Starting phenix.real_space_refine on Mon Mar 11 05:50:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgy_30366/03_2024/7cgy_30366_updated.pdb" } resolution = 3.2 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 9 5.49 5 S 36 5.16 5 C 4533 2.51 5 N 1263 2.21 5 O 1368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7212 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.50, per 1000 atoms: 0.62 Number of scatterers: 7212 At special positions: 0 Unit cell: (94.92, 90.72, 116.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 36 16.00 P 9 15.00 O 1368 8.00 N 1263 7.00 C 4533 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 38.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.888A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.720A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.602A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.594A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 170 through 176 removed outlier: 4.318A pdb=" N ASP A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 196 through 212 removed outlier: 4.137A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.773A pdb=" N GLN A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 34 through 43 removed outlier: 4.961A pdb=" N LYS B 38 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 39 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 41 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 43 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.513A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 67 through 70 No H-bonds generated for 'chain 'B' and resid 67 through 70' Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.603A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.593A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLN B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 170 through 176 removed outlier: 4.319A pdb=" N ASP B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.137A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.829A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 34 through 43 removed outlier: 4.962A pdb=" N LYS C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 39 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 41 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 43 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.514A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 52' Processing helix chain 'C' and resid 67 through 70 No H-bonds generated for 'chain 'C' and resid 67 through 70' Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.603A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.593A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 170 through 176 removed outlier: 4.318A pdb=" N ASP C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 196 through 212 removed outlier: 4.137A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 240 through 259 removed outlier: 4.181A pdb=" N LYS C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 Processing sheet with id= A, first strand: chain 'A' and resid 334 through 336 removed outlier: 3.840A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 264 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA A 124 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 266 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LYS A 155 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 220 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 157 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE A 222 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 159 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.747A pdb=" N VAL B 264 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA B 124 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 266 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LYS B 155 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 220 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 157 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B 222 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 159 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.747A pdb=" N VAL C 264 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA C 124 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C 266 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS C 155 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 220 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 157 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE C 222 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 159 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 329 through 331 189 hydrogen bonds defined for protein. 519 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: 1.74 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2357 1.34 - 1.46: 1134 1.46 - 1.57: 3762 1.57 - 1.69: 7 1.69 - 1.81: 63 Bond restraints: 7323 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 7318 not shown) Histogram of bond angle deviations from ideal: 97.92 - 104.80: 102 104.80 - 111.69: 3198 111.69 - 118.57: 2546 118.57 - 125.46: 3943 125.46 - 132.34: 69 Bond angle restraints: 9858 Sorted by residual: angle pdb=" N VAL B 231 " pdb=" CA VAL B 231 " pdb=" C VAL B 231 " ideal model delta sigma weight residual 110.62 118.33 -7.71 1.02e+00 9.61e-01 5.71e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 106.34 20.61 3.00e+00 1.11e-01 4.72e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 111.36 118.01 -6.65 1.17e+00 7.31e-01 3.23e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 110.30 16.65 3.00e+00 1.11e-01 3.08e+01 ... (remaining 9853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4189 25.74 - 51.47: 230 51.47 - 77.20: 59 77.20 - 102.94: 14 102.94 - 128.67: 2 Dihedral angle restraints: 4494 sinusoidal: 1890 harmonic: 2604 Sorted by residual: dihedral pdb=" CA SER B 66 " pdb=" C SER B 66 " pdb=" N GLU B 67 " pdb=" CA GLU B 67 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA SER C 66 " pdb=" C SER C 66 " pdb=" N GLU C 67 " pdb=" CA GLU C 67 " ideal model delta harmonic sigma weight residual 180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA ILE C 24 " pdb=" C ILE C 24 " pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 4491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 896 0.069 - 0.139: 184 0.139 - 0.208: 28 0.208 - 0.277: 0 0.277 - 0.346: 5 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA GLU B 241 " pdb=" N GLU B 241 " pdb=" C GLU B 241 " pdb=" CB GLU B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA GLU C 241 " pdb=" N GLU C 241 " pdb=" C GLU C 241 " pdb=" CB GLU C 241 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1110 not shown) Planarity restraints: 1251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 165 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C PHE A 165 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 165 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 166 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 165 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C PHE C 165 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE C 165 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 166 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C PHE B 165 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 166 " 0.013 2.00e-02 2.50e+03 ... (remaining 1248 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 2696 2.89 - 3.56: 8868 3.56 - 4.23: 16217 4.23 - 4.90: 27691 Nonbonded interactions: 55485 Sorted by model distance: nonbonded pdb=" OE1 GLU B 238 " pdb=" OE2 GLU B 241 " model vdw 1.554 3.040 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.069 2.510 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.070 2.510 nonbonded pdb=" OG1 THR B 133 " pdb="CA CA B 401 " model vdw 2.074 2.510 nonbonded pdb=" OG1 THR A 133 " pdb="CA CA A 401 " model vdw 2.089 2.510 ... (remaining 55480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } 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: 4.210 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: 12.420 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 23.270 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 0.154 7323 Z= 0.455 Angle : 1.151 20.608 9858 Z= 0.628 Chirality : 0.060 0.346 1113 Planarity : 0.005 0.034 1251 Dihedral : 18.085 128.673 2820 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 0.27 % Allowed : 10.76 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.82 (0.21), residues: 903 helix: -4.64 (0.10), residues: 375 sheet: -0.79 (0.37), residues: 162 loop : -2.50 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 295 PHE 0.025 0.003 PHE C 128 TYR 0.009 0.002 TYR A 194 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.6469 (m-30) cc_final: 0.6136 (t0) REVERT: A 79 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6450 (ptmm) REVERT: A 106 GLN cc_start: 0.7679 (mp10) cc_final: 0.7087 (mt0) REVERT: A 178 ASN cc_start: 0.6998 (m-40) cc_final: 0.6781 (m-40) REVERT: A 182 ASP cc_start: 0.6985 (p0) cc_final: 0.6543 (m-30) REVERT: A 205 TYR cc_start: 0.8337 (m-80) cc_final: 0.7920 (m-80) REVERT: A 254 GLN cc_start: 0.8231 (tp40) cc_final: 0.7844 (tp40) REVERT: A 261 ASN cc_start: 0.8745 (t0) cc_final: 0.8501 (t0) REVERT: A 304 ARG cc_start: 0.7298 (ptt90) cc_final: 0.6970 (ptt90) REVERT: B 49 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8026 (ttmm) REVERT: B 72 LYS cc_start: 0.7929 (ptmt) cc_final: 0.7607 (ttpp) REVERT: B 155 LYS cc_start: 0.8257 (mttt) cc_final: 0.7912 (mtpt) REVERT: B 242 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: B 249 MET cc_start: 0.8404 (ptm) cc_final: 0.8005 (ptp) REVERT: C 175 ASP cc_start: 0.7675 (m-30) cc_final: 0.7444 (m-30) REVERT: C 286 LYS cc_start: 0.7713 (pttt) cc_final: 0.7146 (ptmm) REVERT: C 320 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7029 (mt-10) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.2677 time to fit residues: 85.1519 Evaluate side-chains 162 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 242 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 199 GLN A 269 GLN B 22 GLN C 22 GLN C 52 GLN C 181 HIS C 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7323 Z= 0.175 Angle : 0.545 7.831 9858 Z= 0.287 Chirality : 0.045 0.159 1113 Planarity : 0.004 0.031 1251 Dihedral : 12.527 161.790 1085 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 14.61 % Favored : 83.27 % 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: -3.96 (0.22), residues: 903 helix: -3.57 (0.16), residues: 414 sheet: -0.20 (0.34), residues: 162 loop : -2.32 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 211 PHE 0.019 0.002 PHE B 128 TYR 0.011 0.001 TYR A 194 ARG 0.004 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 0.765 Fit side-chains REVERT: A 71 ASP cc_start: 0.6570 (m-30) cc_final: 0.6174 (t0) REVERT: A 211 HIS cc_start: 0.7925 (t-170) cc_final: 0.7564 (t-170) REVERT: A 304 ARG cc_start: 0.7221 (ptt90) cc_final: 0.6875 (ptt90) REVERT: B 49 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7999 (ttmm) REVERT: B 72 LYS cc_start: 0.7897 (ptmt) cc_final: 0.7647 (ttpp) REVERT: B 186 ASP cc_start: 0.7182 (p0) cc_final: 0.6827 (p0) REVERT: B 239 LEU cc_start: 0.7347 (tp) cc_final: 0.7130 (tp) REVERT: B 242 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8047 (ttp-170) REVERT: B 252 ARG cc_start: 0.7343 (tpt90) cc_final: 0.6972 (tpt-90) REVERT: C 175 ASP cc_start: 0.7590 (m-30) cc_final: 0.7312 (m-30) REVERT: C 204 ASP cc_start: 0.7628 (m-30) cc_final: 0.7230 (m-30) REVERT: C 241 GLU cc_start: 0.7498 (tt0) cc_final: 0.7204 (tt0) REVERT: C 286 LYS cc_start: 0.7717 (pttt) cc_final: 0.7292 (ptmm) outliers start: 16 outliers final: 10 residues processed: 195 average time/residue: 0.2647 time to fit residues: 63.8120 Evaluate side-chains 171 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.0070 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN B 291 HIS C 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7323 Z= 0.129 Angle : 0.465 6.710 9858 Z= 0.247 Chirality : 0.043 0.149 1113 Planarity : 0.003 0.025 1251 Dihedral : 11.420 156.997 1081 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.99 % Allowed : 15.54 % Favored : 82.47 % 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: -3.23 (0.24), residues: 903 helix: -2.77 (0.20), residues: 417 sheet: 0.07 (0.34), residues: 162 loop : -2.19 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 30 PHE 0.019 0.001 PHE B 128 TYR 0.007 0.001 TYR A 151 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 0.859 Fit side-chains REVERT: A 71 ASP cc_start: 0.6674 (m-30) cc_final: 0.6290 (t0) REVERT: A 211 HIS cc_start: 0.7997 (t-170) cc_final: 0.7591 (t-170) REVERT: A 304 ARG cc_start: 0.7332 (ptt90) cc_final: 0.6962 (ptt90) REVERT: A 320 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5897 (mt-10) REVERT: B 72 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7680 (ttpp) REVERT: B 241 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 243 GLN cc_start: 0.8295 (mm110) cc_final: 0.8075 (mm-40) REVERT: B 252 ARG cc_start: 0.7399 (tpt90) cc_final: 0.7092 (ttt90) REVERT: C 52 GLN cc_start: 0.7616 (tt0) cc_final: 0.7346 (tt0) REVERT: C 175 ASP cc_start: 0.7497 (m-30) cc_final: 0.7227 (m-30) REVERT: C 204 ASP cc_start: 0.7691 (m-30) cc_final: 0.7352 (m-30) REVERT: C 205 TYR cc_start: 0.8379 (m-80) cc_final: 0.7807 (m-80) REVERT: C 241 GLU cc_start: 0.7426 (tt0) cc_final: 0.7174 (tt0) REVERT: C 286 LYS cc_start: 0.7754 (pttt) cc_final: 0.7277 (ptmt) outliers start: 15 outliers final: 7 residues processed: 185 average time/residue: 0.2607 time to fit residues: 60.0545 Evaluate side-chains 162 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 178 ASN B 100 HIS B 269 GLN C 100 HIS C 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7323 Z= 0.232 Angle : 0.537 6.231 9858 Z= 0.281 Chirality : 0.045 0.173 1113 Planarity : 0.003 0.035 1251 Dihedral : 11.607 166.198 1077 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.39 % Allowed : 16.07 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.94 (0.25), residues: 903 helix: -2.45 (0.21), residues: 417 sheet: 0.32 (0.34), residues: 162 loop : -2.22 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 30 PHE 0.021 0.002 PHE B 128 TYR 0.008 0.001 TYR A 151 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.904 Fit side-chains REVERT: A 71 ASP cc_start: 0.6645 (m-30) cc_final: 0.6360 (t0) REVERT: A 304 ARG cc_start: 0.7422 (ptt90) cc_final: 0.7046 (ptt90) REVERT: A 320 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5802 (mt-10) REVERT: B 41 LYS cc_start: 0.7295 (mttt) cc_final: 0.6985 (mttm) REVERT: B 72 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7798 (ttpp) REVERT: B 252 ARG cc_start: 0.7442 (tpt90) cc_final: 0.7159 (ttt90) REVERT: C 175 ASP cc_start: 0.7560 (m-30) cc_final: 0.7321 (m-30) REVERT: C 204 ASP cc_start: 0.7726 (m-30) cc_final: 0.7377 (m-30) REVERT: C 205 TYR cc_start: 0.8408 (m-80) cc_final: 0.7753 (m-80) REVERT: C 286 LYS cc_start: 0.7706 (pttt) cc_final: 0.7254 (ptmt) outliers start: 18 outliers final: 15 residues processed: 175 average time/residue: 0.2355 time to fit residues: 52.2581 Evaluate side-chains 160 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 243 GLN B 269 GLN C 52 GLN C 261 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7323 Z= 0.254 Angle : 0.548 6.391 9858 Z= 0.285 Chirality : 0.046 0.182 1113 Planarity : 0.003 0.035 1251 Dihedral : 11.438 173.989 1077 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.32 % Allowed : 17.26 % Favored : 79.42 % 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: -2.73 (0.25), residues: 903 helix: -2.22 (0.22), residues: 417 sheet: 0.37 (0.35), residues: 162 loop : -2.19 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 291 PHE 0.022 0.002 PHE B 128 TYR 0.008 0.001 TYR C 151 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 0.873 Fit side-chains REVERT: A 71 ASP cc_start: 0.6666 (m-30) cc_final: 0.6294 (t0) REVERT: A 304 ARG cc_start: 0.7448 (ptt90) cc_final: 0.7033 (ptt180) REVERT: B 72 LYS cc_start: 0.8077 (ptmt) cc_final: 0.7870 (ttpp) REVERT: B 230 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7647 (ptm-80) REVERT: B 244 MET cc_start: 0.7934 (ptp) cc_final: 0.7379 (tmm) REVERT: B 252 ARG cc_start: 0.7557 (tpt90) cc_final: 0.7307 (ttt90) REVERT: C 175 ASP cc_start: 0.7543 (m-30) cc_final: 0.7298 (m-30) REVERT: C 204 ASP cc_start: 0.7669 (m-30) cc_final: 0.7376 (m-30) REVERT: C 205 TYR cc_start: 0.8469 (m-80) cc_final: 0.7816 (m-80) REVERT: C 286 LYS cc_start: 0.7755 (pttt) cc_final: 0.7087 (ptmt) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.2461 time to fit residues: 53.0953 Evaluate side-chains 169 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 269 GLN B 248 GLN B 269 GLN C 52 GLN C 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7323 Z= 0.126 Angle : 0.446 5.994 9858 Z= 0.235 Chirality : 0.043 0.156 1113 Planarity : 0.002 0.021 1251 Dihedral : 10.427 146.460 1077 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.52 % Allowed : 18.19 % Favored : 79.28 % 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: -2.33 (0.26), residues: 903 helix: -1.86 (0.23), residues: 420 sheet: 0.55 (0.36), residues: 162 loop : -2.02 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 291 PHE 0.023 0.001 PHE C 89 TYR 0.008 0.001 TYR C 151 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 0.920 Fit side-chains REVERT: A 71 ASP cc_start: 0.6666 (m-30) cc_final: 0.6329 (t0) REVERT: A 304 ARG cc_start: 0.7346 (ptt90) cc_final: 0.7001 (ptt90) REVERT: B 36 ASP cc_start: 0.6641 (m-30) cc_final: 0.6166 (p0) REVERT: B 41 LYS cc_start: 0.7371 (mttt) cc_final: 0.7063 (mttm) REVERT: B 72 LYS cc_start: 0.8030 (ptmt) cc_final: 0.7825 (ttpp) REVERT: B 230 ARG cc_start: 0.7972 (ptm160) cc_final: 0.7569 (ptm-80) REVERT: B 242 ARG cc_start: 0.8582 (ttm170) cc_final: 0.8374 (ttt-90) REVERT: B 244 MET cc_start: 0.7920 (ptp) cc_final: 0.7451 (tmm) REVERT: B 252 ARG cc_start: 0.7474 (tpt90) cc_final: 0.7230 (ttt90) REVERT: B 286 LYS cc_start: 0.8115 (ptpt) cc_final: 0.7438 (pttm) REVERT: C 175 ASP cc_start: 0.7513 (m-30) cc_final: 0.7240 (m-30) REVERT: C 204 ASP cc_start: 0.7646 (m-30) cc_final: 0.7347 (m-30) REVERT: C 205 TYR cc_start: 0.8407 (m-80) cc_final: 0.7697 (m-80) REVERT: C 245 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8434 (mmtp) REVERT: C 286 LYS cc_start: 0.7691 (pttt) cc_final: 0.7376 (ptmt) outliers start: 19 outliers final: 10 residues processed: 171 average time/residue: 0.2478 time to fit residues: 53.4077 Evaluate side-chains 158 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7323 Z= 0.144 Angle : 0.457 5.847 9858 Z= 0.238 Chirality : 0.043 0.158 1113 Planarity : 0.002 0.020 1251 Dihedral : 10.192 145.836 1077 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.05 % Allowed : 17.66 % Favored : 79.28 % 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: -2.08 (0.26), residues: 903 helix: -1.59 (0.24), residues: 417 sheet: 0.65 (0.37), residues: 162 loop : -1.97 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 211 PHE 0.024 0.001 PHE C 89 TYR 0.006 0.001 TYR C 151 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.832 Fit side-chains REVERT: A 71 ASP cc_start: 0.6662 (m-30) cc_final: 0.6282 (t0) REVERT: A 90 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 304 ARG cc_start: 0.7385 (ptt90) cc_final: 0.7057 (ptt90) REVERT: B 36 ASP cc_start: 0.6592 (m-30) cc_final: 0.6154 (p0) REVERT: B 41 LYS cc_start: 0.7370 (mttt) cc_final: 0.7070 (mttm) REVERT: B 230 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7552 (ptm-80) REVERT: B 242 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8366 (ttt-90) REVERT: B 244 MET cc_start: 0.7935 (ptp) cc_final: 0.7455 (tmm) REVERT: B 286 LYS cc_start: 0.8091 (ptpt) cc_final: 0.7420 (pttm) REVERT: C 61 ASN cc_start: 0.7419 (m-40) cc_final: 0.7084 (m-40) REVERT: C 175 ASP cc_start: 0.7541 (m-30) cc_final: 0.7254 (m-30) REVERT: C 204 ASP cc_start: 0.7650 (m-30) cc_final: 0.7352 (m-30) REVERT: C 205 TYR cc_start: 0.8420 (m-80) cc_final: 0.7720 (m-80) REVERT: C 245 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8429 (mmtp) REVERT: C 286 LYS cc_start: 0.7792 (pttt) cc_final: 0.7509 (ptmt) outliers start: 23 outliers final: 16 residues processed: 169 average time/residue: 0.2529 time to fit residues: 53.9217 Evaluate side-chains 164 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7323 Z= 0.175 Angle : 0.484 5.867 9858 Z= 0.250 Chirality : 0.044 0.162 1113 Planarity : 0.003 0.023 1251 Dihedral : 10.216 145.345 1077 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.66 % Allowed : 18.73 % Favored : 78.62 % 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: -1.94 (0.26), residues: 903 helix: -1.46 (0.24), residues: 420 sheet: 0.68 (0.38), residues: 162 loop : -1.92 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 211 PHE 0.025 0.002 PHE C 89 TYR 0.007 0.001 TYR A 151 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.869 Fit side-chains REVERT: A 71 ASP cc_start: 0.6629 (m-30) cc_final: 0.6254 (t0) REVERT: A 90 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 304 ARG cc_start: 0.7362 (ptt90) cc_final: 0.7031 (ptt90) REVERT: B 36 ASP cc_start: 0.6598 (m-30) cc_final: 0.6201 (p0) REVERT: B 41 LYS cc_start: 0.7361 (mttt) cc_final: 0.7062 (mttm) REVERT: B 230 ARG cc_start: 0.7930 (ptm160) cc_final: 0.7511 (ptm-80) REVERT: B 242 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8316 (ttt-90) REVERT: B 244 MET cc_start: 0.7922 (ptp) cc_final: 0.7434 (tmm) REVERT: B 286 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7447 (pttm) REVERT: C 175 ASP cc_start: 0.7542 (m-30) cc_final: 0.7259 (m-30) REVERT: C 204 ASP cc_start: 0.7691 (m-30) cc_final: 0.7362 (m-30) REVERT: C 205 TYR cc_start: 0.8445 (m-80) cc_final: 0.7734 (m-80) REVERT: C 245 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8473 (mmtp) REVERT: C 286 LYS cc_start: 0.7829 (pttt) cc_final: 0.7548 (ptmt) outliers start: 20 outliers final: 17 residues processed: 165 average time/residue: 0.2695 time to fit residues: 56.1700 Evaluate side-chains 168 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 chunk 52 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 163 ASN B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7323 Z= 0.130 Angle : 0.446 6.764 9858 Z= 0.232 Chirality : 0.043 0.152 1113 Planarity : 0.002 0.021 1251 Dihedral : 9.965 145.904 1077 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.66 % Allowed : 18.59 % Favored : 78.75 % 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: -1.68 (0.27), residues: 903 helix: -1.14 (0.25), residues: 414 sheet: 0.74 (0.38), residues: 162 loop : -1.89 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 211 PHE 0.023 0.001 PHE C 89 TYR 0.006 0.001 TYR C 151 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.854 Fit side-chains REVERT: A 71 ASP cc_start: 0.6675 (m-30) cc_final: 0.6227 (t0) REVERT: A 211 HIS cc_start: 0.8025 (t-170) cc_final: 0.7562 (t-170) REVERT: A 304 ARG cc_start: 0.7359 (ptt90) cc_final: 0.7033 (ptt90) REVERT: B 230 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7523 (ptm-80) REVERT: B 242 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8325 (ttt-90) REVERT: B 244 MET cc_start: 0.7927 (ptp) cc_final: 0.7462 (tmm) REVERT: C 23 ASP cc_start: 0.7878 (p0) cc_final: 0.7673 (t70) REVERT: C 67 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6242 (mm-30) REVERT: C 175 ASP cc_start: 0.7518 (m-30) cc_final: 0.7254 (m-30) REVERT: C 204 ASP cc_start: 0.7641 (m-30) cc_final: 0.7339 (m-30) REVERT: C 205 TYR cc_start: 0.8399 (m-80) cc_final: 0.7662 (m-80) REVERT: C 245 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8417 (mmtp) REVERT: C 286 LYS cc_start: 0.7788 (pttt) cc_final: 0.7541 (ptmt) outliers start: 20 outliers final: 17 residues processed: 169 average time/residue: 0.2449 time to fit residues: 51.8330 Evaluate side-chains 169 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7323 Z= 0.257 Angle : 0.547 7.337 9858 Z= 0.280 Chirality : 0.046 0.172 1113 Planarity : 0.003 0.032 1251 Dihedral : 10.373 145.758 1077 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.39 % Allowed : 19.79 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.26), residues: 903 helix: -1.22 (0.25), residues: 411 sheet: 0.67 (0.37), residues: 162 loop : -1.96 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 211 PHE 0.025 0.002 PHE C 89 TYR 0.008 0.001 TYR A 151 ARG 0.004 0.001 ARG C 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.921 Fit side-chains REVERT: A 71 ASP cc_start: 0.6612 (m-30) cc_final: 0.6308 (t0) REVERT: A 90 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 304 ARG cc_start: 0.7438 (ptt90) cc_final: 0.7160 (ptm-80) REVERT: B 230 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7541 (ptm-80) REVERT: C 25 ASP cc_start: 0.6601 (m-30) cc_final: 0.6210 (m-30) REVERT: C 175 ASP cc_start: 0.7547 (m-30) cc_final: 0.7258 (m-30) REVERT: C 204 ASP cc_start: 0.7659 (m-30) cc_final: 0.7362 (m-30) REVERT: C 205 TYR cc_start: 0.8475 (m-80) cc_final: 0.7797 (m-80) REVERT: C 245 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8488 (mmtp) REVERT: C 286 LYS cc_start: 0.7952 (pttt) cc_final: 0.7531 (ptmt) outliers start: 18 outliers final: 16 residues processed: 170 average time/residue: 0.2636 time to fit residues: 56.3824 Evaluate side-chains 170 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117423 restraints weight = 9903.298| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.23 r_work: 0.3076 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7323 Z= 0.139 Angle : 0.464 7.433 9858 Z= 0.240 Chirality : 0.043 0.156 1113 Planarity : 0.003 0.021 1251 Dihedral : 10.048 146.044 1077 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.52 % Allowed : 19.52 % Favored : 77.95 % 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: -1.58 (0.27), residues: 903 helix: -1.04 (0.25), residues: 414 sheet: 0.73 (0.37), residues: 162 loop : -1.84 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 211 PHE 0.023 0.001 PHE C 89 TYR 0.006 0.001 TYR C 151 ARG 0.004 0.000 ARG B 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.29 seconds wall clock time: 41 minutes 28.57 seconds (2488.57 seconds total)