Starting phenix.real_space_refine on Mon Dec 30 06:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gqd_34200/12_2024/8gqd_34200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gqd_34200/12_2024/8gqd_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_34200/12_2024/8gqd_34200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gqd_34200/12_2024/8gqd_34200.map" model { file = "/net/cci-nas-00/data/ceres_data/8gqd_34200/12_2024/8gqd_34200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gqd_34200/12_2024/8gqd_34200.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 96 5.16 5 C 7872 2.51 5 N 2232 2.21 5 O 2440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.82, per 1000 atoms: 0.62 Number of scatterers: 12644 At special positions: 0 Unit cell: (97.9, 89.1, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 96 16.00 O 2440 8.00 N 2232 7.00 C 7872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 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: 1.14 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: 3.82 Time building geometry restraints manager: 3.18 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: 0.820 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.260 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- 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 : 0.008 0.076 12828 Z= 0.510 Angle : 1.103 6.917 17284 Z= 0.698 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 *********************** 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 : 1.557 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: 0.2439 time to fit residues: 118.4378 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 : 1.508 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 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 12828 Z= 0.200 Angle : 0.688 7.635 17284 Z= 0.362 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 *********************** 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 : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6703 (ttp) REVERT: D 115 ARG cc_start: 0.6408 (ttm170) cc_final: 0.6126 (ttm170) REVERT: D 135 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7031 (tp) REVERT: A 297 GLN cc_start: 0.0174 (OUTLIER) cc_final: -0.0204 (mm-40) REVERT: B 79 VAL cc_start: 0.7299 (t) cc_final: 0.7087 (t) REVERT: B 300 LYS cc_start: 0.4009 (OUTLIER) cc_final: 0.2859 (mttt) REVERT: B 301 PHE cc_start: 0.4346 (m-80) cc_final: 0.3370 (m-80) REVERT: B 305 MET cc_start: 0.3615 (mtt) cc_final: 0.3163 (mtt) REVERT: C 97 LEU cc_start: 0.7571 (tp) cc_final: 0.7313 (tp) REVERT: C 109 ASN cc_start: 0.7962 (t0) cc_final: 0.7750 (t0) outliers start: 42 outliers final: 18 residues processed: 254 average time/residue: 0.2386 time to fit residues: 89.5146 Evaluate side-chains 219 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 76 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 172 HIS ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 172 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS C 268 GLN E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN H 127 GLN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12828 Z= 0.459 Angle : 0.903 10.190 17284 Z= 0.472 Chirality : 0.050 0.167 1960 Planarity : 0.006 0.044 2252 Dihedral : 6.575 43.104 1722 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.71 % Favored : 89.23 % Rotamer: Outliers : 4.99 % Allowed : 17.63 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.18), residues: 1560 helix: -1.34 (0.17), residues: 784 sheet: -1.40 (0.50), residues: 96 loop : -4.03 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 12 HIS 0.018 0.002 HIS E 130 PHE 0.036 0.002 PHE C 301 TYR 0.028 0.003 TYR B 280 ARG 0.006 0.001 ARG A 26 *********************** 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 272 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 TYR cc_start: 0.5521 (OUTLIER) cc_final: 0.4914 (m-10) REVERT: D 78 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6812 (ttp) REVERT: D 115 ARG cc_start: 0.6736 (ttm170) cc_final: 0.6390 (ttm170) REVERT: D 305 MET cc_start: 0.7270 (tpt) cc_final: 0.6993 (tpt) REVERT: D 317 GLU cc_start: 0.3136 (OUTLIER) cc_final: 0.2827 (mm-30) REVERT: A 23 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.5571 (mtt) REVERT: A 109 ASN cc_start: 0.7959 (t0) cc_final: 0.7692 (t0) REVERT: B 115 ARG cc_start: 0.6749 (ttm170) cc_final: 0.6346 (ttm170) REVERT: B 272 MET cc_start: 0.7094 (ttm) cc_final: 0.6214 (tmm) REVERT: B 298 ASN cc_start: 0.2834 (OUTLIER) cc_final: 0.1551 (p0) REVERT: B 300 LYS cc_start: 0.4822 (OUTLIER) cc_final: 0.3717 (mttt) REVERT: B 301 PHE cc_start: 0.4523 (m-80) cc_final: 0.3365 (m-80) REVERT: B 305 MET cc_start: 0.3951 (mtt) cc_final: 0.3223 (mtt) REVERT: B 309 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6525 (mp10) REVERT: B 324 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7014 (tt0) REVERT: C 23 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.5550 (mtt) REVERT: C 64 LEU cc_start: 0.8356 (tt) cc_final: 0.8107 (tt) REVERT: C 65 MET cc_start: 0.7931 (mmm) cc_final: 0.7500 (mmt) REVERT: E 130 HIS cc_start: 0.5376 (OUTLIER) cc_final: 0.4864 (t-90) REVERT: F 109 TYR cc_start: 0.5863 (t80) cc_final: 0.5553 (t80) REVERT: G 103 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5486 (m-80) outliers start: 71 outliers final: 35 residues processed: 256 average time/residue: 0.2235 time to fit residues: 85.1626 Evaluate side-chains 234 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 71 ASP Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 236 GLN 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 317 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR 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 235 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 103 PHE 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 139 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 302 ASN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 113 HIS A 172 HIS B 113 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 113 HIS C 236 GLN E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12828 Z= 0.184 Angle : 0.648 10.107 17284 Z= 0.337 Chirality : 0.042 0.214 1960 Planarity : 0.004 0.034 2252 Dihedral : 5.668 46.653 1720 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 3.65 % Allowed : 20.08 % Favored : 76.26 % 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: -2.78 (0.20), residues: 1560 helix: -0.47 (0.18), residues: 784 sheet: -1.07 (0.51), residues: 96 loop : -3.76 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 12 HIS 0.007 0.001 HIS C 209 PHE 0.029 0.002 PHE H 128 TYR 0.025 0.002 TYR B 42 ARG 0.005 0.000 ARG D 197 *********************** 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 259 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 VAL cc_start: 0.7277 (t) cc_final: 0.7018 (t) REVERT: D 185 ILE cc_start: 0.7587 (pt) cc_final: 0.7252 (mm) REVERT: D 272 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6277 (tmm) REVERT: B 185 ILE cc_start: 0.7509 (pt) cc_final: 0.7294 (mm) REVERT: B 272 MET cc_start: 0.6776 (ttm) cc_final: 0.6044 (tmm) REVERT: B 300 LYS cc_start: 0.4225 (OUTLIER) cc_final: 0.3303 (mttt) REVERT: B 305 MET cc_start: 0.3334 (mtt) cc_final: 0.2958 (mtt) REVERT: B 324 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6840 (tt0) REVERT: C 65 MET cc_start: 0.7846 (mmm) cc_final: 0.7343 (mmt) REVERT: C 294 ILE cc_start: 0.7278 (mt) cc_final: 0.6695 (mt) REVERT: F 92 MET cc_start: 0.6655 (ppp) cc_final: 0.6088 (ppp) outliers start: 52 outliers final: 29 residues processed: 240 average time/residue: 0.2210 time to fit residues: 80.2294 Evaluate side-chains 221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 ILE 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 A residue 1 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 40 LEU 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 24 SER Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 131 VAL 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 122 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 8 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 187 GLN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 109 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN G 124 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12828 Z= 0.218 Angle : 0.667 9.838 17284 Z= 0.347 Chirality : 0.042 0.230 1960 Planarity : 0.004 0.041 2252 Dihedral : 5.561 45.788 1720 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.94 % Favored : 90.00 % Rotamer: Outliers : 4.71 % Allowed : 20.72 % Favored : 74.58 % 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: -2.62 (0.20), residues: 1560 helix: -0.33 (0.18), residues: 788 sheet: -1.55 (0.47), residues: 112 loop : -3.64 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 12 HIS 0.008 0.001 HIS D 38 PHE 0.022 0.002 PHE C 301 TYR 0.030 0.002 TYR D 42 ARG 0.003 0.000 ARG D 181 *********************** 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 278 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6261 (tmm) REVERT: A 23 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.5186 (mtp) REVERT: B 272 MET cc_start: 0.6893 (ttm) cc_final: 0.6199 (tmm) REVERT: B 300 LYS cc_start: 0.4361 (OUTLIER) cc_final: 0.3458 (mttt) REVERT: B 305 MET cc_start: 0.3643 (mtt) cc_final: 0.3224 (mtt) REVERT: B 309 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6379 (mp10) REVERT: B 324 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6903 (tt0) REVERT: C 23 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.4796 (mtp) REVERT: C 65 MET cc_start: 0.7932 (mmm) cc_final: 0.7366 (mmp) REVERT: C 294 ILE cc_start: 0.7360 (mt) cc_final: 0.7157 (mp) REVERT: F 92 MET cc_start: 0.6585 (ppp) cc_final: 0.5916 (ppp) REVERT: G 103 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.5334 (m-80) outliers start: 67 outliers final: 38 residues processed: 254 average time/residue: 0.2131 time to fit residues: 81.0812 Evaluate side-chains 245 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 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 78 MET 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 40 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain 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 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN B 302 ASN ** C 8 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12828 Z= 0.326 Angle : 0.768 9.581 17284 Z= 0.398 Chirality : 0.045 0.275 1960 Planarity : 0.005 0.056 2252 Dihedral : 5.946 44.255 1720 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.71 % Favored : 89.23 % Rotamer: Outliers : 4.63 % Allowed : 21.70 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.20), residues: 1560 helix: -0.55 (0.18), residues: 784 sheet: -0.75 (0.55), residues: 88 loop : -3.73 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 12 HIS 0.021 0.002 HIS A 113 PHE 0.028 0.002 PHE C 301 TYR 0.024 0.002 TYR D 42 ARG 0.009 0.001 ARG C 115 *********************** 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 273 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6256 (tmm) REVERT: D 275 MET cc_start: 0.6437 (tpp) cc_final: 0.6009 (tpt) REVERT: D 317 GLU cc_start: 0.3222 (OUTLIER) cc_final: 0.2888 (mm-30) REVERT: A 23 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.5317 (mtp) REVERT: A 65 MET cc_start: 0.7069 (mmt) cc_final: 0.6861 (mmp) REVERT: B 182 MET cc_start: 0.7058 (tpp) cc_final: 0.6712 (mmt) REVERT: B 272 MET cc_start: 0.6965 (ttm) cc_final: 0.6173 (tmm) REVERT: B 275 MET cc_start: 0.6394 (tpp) cc_final: 0.6190 (tpp) REVERT: B 300 LYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4051 (mttt) REVERT: B 301 PHE cc_start: 0.4434 (m-80) cc_final: 0.3199 (m-80) REVERT: B 305 MET cc_start: 0.3952 (mtt) cc_final: 0.3466 (mtt) REVERT: B 309 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: B 324 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6991 (tt0) REVERT: C 23 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.5446 (mtt) REVERT: C 65 MET cc_start: 0.8023 (mmm) cc_final: 0.7392 (mmp) REVERT: F 92 MET cc_start: 0.6670 (ppp) cc_final: 0.6196 (ppp) outliers start: 66 outliers final: 46 residues processed: 253 average time/residue: 0.2314 time to fit residues: 86.7573 Evaluate side-chains 249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 78 MET 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 A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 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 67 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL 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 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 114 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12828 Z= 0.180 Angle : 0.647 9.224 17284 Z= 0.335 Chirality : 0.042 0.264 1960 Planarity : 0.004 0.035 2252 Dihedral : 5.434 45.240 1720 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.72 % Allowed : 23.31 % Favored : 72.96 % 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: -2.23 (0.20), residues: 1560 helix: 0.08 (0.18), residues: 772 sheet: -0.53 (0.54), residues: 88 loop : -3.57 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 12 HIS 0.015 0.001 HIS A 113 PHE 0.016 0.001 PHE D 49 TYR 0.022 0.001 TYR B 42 ARG 0.007 0.000 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7012 (mmm) cc_final: 0.6396 (tmm) REVERT: D 275 MET cc_start: 0.6109 (tpp) cc_final: 0.5766 (tpt) REVERT: A 23 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.4640 (mtp) REVERT: B 272 MET cc_start: 0.6701 (ttm) cc_final: 0.6062 (tmm) REVERT: B 300 LYS cc_start: 0.4616 (OUTLIER) cc_final: 0.3777 (mttt) REVERT: B 305 MET cc_start: 0.3517 (mtt) cc_final: 0.3032 (mtt) REVERT: C 23 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.4411 (mtp) REVERT: C 65 MET cc_start: 0.7878 (mmm) cc_final: 0.7327 (mmp) REVERT: F 92 MET cc_start: 0.6567 (ppp) cc_final: 0.6175 (ppp) REVERT: F 130 HIS cc_start: 0.4829 (m-70) cc_final: 0.4428 (t-90) outliers start: 53 outliers final: 44 residues processed: 246 average time/residue: 0.2185 time to fit residues: 81.6464 Evaluate side-chains 251 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 282 LEU 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 165 MET Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL 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 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN ** C 8 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12828 Z= 0.349 Angle : 0.779 9.601 17284 Z= 0.404 Chirality : 0.045 0.275 1960 Planarity : 0.005 0.054 2252 Dihedral : 5.920 44.527 1720 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.51 % Favored : 89.42 % Rotamer: Outliers : 4.63 % Allowed : 22.54 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.20), residues: 1560 helix: -0.40 (0.18), residues: 784 sheet: -0.56 (0.55), residues: 88 loop : -3.61 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 12 HIS 0.014 0.002 HIS C 113 PHE 0.029 0.002 PHE C 301 TYR 0.033 0.002 TYR B 42 ARG 0.006 0.001 ARG A 26 *********************** 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 263 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 ILE cc_start: 0.6339 (mt) cc_final: 0.6049 (mt) REVERT: D 272 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6378 (tmm) REVERT: D 309 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: D 317 GLU cc_start: 0.3443 (OUTLIER) cc_final: 0.3039 (mm-30) REVERT: A 23 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.5315 (mtp) REVERT: B 272 MET cc_start: 0.6925 (ttm) cc_final: 0.6155 (tmm) REVERT: B 275 MET cc_start: 0.6481 (tpp) cc_final: 0.6225 (tpp) REVERT: B 300 LYS cc_start: 0.5127 (OUTLIER) cc_final: 0.4025 (mtmt) REVERT: B 301 PHE cc_start: 0.4425 (m-80) cc_final: 0.3210 (m-80) REVERT: B 305 MET cc_start: 0.3956 (mtt) cc_final: 0.3501 (mtt) REVERT: B 309 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6231 (mp10) REVERT: C 23 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5493 (mtt) REVERT: C 65 MET cc_start: 0.8016 (mmm) cc_final: 0.7398 (mmp) REVERT: C 294 ILE cc_start: 0.7600 (mp) cc_final: 0.7360 (mt) REVERT: F 92 MET cc_start: 0.6702 (ppp) cc_final: 0.6286 (ppp) outliers start: 66 outliers final: 50 residues processed: 244 average time/residue: 0.2262 time to fit residues: 82.4445 Evaluate side-chains 252 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 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 67 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0270 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12828 Z= 0.173 Angle : 0.652 10.451 17284 Z= 0.335 Chirality : 0.042 0.263 1960 Planarity : 0.004 0.043 2252 Dihedral : 5.376 45.852 1720 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.23 % Allowed : 24.16 % Favored : 72.61 % 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: -2.02 (0.20), residues: 1560 helix: 0.20 (0.18), residues: 780 sheet: -0.36 (0.54), residues: 88 loop : -3.46 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 12 HIS 0.012 0.001 HIS C 113 PHE 0.017 0.001 PHE D 49 TYR 0.025 0.001 TYR B 42 ARG 0.003 0.000 ARG C 181 *********************** 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 259 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.6965 (mmm) cc_final: 0.6344 (tmm) REVERT: D 309 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6106 (mp10) REVERT: B 272 MET cc_start: 0.6826 (ttm) cc_final: 0.6178 (tmm) REVERT: B 300 LYS cc_start: 0.4649 (OUTLIER) cc_final: 0.3784 (mttt) REVERT: B 305 MET cc_start: 0.3477 (mtt) cc_final: 0.3024 (mtt) REVERT: B 309 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6112 (mp10) REVERT: C 23 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.4557 (mtp) REVERT: C 65 MET cc_start: 0.7847 (mmm) cc_final: 0.7340 (mmt) REVERT: F 92 MET cc_start: 0.6541 (ppp) cc_final: 0.6133 (ppp) REVERT: F 130 HIS cc_start: 0.4772 (m-70) cc_final: 0.4430 (t-90) outliers start: 46 outliers final: 37 residues processed: 246 average time/residue: 0.2484 time to fit residues: 89.6583 Evaluate side-chains 243 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain 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 309 GLN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 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 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 109 TYR 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 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 0.0000 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12828 Z= 0.176 Angle : 0.653 10.657 17284 Z= 0.334 Chirality : 0.042 0.254 1960 Planarity : 0.004 0.053 2252 Dihedral : 5.083 43.388 1718 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.81 % Allowed : 24.79 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.83 (0.21), residues: 1560 helix: 0.43 (0.18), residues: 780 sheet: -0.22 (0.54), residues: 88 loop : -3.46 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 12 HIS 0.014 0.001 HIS C 113 PHE 0.018 0.002 PHE C 49 TYR 0.020 0.001 TYR B 42 ARG 0.012 0.000 ARG B 50 ********************** 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 246 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.6965 (mmm) cc_final: 0.6400 (tmm) REVERT: D 294 ILE cc_start: 0.7275 (mp) cc_final: 0.6299 (mt) REVERT: A 23 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.4565 (mtp) REVERT: A 143 LEU cc_start: 0.7326 (mm) cc_final: 0.6871 (tp) REVERT: B 115 ARG cc_start: 0.6427 (ttm170) cc_final: 0.5968 (ttm170) REVERT: B 272 MET cc_start: 0.6773 (ttm) cc_final: 0.6134 (tmm) REVERT: B 300 LYS cc_start: 0.4470 (OUTLIER) cc_final: 0.3707 (mttt) REVERT: B 305 MET cc_start: 0.3560 (mtt) cc_final: 0.3203 (mtt) REVERT: C 23 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.4483 (mtp) REVERT: C 65 MET cc_start: 0.7848 (mmm) cc_final: 0.7355 (mmt) REVERT: C 143 LEU cc_start: 0.7196 (mm) cc_final: 0.6703 (tp) REVERT: F 92 MET cc_start: 0.6569 (ppp) cc_final: 0.6154 (ppp) REVERT: F 130 HIS cc_start: 0.4830 (m-70) cc_final: 0.4494 (t-90) outliers start: 40 outliers final: 35 residues processed: 233 average time/residue: 0.2218 time to fit residues: 77.7943 Evaluate side-chains 237 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 266 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain 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 309 GLN Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 169 VAL 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 131 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 HIS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 109 TYR 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.227587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.195687 restraints weight = 13284.837| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.20 r_work: 0.4258 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12828 Z= 0.215 Angle : 0.686 10.654 17284 Z= 0.350 Chirality : 0.043 0.272 1960 Planarity : 0.004 0.050 2252 Dihedral : 5.180 43.125 1718 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.09 % Allowed : 25.07 % Favored : 71.84 % 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: -1.87 (0.20), residues: 1560 helix: 0.33 (0.18), residues: 784 sheet: -0.21 (0.55), residues: 88 loop : -3.42 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 12 HIS 0.012 0.001 HIS C 113 PHE 0.021 0.002 PHE C 49 TYR 0.024 0.002 TYR A 129 ARG 0.011 0.001 ARG C 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.19 seconds wall clock time: 47 minutes 54.00 seconds (2874.00 seconds total)