Starting phenix.real_space_refine on Wed Jul 30 14:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gqd_34200/07_2025/8gqd_34200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gqd_34200/07_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_34200/07_2025/8gqd_34200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gqd_34200/07_2025/8gqd_34200.map" model { file = "/net/cci-nas-00/data/ceres_data/8gqd_34200/07_2025/8gqd_34200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gqd_34200/07_2025/8gqd_34200.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.74, per 1000 atoms: 0.61 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: 2.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.19 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: 3.74 Time building geometry restraints manager: 3.43 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.110 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.003 TRP C 12 HIS 0.010 0.002 HIS A 3 PHE 0.020 0.002 PHE A 301 TYR 0.019 0.002 TYR C 200 ARG 0.006 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.20252 ( 593) hydrogen bonds : angle 6.98279 ( 1713) metal coordination : bond 0.36133 ( 13) metal coordination : angle 14.16017 ( 6) covalent geometry : bond 0.00780 (12828) covalent geometry : angle 1.10315 (17284) *********************** 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 : 1.330 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: 0.2299 time to fit residues: 111.8307 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 : 1.418 ------------------------------------------------------------------------------- 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 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 = 0.4884 r_free = 0.4884 target = 0.234330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.201014 restraints weight = 13051.000| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 1.68 r_work: 0.4258 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2644 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= 0.142 Angle : 0.702 10.472 17290 Z= 0.363 Chirality : 0.044 0.255 1960 Planarity : 0.004 0.031 2252 Dihedral : 7.280 88.058 1743 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.95 % Allowed : 13.83 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.19), residues: 1560 helix: -1.02 (0.17), residues: 788 sheet: -1.82 (0.46), residues: 120 loop : -3.96 (0.19), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 12 HIS 0.006 0.001 HIS B 209 PHE 0.020 0.001 PHE B 299 TYR 0.018 0.002 TYR E 109 ARG 0.005 0.001 ARG C 26 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 593) hydrogen bonds : angle 5.38031 ( 1713) metal coordination : bond 0.00691 ( 13) metal coordination : angle 7.62015 ( 6) covalent geometry : bond 0.00302 (12828) covalent geometry : angle 0.68798 (17284) *********************** 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 : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6924 (ttp) REVERT: D 115 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6760 (ttm170) REVERT: D 135 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7122 (tp) REVERT: A 109 ASN cc_start: 0.8401 (t0) cc_final: 0.8188 (t0) REVERT: A 297 GLN cc_start: 0.0239 (OUTLIER) cc_final: -0.0266 (mm-40) REVERT: A 301 PHE cc_start: 0.3878 (m-80) cc_final: 0.3509 (t80) REVERT: B 79 VAL cc_start: 0.7454 (t) cc_final: 0.7244 (t) REVERT: B 300 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.2949 (mttt) REVERT: B 301 PHE cc_start: 0.4748 (m-80) cc_final: 0.3517 (m-80) REVERT: B 305 MET cc_start: 0.4662 (mtt) cc_final: 0.3809 (mtt) REVERT: C 49 PHE cc_start: 0.6580 (m-80) cc_final: 0.6228 (m-10) REVERT: C 97 LEU cc_start: 0.7753 (tp) cc_final: 0.7429 (tp) REVERT: C 109 ASN cc_start: 0.8535 (t0) cc_final: 0.8288 (t0) outliers start: 42 outliers final: 18 residues processed: 254 average time/residue: 0.2304 time to fit residues: 86.1435 Evaluate side-chains 220 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 119 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 126 GLN D 172 HIS ** 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** A 32 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 127 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 = 0.4831 r_free = 0.4831 target = 0.228328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.192868 restraints weight = 13444.763| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 2.22 r_work: 0.4106 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12841 Z= 0.177 Angle : 0.730 11.228 17290 Z= 0.377 Chirality : 0.044 0.154 1960 Planarity : 0.004 0.032 2252 Dihedral : 5.933 52.907 1722 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.49 % Favored : 90.45 % Rotamer: Outliers : 4.07 % Allowed : 16.43 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.19), residues: 1560 helix: -0.82 (0.17), residues: 792 sheet: -1.77 (0.44), residues: 120 loop : -3.78 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 12 HIS 0.016 0.001 HIS E 130 PHE 0.023 0.002 PHE C 301 TYR 0.020 0.002 TYR C 129 ARG 0.005 0.001 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 593) hydrogen bonds : angle 5.24434 ( 1713) metal coordination : bond 0.00734 ( 13) metal coordination : angle 7.58999 ( 6) covalent geometry : bond 0.00408 (12828) covalent geometry : angle 0.71678 (17284) *********************** 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 264 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5269 (m-10) REVERT: D 78 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7217 (ttp) REVERT: D 115 ARG cc_start: 0.7374 (ttm170) cc_final: 0.7122 (ttm170) REVERT: D 272 MET cc_start: 0.7551 (mmm) cc_final: 0.6682 (tmm) REVERT: D 275 MET cc_start: 0.6510 (tpp) cc_final: 0.6308 (tpp) REVERT: A 65 MET cc_start: 0.8030 (mmm) cc_final: 0.7760 (mmp) REVERT: A 109 ASN cc_start: 0.8415 (t0) cc_final: 0.8156 (t0) REVERT: A 297 GLN cc_start: 0.0658 (OUTLIER) cc_final: 0.0068 (mm-40) REVERT: A 301 PHE cc_start: 0.4288 (m-80) cc_final: 0.3621 (t80) REVERT: B 79 VAL cc_start: 0.7589 (t) cc_final: 0.7384 (t) REVERT: B 115 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7145 (ttm170) REVERT: B 272 MET cc_start: 0.7552 (ttm) cc_final: 0.6596 (tmm) REVERT: B 300 LYS cc_start: 0.4680 (OUTLIER) cc_final: 0.3439 (mttt) REVERT: B 301 PHE cc_start: 0.4856 (m-80) cc_final: 0.3482 (m-80) REVERT: B 305 MET cc_start: 0.4877 (mtt) cc_final: 0.3974 (mtt) REVERT: C 23 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.4881 (mtp) REVERT: C 49 PHE cc_start: 0.6435 (m-80) cc_final: 0.6147 (m-10) REVERT: C 64 LEU cc_start: 0.8415 (tt) cc_final: 0.8168 (tt) REVERT: C 65 MET cc_start: 0.7985 (mmm) cc_final: 0.7432 (mmt) REVERT: C 109 ASN cc_start: 0.8571 (t0) cc_final: 0.8348 (t0) REVERT: C 294 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6692 (mt) REVERT: E 130 HIS cc_start: 0.5858 (OUTLIER) cc_final: 0.5161 (t-90) REVERT: F 109 TYR cc_start: 0.6371 (t80) cc_final: 0.6085 (t80) outliers start: 58 outliers final: 31 residues processed: 248 average time/residue: 0.2199 time to fit residues: 81.1293 Evaluate side-chains 232 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 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 A residue 1 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 32 ASN 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 A residue 306 VAL Chi-restraints excluded: chain B residue 9 ILE 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 8 ASN A 113 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 113 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.230334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.196996 restraints weight = 13275.448| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 1.74 r_work: 0.4185 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12841 Z= 0.115 Angle : 0.617 9.595 17290 Z= 0.316 Chirality : 0.041 0.188 1960 Planarity : 0.004 0.037 2252 Dihedral : 5.372 46.057 1722 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.95 % Allowed : 18.96 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1560 helix: -0.17 (0.18), residues: 788 sheet: -1.55 (0.45), residues: 120 loop : -3.59 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 12 HIS 0.006 0.001 HIS D 209 PHE 0.019 0.001 PHE B 299 TYR 0.023 0.001 TYR B 42 ARG 0.004 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 593) hydrogen bonds : angle 4.71234 ( 1713) metal coordination : bond 0.00486 ( 13) metal coordination : angle 6.06864 ( 6) covalent geometry : bond 0.00242 (12828) covalent geometry : angle 0.60651 (17284) *********************** 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 254 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.5689 (m-10) REVERT: D 76 MET cc_start: 0.5859 (mmt) cc_final: 0.5622 (mmt) REVERT: D 79 VAL cc_start: 0.7591 (t) cc_final: 0.7350 (t) REVERT: D 272 MET cc_start: 0.7489 (mmm) cc_final: 0.6598 (tmm) REVERT: A 23 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.4401 (mtp) REVERT: A 65 MET cc_start: 0.7926 (mmm) cc_final: 0.7622 (mmp) REVERT: A 297 GLN cc_start: 0.0806 (OUTLIER) cc_final: 0.0392 (mm-40) REVERT: B 79 VAL cc_start: 0.7462 (t) cc_final: 0.7253 (t) REVERT: B 272 MET cc_start: 0.7356 (ttm) cc_final: 0.6408 (tmm) REVERT: B 300 LYS cc_start: 0.4592 (OUTLIER) cc_final: 0.3617 (mttt) REVERT: B 301 PHE cc_start: 0.4723 (m-80) cc_final: 0.3418 (m-80) REVERT: B 305 MET cc_start: 0.4527 (mtt) cc_final: 0.3690 (mtt) REVERT: B 309 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: B 324 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7208 (tt0) REVERT: C 65 MET cc_start: 0.7839 (mmm) cc_final: 0.7379 (mmt) REVERT: C 109 ASN cc_start: 0.8484 (t0) cc_final: 0.8254 (t0) REVERT: F 92 MET cc_start: 0.7326 (ppp) cc_final: 0.6895 (ppp) outliers start: 42 outliers final: 29 residues processed: 238 average time/residue: 0.2621 time to fit residues: 93.8457 Evaluate side-chains 227 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 TYR 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 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 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 182 MET 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 40 LEU 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 C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 135 ILE 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 131 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 ASN D 109 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN B 172 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 130 HIS F 130 HIS ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.216423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.189791 restraints weight = 13471.534| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.43 r_work: 0.4167 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 12841 Z= 0.326 Angle : 0.936 11.349 17290 Z= 0.484 Chirality : 0.051 0.235 1960 Planarity : 0.006 0.054 2252 Dihedral : 6.539 44.300 1720 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.64 % Favored : 89.29 % Rotamer: Outliers : 6.32 % Allowed : 19.38 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.19), residues: 1560 helix: -1.06 (0.17), residues: 784 sheet: -1.02 (0.52), residues: 88 loop : -3.91 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 12 HIS 0.007 0.002 HIS A 209 PHE 0.049 0.003 PHE C 301 TYR 0.030 0.004 TYR D 200 ARG 0.007 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.08481 ( 593) hydrogen bonds : angle 5.68644 ( 1713) metal coordination : bond 0.00715 ( 13) metal coordination : angle 6.24910 ( 6) covalent geometry : bond 0.00789 (12828) covalent geometry : angle 0.92906 (17284) *********************** 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 291 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 201 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.5172 (m-10) REVERT: D 52 ILE cc_start: 0.6190 (mt) cc_final: 0.5898 (mt) REVERT: D 78 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7432 (ttp) REVERT: D 272 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6783 (tmm) REVERT: D 305 MET cc_start: 0.6901 (tpt) cc_final: 0.6676 (tpt) REVERT: D 309 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.6123 (mp10) REVERT: A 23 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.5695 (mtt) REVERT: A 65 MET cc_start: 0.8145 (mmm) cc_final: 0.7866 (mmt) REVERT: A 119 MET cc_start: 0.7875 (mmt) cc_final: 0.7656 (mmt) REVERT: A 210 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7624 (m) REVERT: A 301 PHE cc_start: 0.5100 (m-80) cc_final: 0.4438 (t80) REVERT: B 272 MET cc_start: 0.7716 (ttm) cc_final: 0.6786 (tmm) REVERT: B 300 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4181 (mttt) REVERT: B 301 PHE cc_start: 0.4783 (m-80) cc_final: 0.3518 (m-80) REVERT: B 305 MET cc_start: 0.4820 (mtt) cc_final: 0.3752 (mtt) REVERT: B 309 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6193 (mp10) REVERT: C 23 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.5699 (mtt) REVERT: C 65 MET cc_start: 0.8006 (mmm) cc_final: 0.7517 (mmp) REVERT: F 92 MET cc_start: 0.6719 (ppp) cc_final: 0.6036 (ppp) REVERT: G 103 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.5164 (m-80) outliers start: 90 outliers final: 47 residues processed: 267 average time/residue: 0.2245 time to fit residues: 90.2945 Evaluate side-chains 249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 TYR 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 272 MET Chi-restraints excluded: chain D residue 289 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 27 ILE 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 169 VAL Chi-restraints excluded: chain A residue 210 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 A residue 310 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 124 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 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 67 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 SER 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 E residue 131 VAL Chi-restraints excluded: chain F residue 130 HIS 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 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 136 HIS 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 139 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 9 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 6 HIS D 109 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN F 130 HIS G 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.225005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.191847 restraints weight = 13372.971| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.28 r_work: 0.4099 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4515 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= 0.142 Angle : 0.691 10.128 17290 Z= 0.353 Chirality : 0.043 0.285 1960 Planarity : 0.004 0.036 2252 Dihedral : 5.661 46.086 1720 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 4.49 % Allowed : 21.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1560 helix: -0.27 (0.18), residues: 776 sheet: -0.71 (0.53), residues: 88 loop : -3.58 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 12 HIS 0.018 0.002 HIS C 113 PHE 0.017 0.002 PHE B 299 TYR 0.020 0.002 TYR B 42 ARG 0.008 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 593) hydrogen bonds : angle 4.85575 ( 1713) metal coordination : bond 0.00375 ( 13) metal coordination : angle 4.94029 ( 6) covalent geometry : bond 0.00313 (12828) covalent geometry : angle 0.68529 (17284) *********************** 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 270 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5913 (m-10) REVERT: D 79 VAL cc_start: 0.7542 (t) cc_final: 0.7286 (t) REVERT: D 182 MET cc_start: 0.7133 (tpp) cc_final: 0.6845 (mmt) REVERT: D 272 MET cc_start: 0.7674 (mmm) cc_final: 0.6562 (tmm) REVERT: D 309 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.6221 (mp10) REVERT: A 23 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.4535 (mtp) REVERT: A 65 MET cc_start: 0.7960 (mmm) cc_final: 0.7539 (mmt) REVERT: A 297 GLN cc_start: 0.0708 (OUTLIER) cc_final: 0.0501 (mm-40) REVERT: B 272 MET cc_start: 0.7451 (ttm) cc_final: 0.6443 (tmm) REVERT: B 300 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.3676 (mttt) REVERT: B 305 MET cc_start: 0.4728 (mtt) cc_final: 0.3730 (mtt) REVERT: B 324 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7460 (tt0) REVERT: C 23 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.4634 (mtp) REVERT: C 65 MET cc_start: 0.8079 (mmm) cc_final: 0.7427 (mmp) REVERT: C 78 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7052 (ptm) REVERT: C 109 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (t0) REVERT: C 294 ILE cc_start: 0.7691 (mt) cc_final: 0.7439 (mp) REVERT: E 130 HIS cc_start: 0.5842 (OUTLIER) cc_final: 0.5523 (t-90) REVERT: F 92 MET cc_start: 0.7347 (ppp) cc_final: 0.6810 (ppp) REVERT: G 103 PHE cc_start: 0.5555 (OUTLIER) cc_final: 0.5098 (m-80) outliers start: 64 outliers final: 37 residues processed: 246 average time/residue: 0.2146 time to fit residues: 79.4509 Evaluate side-chains 246 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS 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 309 GLN 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 155 THR Chi-restraints excluded: chain A residue 182 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 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 78 MET Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 289 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 130 HIS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain G residue 103 PHE 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 114 ASP Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 134 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 148 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 109 ASN C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.224643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 187)---------------| | r_work = 0.4465 r_free = 0.4465 target = 0.181711 restraints weight = 13603.521| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.62 r_work: 0.4122 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4676 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= 0.157 Angle : 0.699 8.862 17290 Z= 0.358 Chirality : 0.043 0.241 1960 Planarity : 0.004 0.036 2252 Dihedral : 5.631 45.510 1720 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 4.21 % Allowed : 22.33 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1560 helix: -0.19 (0.18), residues: 780 sheet: -0.51 (0.55), residues: 88 loop : -3.54 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 12 HIS 0.015 0.002 HIS C 113 PHE 0.025 0.002 PHE C 301 TYR 0.022 0.002 TYR B 42 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 593) hydrogen bonds : angle 4.82216 ( 1713) metal coordination : bond 0.00386 ( 13) metal coordination : angle 4.75354 ( 6) covalent geometry : bond 0.00359 (12828) covalent geometry : angle 0.69362 (17284) *********************** 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 265 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5870 (m-10) REVERT: D 182 MET cc_start: 0.7170 (tpp) cc_final: 0.6921 (mmt) REVERT: D 272 MET cc_start: 0.7639 (mmm) cc_final: 0.6619 (tmm) REVERT: D 309 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6336 (mp10) REVERT: A 23 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.4703 (mtp) REVERT: A 65 MET cc_start: 0.8068 (mmm) cc_final: 0.7645 (mmt) REVERT: B 272 MET cc_start: 0.7544 (ttm) cc_final: 0.6575 (tmm) REVERT: B 300 LYS cc_start: 0.5030 (OUTLIER) cc_final: 0.3791 (mttt) REVERT: B 305 MET cc_start: 0.4641 (mtt) cc_final: 0.3719 (mtt) REVERT: B 324 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7333 (tt0) REVERT: C 23 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.4806 (mtp) REVERT: C 65 MET cc_start: 0.8055 (mmm) cc_final: 0.7404 (mmp) REVERT: C 236 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: C 294 ILE cc_start: 0.7759 (mt) cc_final: 0.7463 (mp) REVERT: F 92 MET cc_start: 0.7412 (ppp) cc_final: 0.7029 (ppp) REVERT: G 103 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.5277 (m-80) outliers start: 60 outliers final: 41 residues processed: 246 average time/residue: 0.2212 time to fit residues: 81.1898 Evaluate side-chains 246 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 TYR 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 310 SER 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 155 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 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 289 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 322 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 G residue 103 PHE 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 114 ASP Chi-restraints excluded: chain H residue 131 VAL 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 127 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 82 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.233214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.201842 restraints weight = 13457.590| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 1.87 r_work: 0.4234 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12841 Z= 0.114 Angle : 0.633 10.341 17290 Z= 0.321 Chirality : 0.042 0.199 1960 Planarity : 0.004 0.050 2252 Dihedral : 5.145 48.913 1720 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.37 % Allowed : 23.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1560 helix: 0.30 (0.18), residues: 780 sheet: -1.38 (0.46), residues: 120 loop : -3.42 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 12 HIS 0.012 0.001 HIS A 113 PHE 0.019 0.001 PHE D 49 TYR 0.026 0.001 TYR B 42 ARG 0.009 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 593) hydrogen bonds : angle 4.48097 ( 1713) metal coordination : bond 0.00274 ( 13) metal coordination : angle 4.11504 ( 6) covalent geometry : bond 0.00234 (12828) covalent geometry : angle 0.62832 (17284) *********************** 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 268 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7506 (mmm) cc_final: 0.6498 (tmm) REVERT: D 275 MET cc_start: 0.6487 (tpp) cc_final: 0.6259 (tpt) REVERT: D 309 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: A 23 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.4169 (mtp) REVERT: A 65 MET cc_start: 0.7882 (mmm) cc_final: 0.7353 (mmt) REVERT: B 12 TRP cc_start: 0.2875 (p90) cc_final: 0.2584 (p90) REVERT: B 115 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6887 (ttm170) REVERT: B 272 MET cc_start: 0.7269 (ttm) cc_final: 0.6403 (tmm) REVERT: B 300 LYS cc_start: 0.4691 (OUTLIER) cc_final: 0.3929 (mttt) REVERT: B 305 MET cc_start: 0.4323 (mtt) cc_final: 0.3622 (mtt) REVERT: B 324 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7349 (tt0) REVERT: C 65 MET cc_start: 0.7826 (mmm) cc_final: 0.7298 (mmt) REVERT: C 161 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7643 (mm) REVERT: C 294 ILE cc_start: 0.7463 (mt) cc_final: 0.7127 (mp) REVERT: F 92 MET cc_start: 0.7129 (ppp) cc_final: 0.6703 (ppp) REVERT: G 85 LYS cc_start: 0.6211 (tptp) cc_final: 0.5905 (mtmm) REVERT: G 103 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.5436 (m-80) outliers start: 48 outliers final: 33 residues processed: 252 average time/residue: 0.2162 time to fit residues: 81.6033 Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 283 SER 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 310 SER Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 2 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 C residue 155 THR Chi-restraints excluded: chain C residue 161 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 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 139 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.225420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.191316 restraints weight = 13425.103| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 1.69 r_work: 0.4178 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12841 Z= 0.166 Angle : 0.720 9.848 17290 Z= 0.369 Chirality : 0.044 0.274 1960 Planarity : 0.004 0.052 2252 Dihedral : 5.446 44.345 1720 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.51 % Allowed : 24.58 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1560 helix: 0.04 (0.18), residues: 788 sheet: -0.48 (0.54), residues: 96 loop : -3.45 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 12 HIS 0.015 0.001 HIS A 113 PHE 0.029 0.002 PHE C 301 TYR 0.030 0.002 TYR D 42 ARG 0.006 0.001 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 593) hydrogen bonds : angle 4.66343 ( 1713) metal coordination : bond 0.00401 ( 13) metal coordination : angle 4.23623 ( 6) covalent geometry : bond 0.00384 (12828) covalent geometry : angle 0.71555 (17284) *********************** 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 247 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6765 (tmm) REVERT: D 309 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: A 23 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.4837 (mtp) REVERT: A 65 MET cc_start: 0.8135 (mmm) cc_final: 0.7635 (mmt) REVERT: A 115 ARG cc_start: 0.7265 (tmt-80) cc_final: 0.6691 (tmt-80) REVERT: B 12 TRP cc_start: 0.3025 (p90) cc_final: 0.2821 (p90) REVERT: B 272 MET cc_start: 0.7540 (ttm) cc_final: 0.6574 (tmm) REVERT: B 300 LYS cc_start: 0.4880 (OUTLIER) cc_final: 0.3818 (mttt) REVERT: B 305 MET cc_start: 0.4732 (mtt) cc_final: 0.3779 (mtt) REVERT: B 324 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7404 (tt0) REVERT: C 23 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.5087 (mtp) REVERT: C 65 MET cc_start: 0.8066 (mmm) cc_final: 0.7551 (mmt) REVERT: C 294 ILE cc_start: 0.7766 (mt) cc_final: 0.7482 (mp) REVERT: E 130 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.4703 (t-90) REVERT: F 92 MET cc_start: 0.7087 (ppp) cc_final: 0.6726 (ppp) REVERT: G 85 LYS cc_start: 0.6118 (tptp) cc_final: 0.5842 (mtmm) outliers start: 50 outliers final: 34 residues processed: 228 average time/residue: 0.2334 time to fit residues: 79.4941 Evaluate side-chains 233 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 289 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 310 SER Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 182 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 C residue 23 MET Chi-restraints excluded: chain C residue 155 THR 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 130 HIS 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 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.0010 chunk 135 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 216 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 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 = 0.4862 r_free = 0.4862 target = 0.231228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.198158 restraints weight = 13351.503| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 1.98 r_work: 0.4192 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12841 Z= 0.119 Angle : 0.655 10.509 17290 Z= 0.333 Chirality : 0.042 0.239 1960 Planarity : 0.004 0.046 2252 Dihedral : 5.231 47.285 1720 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.88 % Allowed : 25.14 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1560 helix: 0.37 (0.18), residues: 788 sheet: -0.39 (0.53), residues: 96 loop : -3.33 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 12 HIS 0.011 0.001 HIS A 113 PHE 0.015 0.001 PHE D 49 TYR 0.021 0.001 TYR B 42 ARG 0.008 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 593) hydrogen bonds : angle 4.42912 ( 1713) metal coordination : bond 0.00303 ( 13) metal coordination : angle 3.98785 ( 6) covalent geometry : bond 0.00249 (12828) covalent geometry : angle 0.65045 (17284) ********************** 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 240 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7666 (mmm) cc_final: 0.6631 (tmm) REVERT: D 309 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6245 (mp10) REVERT: A 23 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.4533 (mtp) REVERT: A 65 MET cc_start: 0.7940 (mmm) cc_final: 0.7431 (mmt) REVERT: A 275 MET cc_start: 0.6757 (tpp) cc_final: 0.6241 (tpt) REVERT: B 12 TRP cc_start: 0.2910 (p90) cc_final: 0.2705 (p90) REVERT: B 115 ARG cc_start: 0.7237 (ttm170) cc_final: 0.6878 (ttm170) REVERT: B 272 MET cc_start: 0.7433 (ttm) cc_final: 0.6467 (tmm) REVERT: B 300 LYS cc_start: 0.4621 (OUTLIER) cc_final: 0.3736 (mttt) REVERT: B 305 MET cc_start: 0.4453 (mtt) cc_final: 0.3750 (tpt) REVERT: B 324 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7346 (tt0) REVERT: C 65 MET cc_start: 0.7950 (mmm) cc_final: 0.7441 (mmt) REVERT: E 130 HIS cc_start: 0.5547 (OUTLIER) cc_final: 0.4829 (t-90) REVERT: F 92 MET cc_start: 0.7058 (ppp) cc_final: 0.6630 (ppp) REVERT: G 85 LYS cc_start: 0.6284 (tptp) cc_final: 0.6016 (mtmm) outliers start: 41 outliers final: 31 residues processed: 226 average time/residue: 0.2154 time to fit residues: 73.2037 Evaluate side-chains 227 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 283 SER 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 310 SER Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 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 C residue 155 THR 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 130 HIS 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 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 134 optimal weight: 7.9990 chunk 48 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 82 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.233742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.201411 restraints weight = 13390.500| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.18 r_work: 0.4221 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12841 Z= 0.113 Angle : 0.635 9.865 17290 Z= 0.321 Chirality : 0.041 0.223 1960 Planarity : 0.004 0.046 2252 Dihedral : 5.044 47.564 1720 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.95 % Allowed : 24.86 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1560 helix: 0.68 (0.19), residues: 784 sheet: -1.09 (0.47), residues: 120 loop : -3.24 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 12 HIS 0.011 0.001 HIS A 113 PHE 0.016 0.001 PHE B 49 TYR 0.024 0.001 TYR A 129 ARG 0.006 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 593) hydrogen bonds : angle 4.27543 ( 1713) metal coordination : bond 0.00259 ( 13) metal coordination : angle 3.65663 ( 6) covalent geometry : bond 0.00236 (12828) covalent geometry : angle 0.63193 (17284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.60 seconds wall clock time: 108 minutes 26.43 seconds (6506.43 seconds total)