764 (mtp) REVERT: C 65 MET cc_start: 0.7802 (mmm) cc_final: 0.7484 (mmt) REVERT: C 115 ARG cc_start: 0.6415 (ttt90) cc_final: 0.6186 (ttt90) REVERT: F 92 MET cc_start: 0.6219 (ppp) cc_final: 0.5932 (ppp) outliers start: 59 outliers final: 43 residues processed: 242 average time/residue: 0.0848 time to fit residues: 31.0949 Evaluate side-chains 241 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.228499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.196241 restraints weight = 13338.265| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 2.23 r_work: 0.4169 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12841 Z= 0.135 Angle : 0.654 10.033 17290 Z= 0.334 Chirality : 0.042 0.253 1960 Planarity : 0.004 0.046 2252 Dihedral : 5.225 46.005 1720 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.86 % Allowed : 23.31 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.20), residues: 1560 helix: 0.31 (0.18), residues: 780 sheet: -0.55 (0.52), residues: 96 loop : -3.43 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 141 TYR 0.028 0.002 TYR B 42 PHE 0.017 0.001 PHE A 301 TRP 0.010 0.002 TRP C 12 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00302 (12828) covalent geometry : angle 0.64896 (17284) hydrogen bonds : bond 0.04954 ( 593) hydrogen bonds : angle 4.55958 ( 1713) metal coordination : bond 0.00337 ( 13) metal coordination : angle 4.41265 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7529 (ttm) cc_final: 0.6579 (tmm) REVERT: D 275 MET cc_start: 0.6543 (tpp) cc_final: 0.6292 (tpt) REVERT: D 305 MET cc_start: 0.6666 (tpt) cc_final: 0.6460 (tpt) REVERT: D 309 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6297 (mp10) REVERT: A 23 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.4879 (mtp) REVERT: B 115 ARG cc_start: 0.7227 (ttm170) cc_final: 0.6903 (ttm170) REVERT: B 185 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7191 (mt) REVERT: B 272 MET cc_start: 0.7391 (ttm) cc_final: 0.6495 (tmm) REVERT: B 300 LYS cc_start: 0.4559 (OUTLIER) cc_final: 0.3239 (mttt) REVERT: B 305 MET cc_start: 0.4641 (mtt) cc_final: 0.3806 (mtt) REVERT: B 309 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6269 (mp10) REVERT: C 23 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.4382 (mtp) REVERT: C 65 MET cc_start: 0.8016 (mmm) cc_final: 0.7529 (mmt) REVERT: F 92 MET cc_start: 0.6949 (ppp) cc_final: 0.6627 (ppp) outliers start: 55 outliers final: 46 residues processed: 239 average time/residue: 0.0840 time to fit residues: 30.3685 Evaluate side-chains 242 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 134 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.230056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.193951 restraints weight = 13415.435| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.26 r_work: 0.4177 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12841 Z= 0.125 Angle : 0.653 10.050 17290 Z= 0.334 Chirality : 0.041 0.236 1960 Planarity : 0.004 0.047 2252 Dihedral : 5.157 45.467 1720 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.51 % Allowed : 24.09 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.21), residues: 1560 helix: 0.48 (0.19), residues: 780 sheet: -1.01 (0.51), residues: 104 loop : -3.35 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 141 TYR 0.018 0.001 TYR E 109 PHE 0.016 0.001 PHE D 49 TRP 0.010 0.002 TRP C 12 HIS 0.008 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00273 (12828) covalent geometry : angle 0.64823 (17284) hydrogen bonds : bond 0.04553 ( 593) hydrogen bonds : angle 4.46984 ( 1713) metal coordination : bond 0.00341 ( 13) metal coordination : angle 4.19396 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7313 (ttm) cc_final: 0.6412 (tmm) REVERT: A 23 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.4355 (mtp) REVERT: A 115 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.6498 (tmt-80) REVERT: B 115 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6897 (ttm170) REVERT: B 185 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7132 (mt) REVERT: B 272 MET cc_start: 0.7415 (ttm) cc_final: 0.6469 (tmm) REVERT: B 300 LYS cc_start: 0.4578 (OUTLIER) cc_final: 0.3223 (mttt) REVERT: B 305 MET cc_start: 0.4619 (mtt) cc_final: 0.4031 (tpt) REVERT: B 309 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: C 23 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.4238 (mtp) REVERT: C 65 MET cc_start: 0.7803 (mmm) cc_final: 0.7287 (mmt) REVERT: F 92 MET cc_start: 0.6999 (ppp) cc_final: 0.6677 (ppp) outliers start: 50 outliers final: 41 residues processed: 239 average time/residue: 0.0792 time to fit residues: 28.7037 Evaluate side-chains 239 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 0.0070 chunk 69 optimal weight: 7.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.233597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.199440 restraints weight = 13312.471| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 2.10 r_work: 0.4225 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12841 Z= 0.115 Angle : 0.626 9.982 17290 Z= 0.319 Chirality : 0.041 0.220 1960 Planarity : 0.004 0.044 2252 Dihedral : 4.941 45.609 1720 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.09 % Allowed : 24.37 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.21), residues: 1560 helix: 0.72 (0.19), residues: 780 sheet: -0.38 (0.52), residues: 96 loop : -3.30 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 141 TYR 0.021 0.001 TYR A 129 PHE 0.015 0.001 PHE A 301 TRP 0.009 0.002 TRP C 12 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00241 (12828) covalent geometry : angle 0.62194 (17284) hydrogen bonds : bond 0.03933 ( 593) hydrogen bonds : angle 4.33752 ( 1713) metal coordination : bond 0.00267 ( 13) metal coordination : angle 3.87021 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.73 seconds wall clock time: 40 minutes 39.95 seconds (2439.95 seconds total)