Starting phenix.real_space_refine on Thu May 15 00:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gqd_34200/05_2025/8gqd_34200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gqd_34200/05_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_34200/05_2025/8gqd_34200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gqd_34200/05_2025/8gqd_34200.map" model { file = "/net/cci-nas-00/data/ceres_data/8gqd_34200/05_2025/8gqd_34200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gqd_34200/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.15, per 1000 atoms: 0.57 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 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: 1.17 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: 3.45 Time building geometry restraints manager: 3.48 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.370 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- 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 : 1.511 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: 0.2318 time to fit residues: 112.7226 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 : 1.516 ------------------------------------------------------------------------------- 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 = 13050.996| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 1.68 r_work: 0.4262 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 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 : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6948 (ttp) REVERT: D 115 ARG cc_start: 0.7027 (ttm170) cc_final: 0.6753 (ttm170) REVERT: D 135 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7131 (tp) REVERT: A 109 ASN cc_start: 0.8378 (t0) cc_final: 0.8171 (t0) REVERT: A 297 GLN cc_start: 0.0244 (OUTLIER) cc_final: -0.0259 (mm-40) REVERT: A 301 PHE cc_start: 0.3870 (m-80) cc_final: 0.3513 (t80) REVERT: B 79 VAL cc_start: 0.7461 (t) cc_final: 0.7254 (t) REVERT: B 300 LYS cc_start: 0.4258 (OUTLIER) cc_final: 0.2950 (mttt) REVERT: B 301 PHE cc_start: 0.4732 (m-80) cc_final: 0.3512 (m-80) REVERT: B 305 MET cc_start: 0.4650 (mtt) cc_final: 0.3799 (mtt) REVERT: C 49 PHE cc_start: 0.6508 (m-80) cc_final: 0.6166 (m-10) REVERT: C 97 LEU cc_start: 0.7746 (tp) cc_final: 0.7424 (tp) REVERT: C 109 ASN cc_start: 0.8517 (t0) cc_final: 0.8277 (t0) outliers start: 42 outliers final: 18 residues processed: 254 average time/residue: 0.2246 time to fit residues: 83.9740 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 : 1.452 ------------------------------------------------------------------------------- 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: 0.7980 chunk 146 optimal weight: 0.0030 chunk 140 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 127 GLN H 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.235687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.200046 restraints weight = 13505.163| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 1.87 r_work: 0.4246 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12841 Z= 0.119 Angle : 0.630 9.809 17290 Z= 0.323 Chirality : 0.041 0.152 1960 Planarity : 0.003 0.029 2252 Dihedral : 5.542 55.064 1722 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 3.58 % Allowed : 15.31 % Favored : 81.11 % 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: -2.64 (0.20), residues: 1560 helix: -0.33 (0.18), residues: 784 sheet: -1.71 (0.46), residues: 124 loop : -3.65 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 12 HIS 0.015 0.001 HIS E 130 PHE 0.020 0.001 PHE B 299 TYR 0.021 0.001 TYR C 129 ARG 0.005 0.000 ARG B 50 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 593) hydrogen bonds : angle 4.88896 ( 1713) metal coordination : bond 0.00613 ( 13) metal coordination : angle 7.51958 ( 6) covalent geometry : bond 0.00248 (12828) covalent geometry : angle 0.61467 (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 260 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5498 (m-10) REVERT: D 170 MET cc_start: 0.6570 (tpt) cc_final: 0.6276 (ttm) REVERT: D 272 MET cc_start: 0.7392 (mmm) cc_final: 0.6537 (tmm) REVERT: A 65 MET cc_start: 0.7899 (mmm) cc_final: 0.7654 (mmp) REVERT: A 109 ASN cc_start: 0.8349 (t0) cc_final: 0.8135 (t0) REVERT: A 297 GLN cc_start: 0.0642 (OUTLIER) cc_final: 0.0388 (mm-40) REVERT: A 301 PHE cc_start: 0.3994 (m-80) cc_final: 0.3623 (m-80) REVERT: B 42 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5876 (m-80) REVERT: B 79 VAL cc_start: 0.7487 (t) cc_final: 0.7285 (t) REVERT: B 115 ARG cc_start: 0.7284 (ttm170) cc_final: 0.7058 (ttm170) REVERT: B 272 MET cc_start: 0.7294 (ttm) cc_final: 0.6384 (tmm) REVERT: B 300 LYS cc_start: 0.4295 (OUTLIER) cc_final: 0.3216 (mttt) REVERT: B 301 PHE cc_start: 0.4779 (m-80) cc_final: 0.3533 (m-80) REVERT: B 305 MET cc_start: 0.4632 (mtt) cc_final: 0.3817 (mtt) REVERT: C 49 PHE cc_start: 0.6435 (m-80) cc_final: 0.6186 (m-10) REVERT: C 64 LEU cc_start: 0.8408 (tt) cc_final: 0.8111 (tt) REVERT: C 65 MET cc_start: 0.7830 (mmm) cc_final: 0.7375 (mmt) REVERT: C 97 LEU cc_start: 0.7835 (tp) cc_final: 0.7533 (tp) REVERT: C 109 ASN cc_start: 0.8531 (t0) cc_final: 0.8254 (t0) REVERT: E 130 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5516 (m-70) REVERT: F 109 TYR cc_start: 0.6502 (t80) cc_final: 0.6218 (t80) outliers start: 51 outliers final: 28 residues processed: 246 average time/residue: 0.2216 time to fit residues: 81.6602 Evaluate side-chains 226 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 0.0010 chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** 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 = 0.4864 r_free = 0.4864 target = 0.231798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.198391 restraints weight = 13229.050| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.88 r_work: 0.4218 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12841 Z= 0.131 Angle : 0.626 9.377 17290 Z= 0.321 Chirality : 0.041 0.138 1960 Planarity : 0.004 0.037 2252 Dihedral : 5.412 44.267 1722 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.37 % Allowed : 17.56 % Favored : 79.07 % 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: -2.41 (0.20), residues: 1560 helix: -0.15 (0.18), residues: 788 sheet: -1.59 (0.45), residues: 124 loop : -3.56 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 12 HIS 0.005 0.001 HIS A 209 PHE 0.017 0.002 PHE B 299 TYR 0.018 0.001 TYR E 109 ARG 0.005 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 593) hydrogen bonds : angle 4.72395 ( 1713) metal coordination : bond 0.00506 ( 13) metal coordination : angle 6.21953 ( 6) covalent geometry : bond 0.00293 (12828) covalent geometry : angle 0.61570 (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 269 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5324 (m-10) REVERT: D 79 VAL cc_start: 0.7659 (t) cc_final: 0.7421 (t) REVERT: D 115 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6971 (ttm170) REVERT: D 182 MET cc_start: 0.7163 (tpp) cc_final: 0.6897 (mmt) REVERT: D 272 MET cc_start: 0.7385 (mmm) cc_final: 0.6634 (tmm) REVERT: D 275 MET cc_start: 0.6287 (tpp) cc_final: 0.6019 (tpp) REVERT: A 65 MET cc_start: 0.7976 (mmm) cc_final: 0.7697 (mmp) REVERT: A 297 GLN cc_start: 0.0777 (OUTLIER) cc_final: 0.0176 (mm-40) REVERT: A 301 PHE cc_start: 0.3877 (m-80) cc_final: 0.3484 (t80) REVERT: B 41 MET cc_start: 0.7080 (mmp) cc_final: 0.6666 (mmm) REVERT: B 79 VAL cc_start: 0.7556 (t) cc_final: 0.7281 (t) REVERT: B 115 ARG cc_start: 0.7313 (ttm170) cc_final: 0.7108 (ttm170) REVERT: B 272 MET cc_start: 0.7421 (ttm) cc_final: 0.6483 (tmm) REVERT: B 275 MET cc_start: 0.6160 (tpp) cc_final: 0.5850 (tpp) REVERT: B 300 LYS cc_start: 0.4299 (OUTLIER) cc_final: 0.3405 (mttt) REVERT: B 301 PHE cc_start: 0.4720 (m-80) cc_final: 0.3446 (m-80) REVERT: B 305 MET cc_start: 0.4699 (mtt) cc_final: 0.3834 (mtt) REVERT: B 309 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: B 324 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7263 (tt0) REVERT: C 65 MET cc_start: 0.7911 (mmm) cc_final: 0.7516 (mmp) REVERT: F 92 MET cc_start: 0.7207 (ppp) cc_final: 0.6858 (ppp) outliers start: 48 outliers final: 33 residues processed: 248 average time/residue: 0.2281 time to fit residues: 85.0353 Evaluate side-chains 231 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 185 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 B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL 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 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN G 124 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.226299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.192175 restraints weight = 13211.109| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.19 r_work: 0.4119 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12841 Z= 0.172 Angle : 0.695 9.187 17290 Z= 0.358 Chirality : 0.043 0.208 1960 Planarity : 0.004 0.038 2252 Dihedral : 5.670 57.723 1722 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.64 % Rotamer: Outliers : 4.35 % Allowed : 19.31 % Favored : 76.33 % 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: -0.23 (0.18), residues: 788 sheet: -0.82 (0.52), residues: 96 loop : -3.60 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 12 HIS 0.006 0.001 HIS B 333 PHE 0.023 0.002 PHE C 301 TYR 0.029 0.002 TYR B 42 ARG 0.009 0.001 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.05993 ( 593) hydrogen bonds : angle 4.89519 ( 1713) metal coordination : bond 0.00534 ( 13) metal coordination : angle 5.61178 ( 6) covalent geometry : bond 0.00398 (12828) covalent geometry : angle 0.68765 (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 267 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5822 (m-10) REVERT: D 52 ILE cc_start: 0.6537 (mt) cc_final: 0.6228 (mt) REVERT: D 78 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7203 (ttp) REVERT: D 182 MET cc_start: 0.7316 (tpp) cc_final: 0.6833 (mmt) REVERT: D 272 MET cc_start: 0.7638 (mmm) cc_final: 0.6656 (tmm) REVERT: D 275 MET cc_start: 0.6513 (tpp) cc_final: 0.6287 (tpp) REVERT: D 305 MET cc_start: 0.6614 (tpt) cc_final: 0.6159 (mmm) REVERT: D 309 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: A 23 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.5408 (mtt) REVERT: A 65 MET cc_start: 0.7981 (mmm) cc_final: 0.7579 (mmt) REVERT: A 109 ASN cc_start: 0.8372 (t0) cc_final: 0.8009 (t0) REVERT: A 182 MET cc_start: 0.8438 (mmm) cc_final: 0.8231 (mmt) REVERT: A 297 GLN cc_start: 0.0419 (OUTLIER) cc_final: -0.0078 (mm-40) REVERT: A 301 PHE cc_start: 0.4513 (m-80) cc_final: 0.3898 (t80) REVERT: B 182 MET cc_start: 0.7440 (tpp) cc_final: 0.7091 (mmt) REVERT: B 272 MET cc_start: 0.7640 (ttm) cc_final: 0.6655 (tmm) REVERT: B 275 MET cc_start: 0.6462 (tpp) cc_final: 0.6233 (tpp) REVERT: B 300 LYS cc_start: 0.4611 (OUTLIER) cc_final: 0.3414 (mttt) REVERT: B 301 PHE cc_start: 0.4673 (m-80) cc_final: 0.3311 (m-80) REVERT: B 305 MET cc_start: 0.4824 (mtt) cc_final: 0.3893 (mtt) REVERT: B 309 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: B 324 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7328 (tt0) REVERT: C 23 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.5261 (mtt) REVERT: C 65 MET cc_start: 0.7891 (mmm) cc_final: 0.7345 (mmp) REVERT: C 109 ASN cc_start: 0.8453 (t0) cc_final: 0.8156 (t0) REVERT: C 236 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: C 294 ILE cc_start: 0.7522 (mt) cc_final: 0.7217 (mp) REVERT: F 92 MET cc_start: 0.7342 (ppp) cc_final: 0.6393 (ppp) outliers start: 62 outliers final: 37 residues processed: 247 average time/residue: 0.2192 time to fit residues: 81.7564 Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 135 ILE 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 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 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.0670 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 4 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 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 = 0.4819 r_free = 0.4819 target = 0.225713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.195264 restraints weight = 13402.007| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.29 r_work: 0.4104 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12841 Z= 0.172 Angle : 0.700 9.636 17290 Z= 0.359 Chirality : 0.043 0.263 1960 Planarity : 0.004 0.033 2252 Dihedral : 5.579 43.695 1720 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 4.85 % Allowed : 20.08 % Favored : 75.07 % 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: -2.42 (0.20), residues: 1560 helix: -0.22 (0.18), residues: 788 sheet: -0.85 (0.51), residues: 96 loop : -3.55 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 12 HIS 0.007 0.001 HIS A 209 PHE 0.021 0.002 PHE D 301 TYR 0.020 0.002 TYR B 42 ARG 0.008 0.001 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 593) hydrogen bonds : angle 4.81085 ( 1713) metal coordination : bond 0.00481 ( 13) metal coordination : angle 5.43004 ( 6) covalent geometry : bond 0.00402 (12828) covalent geometry : angle 0.69285 (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 272 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5820 (m-10) REVERT: D 78 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7264 (ttp) REVERT: D 115 ARG cc_start: 0.7279 (ttm170) cc_final: 0.6933 (ttm170) REVERT: D 182 MET cc_start: 0.7271 (tpp) cc_final: 0.6887 (mmt) REVERT: D 272 MET cc_start: 0.7652 (mmm) cc_final: 0.6603 (tmm) REVERT: D 275 MET cc_start: 0.6480 (tpp) cc_final: 0.6264 (tpp) REVERT: D 305 MET cc_start: 0.6689 (tpt) cc_final: 0.6260 (tpt) REVERT: A 23 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.5023 (mtp) REVERT: A 65 MET cc_start: 0.7982 (mmm) cc_final: 0.7600 (mmt) REVERT: A 182 MET cc_start: 0.8430 (mmm) cc_final: 0.8183 (mmt) REVERT: A 301 PHE cc_start: 0.4501 (m-80) cc_final: 0.3811 (t80) REVERT: B 182 MET cc_start: 0.7491 (tpp) cc_final: 0.7131 (mmt) REVERT: B 272 MET cc_start: 0.7540 (ttm) cc_final: 0.6576 (tmm) REVERT: B 275 MET cc_start: 0.6498 (tpp) cc_final: 0.6282 (tpp) REVERT: B 300 LYS cc_start: 0.4858 (OUTLIER) cc_final: 0.3305 (mttt) REVERT: B 305 MET cc_start: 0.4873 (mtt) cc_final: 0.3842 (mtt) REVERT: B 309 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6349 (mp10) REVERT: B 324 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7406 (tt0) REVERT: C 23 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.4721 (mtp) REVERT: C 65 MET cc_start: 0.8064 (mmm) cc_final: 0.7439 (mmp) REVERT: C 119 MET cc_start: 0.7200 (mmm) cc_final: 0.6747 (mmt) REVERT: C 294 ILE cc_start: 0.7637 (mt) cc_final: 0.7304 (mp) REVERT: C 301 PHE cc_start: 0.4622 (m-80) cc_final: 0.4096 (t80) REVERT: F 92 MET cc_start: 0.6990 (ppp) cc_final: 0.6526 (ppp) outliers start: 69 outliers final: 43 residues processed: 251 average time/residue: 0.2109 time to fit residues: 80.0724 Evaluate side-chains 249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 266 ILE 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 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 235 ASN 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 155 THR Chi-restraints excluded: chain C residue 182 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.189889 restraints weight = 13332.990| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 2.34 r_work: 0.4086 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12841 Z= 0.160 Angle : 0.683 8.581 17290 Z= 0.351 Chirality : 0.042 0.215 1960 Planarity : 0.004 0.033 2252 Dihedral : 5.500 47.733 1720 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.42 % Allowed : 21.28 % Favored : 74.30 % 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: -2.28 (0.20), residues: 1560 helix: -0.10 (0.18), residues: 788 sheet: -0.72 (0.51), residues: 96 loop : -3.49 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 12 HIS 0.007 0.001 HIS D 209 PHE 0.018 0.002 PHE D 301 TYR 0.023 0.002 TYR B 42 ARG 0.007 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 593) hydrogen bonds : angle 4.72089 ( 1713) metal coordination : bond 0.00382 ( 13) metal coordination : angle 5.24353 ( 6) covalent geometry : bond 0.00367 (12828) covalent geometry : angle 0.67560 (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 273 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: D 78 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7347 (ttp) REVERT: D 115 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7079 (ttm170) REVERT: D 182 MET cc_start: 0.7246 (tpp) cc_final: 0.6881 (mmt) REVERT: D 272 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6604 (tmm) REVERT: D 275 MET cc_start: 0.6508 (tpp) cc_final: 0.6279 (tpp) REVERT: A 23 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.4721 (mtp) REVERT: A 65 MET cc_start: 0.8018 (mmm) cc_final: 0.7547 (mmt) REVERT: A 182 MET cc_start: 0.8435 (mmm) cc_final: 0.8196 (mmt) REVERT: A 301 PHE cc_start: 0.4623 (m-80) cc_final: 0.3923 (t80) REVERT: B 115 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7006 (ttm170) REVERT: B 182 MET cc_start: 0.7492 (tpp) cc_final: 0.7159 (mmt) REVERT: B 272 MET cc_start: 0.7607 (ttm) cc_final: 0.6626 (tmm) REVERT: B 275 MET cc_start: 0.6572 (tpp) cc_final: 0.6363 (tpp) REVERT: B 300 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.3388 (mttt) REVERT: B 305 MET cc_start: 0.4846 (mtt) cc_final: 0.3833 (mtt) REVERT: B 309 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6178 (mp10) REVERT: B 324 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7448 (tt0) REVERT: C 23 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.4262 (mtp) REVERT: C 65 MET cc_start: 0.8029 (mmm) cc_final: 0.7438 (mmp) REVERT: C 119 MET cc_start: 0.7331 (mmm) cc_final: 0.6943 (mmt) REVERT: C 294 ILE cc_start: 0.7708 (mt) cc_final: 0.6998 (mt) REVERT: F 92 MET cc_start: 0.7115 (ppp) cc_final: 0.6775 (ppp) REVERT: G 85 LYS cc_start: 0.6502 (tppt) cc_final: 0.6213 (tptp) outliers start: 63 outliers final: 42 residues processed: 252 average time/residue: 0.2259 time to fit residues: 85.1006 Evaluate side-chains 249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 266 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain 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 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 182 MET 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 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 G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET 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 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 97 optimal weight: 0.0670 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 82 HIS A 172 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 216 GLN ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.233537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.201405 restraints weight = 13364.711| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 2.10 r_work: 0.4260 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12841 Z= 0.111 Angle : 0.614 10.231 17290 Z= 0.310 Chirality : 0.041 0.270 1960 Planarity : 0.004 0.039 2252 Dihedral : 5.019 46.236 1720 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.37 % Allowed : 22.40 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.75 (0.21), residues: 1560 helix: 0.42 (0.19), residues: 788 sheet: -0.54 (0.52), residues: 96 loop : -3.36 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 12 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.001 PHE D 49 TYR 0.022 0.001 TYR B 42 ARG 0.009 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 593) hydrogen bonds : angle 4.39507 ( 1713) metal coordination : bond 0.00281 ( 13) metal coordination : angle 4.56399 ( 6) covalent geometry : bond 0.00228 (12828) covalent geometry : angle 0.60844 (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 277 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ARG cc_start: 0.7061 (ttm170) cc_final: 0.6821 (ttm170) REVERT: D 272 MET cc_start: 0.7506 (mmm) cc_final: 0.6535 (tmm) REVERT: A 65 MET cc_start: 0.7870 (mmm) cc_final: 0.7472 (mmt) REVERT: B 12 TRP cc_start: 0.2925 (p90) cc_final: 0.2644 (p90) REVERT: B 115 ARG cc_start: 0.7179 (ttm170) cc_final: 0.6736 (ttm170) REVERT: B 272 MET cc_start: 0.7294 (ttm) cc_final: 0.6419 (tmm) REVERT: B 300 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.3442 (mttt) REVERT: B 301 PHE cc_start: 0.4494 (m-80) cc_final: 0.3244 (m-80) REVERT: B 305 MET cc_start: 0.4460 (mtt) cc_final: 0.4056 (tpt) REVERT: B 324 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7196 (tt0) REVERT: C 23 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.4262 (mtp) REVERT: C 65 MET cc_start: 0.7864 (mmm) cc_final: 0.7460 (mmt) REVERT: C 294 ILE cc_start: 0.7420 (mt) cc_final: 0.7110 (mp) REVERT: F 92 MET cc_start: 0.7046 (ppp) cc_final: 0.6701 (ppp) REVERT: F 130 HIS cc_start: 0.5186 (m-70) cc_final: 0.4676 (t-90) REVERT: G 85 LYS cc_start: 0.6485 (tppt) cc_final: 0.6241 (tptp) outliers start: 48 outliers final: 33 residues processed: 263 average time/residue: 0.2136 time to fit residues: 83.0283 Evaluate side-chains 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 306 VAL 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 283 SER 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 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 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 HIS H 130 HIS H 136 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.224917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.184744 restraints weight = 13493.361| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 1.90 r_work: 0.4115 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12841 Z= 0.197 Angle : 0.759 9.851 17290 Z= 0.391 Chirality : 0.044 0.286 1960 Planarity : 0.005 0.053 2252 Dihedral : 5.393 43.404 1718 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.23 % Allowed : 23.24 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.17 (0.20), residues: 1560 helix: -0.02 (0.18), residues: 788 sheet: -0.56 (0.52), residues: 96 loop : -3.44 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 12 HIS 0.007 0.001 HIS A 113 PHE 0.028 0.002 PHE D 301 TYR 0.035 0.003 TYR D 42 ARG 0.008 0.001 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.06174 ( 593) hydrogen bonds : angle 4.84616 ( 1713) metal coordination : bond 0.00493 ( 13) metal coordination : angle 4.90227 ( 6) covalent geometry : bond 0.00464 (12828) covalent geometry : angle 0.75401 (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 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ARG cc_start: 0.7247 (ttm170) cc_final: 0.6912 (ttm170) REVERT: D 272 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6800 (tmm) REVERT: A 23 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5230 (mtt) REVERT: A 40 LEU cc_start: 0.6576 (tp) cc_final: 0.6289 (tp) REVERT: A 65 MET cc_start: 0.8145 (mmm) cc_final: 0.7657 (mmt) REVERT: A 115 ARG cc_start: 0.7296 (tmt170) cc_final: 0.7079 (tmt-80) REVERT: A 275 MET cc_start: 0.7159 (tpp) cc_final: 0.6285 (tpt) REVERT: A 301 PHE cc_start: 0.4418 (m-80) cc_final: 0.3866 (t80) REVERT: B 272 MET cc_start: 0.7680 (ttm) cc_final: 0.6641 (tmm) REVERT: B 300 LYS cc_start: 0.4820 (OUTLIER) cc_final: 0.3378 (mttt) REVERT: B 305 MET cc_start: 0.4778 (mtt) cc_final: 0.3720 (mtt) REVERT: B 324 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7481 (tt0) REVERT: C 23 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.4943 (mtt) REVERT: C 65 MET cc_start: 0.8064 (mmm) cc_final: 0.7510 (mmt) REVERT: C 115 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6868 (ttt90) REVERT: C 294 ILE cc_start: 0.7848 (mt) cc_final: 0.7431 (mp) REVERT: F 92 MET cc_start: 0.7044 (ppp) cc_final: 0.6724 (ppp) outliers start: 46 outliers final: 35 residues processed: 229 average time/residue: 0.2098 time to fit residues: 72.7334 Evaluate side-chains 231 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain 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 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 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 155 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 32 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS ** 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 = 0.4873 r_free = 0.4873 target = 0.232156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.197682 restraints weight = 13313.392| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 2.33 r_work: 0.4167 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12841 Z= 0.127 Angle : 0.676 10.203 17290 Z= 0.344 Chirality : 0.042 0.244 1960 Planarity : 0.004 0.048 2252 Dihedral : 5.159 45.213 1718 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.02 % Allowed : 23.67 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.21), residues: 1560 helix: 0.38 (0.19), residues: 784 sheet: -0.97 (0.51), residues: 104 loop : -3.30 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 12 HIS 0.011 0.001 HIS B 38 PHE 0.015 0.001 PHE D 49 TYR 0.020 0.001 TYR E 109 ARG 0.007 0.001 ARG B 50 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 593) hydrogen bonds : angle 4.51150 ( 1713) metal coordination : bond 0.00427 ( 13) metal coordination : angle 4.59418 ( 6) covalent geometry : bond 0.00273 (12828) covalent geometry : angle 0.67074 (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 244 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7671 (mmm) cc_final: 0.6614 (tmm) REVERT: A 23 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.4325 (mtp) REVERT: A 65 MET cc_start: 0.8096 (mmm) cc_final: 0.7651 (mmt) REVERT: A 275 MET cc_start: 0.6761 (tpp) cc_final: 0.5965 (tpt) REVERT: A 301 PHE cc_start: 0.4312 (m-80) cc_final: 0.3678 (t80) REVERT: A 303 GLU cc_start: 0.5529 (mp0) cc_final: 0.5237 (mp0) REVERT: B 115 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6923 (ttm170) REVERT: B 272 MET cc_start: 0.7375 (ttm) cc_final: 0.6352 (tmm) REVERT: B 300 LYS cc_start: 0.4529 (OUTLIER) cc_final: 0.3246 (mttt) REVERT: B 305 MET cc_start: 0.4538 (mtt) cc_final: 0.3724 (tpt) REVERT: B 324 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7423 (tt0) REVERT: C 23 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.4191 (mtp) REVERT: C 65 MET cc_start: 0.7957 (mmm) cc_final: 0.7450 (mmt) REVERT: C 294 ILE cc_start: 0.7525 (mt) cc_final: 0.6752 (mt) REVERT: F 92 MET cc_start: 0.7009 (ppp) cc_final: 0.6700 (ppp) REVERT: F 130 HIS cc_start: 0.5160 (m-70) cc_final: 0.4475 (t-90) outliers start: 43 outliers final: 36 residues processed: 231 average time/residue: 0.2198 time to fit residues: 75.4888 Evaluate side-chains 236 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain 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 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain 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 182 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS C 216 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN H 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.233874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.198402 restraints weight = 13304.166| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.29 r_work: 0.4187 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12841 Z= 0.117 Angle : 0.653 11.064 17290 Z= 0.331 Chirality : 0.041 0.232 1960 Planarity : 0.004 0.044 2252 Dihedral : 4.926 44.812 1718 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.74 % Allowed : 24.23 % Favored : 73.03 % 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: -1.55 (0.21), residues: 1560 helix: 0.66 (0.19), residues: 780 sheet: -0.33 (0.52), residues: 96 loop : -3.33 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 12 HIS 0.009 0.001 HIS B 38 PHE 0.027 0.001 PHE C 49 TYR 0.024 0.001 TYR A 129 ARG 0.007 0.001 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 593) hydrogen bonds : angle 4.38013 ( 1713) metal coordination : bond 0.00429 ( 13) metal coordination : angle 4.32420 ( 6) covalent geometry : bond 0.00245 (12828) covalent geometry : angle 0.64842 (17284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5859.76 seconds wall clock time: 102 minutes 10.13 seconds (6130.13 seconds total)