Starting phenix.real_space_refine on Sat Apr 6 19:36:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6l_36007/04_2024/8j6l_36007_updated.pdb" } resolution = 3.05 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5657 2.51 5 N 1505 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8839 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 383 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2403 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.55 Number of scatterers: 8839 At special positions: 0 Unit cell: (105.472, 110.416, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1610 8.00 N 1505 7.00 C 5657 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: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 33.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.267A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.940A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.723A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.672A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'R' and resid 25 through 54 Proline residue: R 31 - end of helix removed outlier: 3.580A pdb=" N ALA R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.939A pdb=" N PHE R 65 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 77 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU R 80 " --> pdb=" O ILE R 77 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.888A pdb=" N MET R 84 " --> pdb=" O PRO R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 141 through 163 removed outlier: 4.502A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU R 163 " --> pdb=" O THR R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 218 removed outlier: 4.271A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.859A pdb=" N ARG R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 259 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 268 through 297 removed outlier: 4.322A pdb=" N ASP R 273 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU R 280 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN R 286 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP R 290 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 4.948A pdb=" N TYR R 295 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE R 296 " --> pdb=" O VAL R 293 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER R 297 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.392A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.031A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.942A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.758A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.463A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.808A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.869A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.682A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.524A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.886A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2207 1.33 - 1.45: 1828 1.45 - 1.57: 4903 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 9035 Sorted by residual: bond pdb=" N ILE R 139 " pdb=" CA ILE R 139 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ILE G 25 " pdb=" CA ILE G 25 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.55e+00 bond pdb=" N LYS G 29 " pdb=" CA LYS G 29 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.53e+00 bond pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.56e+00 bond pdb=" N ILE G 28 " pdb=" CA ILE G 28 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.41e+00 ... (remaining 9030 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 205 106.83 - 113.64: 4946 113.64 - 120.44: 3459 120.44 - 127.25: 3531 127.25 - 134.06: 100 Bond angle restraints: 12241 Sorted by residual: angle pdb=" N PHE R 82 " pdb=" CA PHE R 82 " pdb=" C PHE R 82 " ideal model delta sigma weight residual 112.45 105.56 6.89 1.39e+00 5.18e-01 2.45e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 110.42 105.85 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.36 106.32 5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 111.75 105.93 5.82 1.28e+00 6.10e-01 2.07e+01 angle pdb=" N LEU G 15 " pdb=" CA LEU G 15 " pdb=" C LEU G 15 " ideal model delta sigma weight residual 111.07 106.95 4.12 1.07e+00 8.73e-01 1.49e+01 ... (remaining 12236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4681 17.87 - 35.74: 497 35.74 - 53.60: 115 53.60 - 71.47: 8 71.47 - 89.34: 7 Dihedral angle restraints: 5308 sinusoidal: 2012 harmonic: 3296 Sorted by residual: dihedral pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " pdb=" CG ASP A 328 " pdb=" OD1 ASP A 328 " ideal model delta sinusoidal sigma weight residual -30.00 -88.31 58.31 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG B 283 " pdb=" CD ARG B 283 " pdb=" NE ARG B 283 " pdb=" CZ ARG B 283 " ideal model delta sinusoidal sigma weight residual -180.00 -135.11 -44.89 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 -88.43 88.43 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1181 0.054 - 0.108: 147 0.108 - 0.162: 48 0.162 - 0.217: 8 0.217 - 0.271: 3 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA VAL G 16 " pdb=" N VAL G 16 " pdb=" C VAL G 16 " pdb=" CB VAL G 16 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1384 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 137 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN R 137 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN R 137 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS R 138 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO R 81 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 39 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.81e+00 pdb=" C ILE R 39 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 39 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE R 40 " -0.010 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 114 2.63 - 3.20: 8313 3.20 - 3.76: 13585 3.76 - 4.33: 18866 4.33 - 4.90: 30788 Nonbonded interactions: 71666 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.061 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.144 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 322 " model vdw 2.202 2.440 nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.202 2.440 ... (remaining 71661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.730 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: 3.840 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.480 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 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 : 0.003 0.044 9035 Z= 0.201 Angle : 0.616 7.433 12241 Z= 0.374 Chirality : 0.045 0.271 1387 Planarity : 0.004 0.060 1545 Dihedral : 15.239 89.338 3176 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 0.21 % Allowed : 24.95 % Favored : 74.84 % 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: 0.65 (0.26), residues: 1120 helix: 1.70 (0.28), residues: 352 sheet: 0.80 (0.32), residues: 261 loop : -0.67 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 176 HIS 0.006 0.001 HIS R 131 PHE 0.009 0.001 PHE R 25 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7019 (m-30) cc_final: 0.6695 (m-30) REVERT: A 28 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5613 (mt-10) REVERT: A 32 ARG cc_start: 0.7420 (mtm180) cc_final: 0.6234 (mpt180) REVERT: A 197 LYS cc_start: 0.7144 (mtpp) cc_final: 0.6902 (mtmt) REVERT: A 207 GLU cc_start: 0.6432 (tt0) cc_final: 0.6192 (tt0) REVERT: A 209 LYS cc_start: 0.7773 (ttmm) cc_final: 0.7521 (tttm) REVERT: A 252 SER cc_start: 0.7862 (m) cc_final: 0.7634 (p) REVERT: A 341 ASP cc_start: 0.7316 (t0) cc_final: 0.6724 (m-30) REVERT: B 150 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7324 (mmt-90) REVERT: B 263 THR cc_start: 0.7533 (t) cc_final: 0.7302 (m) REVERT: B 312 ASP cc_start: 0.7020 (p0) cc_final: 0.6753 (p0) REVERT: H 83 MET cc_start: 0.6363 (mtm) cc_final: 0.6117 (mtm) REVERT: H 186 GLN cc_start: 0.6372 (tt0) cc_final: 0.5977 (tm-30) REVERT: H 230 MET cc_start: 0.7677 (ttm) cc_final: 0.7432 (ttp) REVERT: R 12 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6492 (mp0) REVERT: R 17 ASN cc_start: 0.5803 (m-40) cc_final: 0.5529 (m-40) REVERT: R 52 PHE cc_start: 0.5671 (t80) cc_final: 0.4800 (m-10) REVERT: R 106 MET cc_start: 0.4915 (mmp) cc_final: 0.3813 (ttt) REVERT: R 164 LYS cc_start: 0.4454 (tmmt) cc_final: 0.4110 (mptt) REVERT: R 187 GLN cc_start: 0.5649 (pm20) cc_final: 0.5010 (pm20) REVERT: R 264 GLN cc_start: 0.5296 (pp30) cc_final: 0.4240 (mp10) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.2179 time to fit residues: 56.6324 Evaluate side-chains 135 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.0570 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 213 HIS A 294 ASN B 13 GLN B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.198 Angle : 0.601 7.056 12241 Z= 0.311 Chirality : 0.043 0.153 1387 Planarity : 0.004 0.044 1545 Dihedral : 4.238 27.598 1220 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 3.82 % Allowed : 19.21 % Favored : 76.96 % 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: 0.47 (0.25), residues: 1120 helix: 1.45 (0.27), residues: 359 sheet: 0.51 (0.31), residues: 278 loop : -0.65 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS B 54 PHE 0.020 0.002 PHE R 54 TYR 0.012 0.001 TYR R 284 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5984 (mt-10) REVERT: A 29 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6989 (ttmt) REVERT: A 32 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6384 (mpt180) REVERT: A 197 LYS cc_start: 0.7248 (mtpp) cc_final: 0.7038 (mtmt) REVERT: A 209 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7533 (tttm) REVERT: A 216 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 248 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7286 (mptt) REVERT: A 252 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 341 ASP cc_start: 0.7491 (t0) cc_final: 0.6780 (m-30) REVERT: B 234 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: B 250 CYS cc_start: 0.6724 (m) cc_final: 0.6436 (m) REVERT: B 312 ASP cc_start: 0.7312 (p0) cc_final: 0.7061 (p0) REVERT: H 83 MET cc_start: 0.6658 (mtm) cc_final: 0.6267 (mtm) REVERT: H 186 GLN cc_start: 0.6962 (tt0) cc_final: 0.6387 (tm-30) REVERT: R 12 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6498 (mp0) REVERT: R 17 ASN cc_start: 0.5696 (m-40) cc_final: 0.5191 (m110) REVERT: R 52 PHE cc_start: 0.5770 (t80) cc_final: 0.4889 (m-80) REVERT: R 62 SER cc_start: 0.6240 (OUTLIER) cc_final: 0.5708 (p) REVERT: R 106 MET cc_start: 0.4941 (mmp) cc_final: 0.4060 (ttt) REVERT: R 164 LYS cc_start: 0.3975 (tmmt) cc_final: 0.3568 (mptt) REVERT: R 195 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5531 (mp) REVERT: R 264 GLN cc_start: 0.5127 (pp30) cc_final: 0.4483 (mp10) outliers start: 36 outliers final: 20 residues processed: 166 average time/residue: 0.2218 time to fit residues: 49.8059 Evaluate side-chains 147 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.0770 chunk 109 optimal weight: 0.0970 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 293 ASN B 295 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9035 Z= 0.149 Angle : 0.533 7.134 12241 Z= 0.276 Chirality : 0.041 0.167 1387 Planarity : 0.004 0.046 1545 Dihedral : 3.969 24.511 1220 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 3.29 % Allowed : 20.91 % Favored : 75.80 % 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: 0.48 (0.26), residues: 1120 helix: 1.56 (0.27), residues: 357 sheet: 0.35 (0.30), residues: 293 loop : -0.62 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS R 161 PHE 0.037 0.001 PHE R 255 TYR 0.007 0.001 TYR B 59 ARG 0.006 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6267 (mt-10) cc_final: 0.6057 (mt-10) REVERT: A 29 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6949 (ttmt) REVERT: A 32 ARG cc_start: 0.7579 (mtm180) cc_final: 0.6394 (mpt180) REVERT: A 197 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7181 (mtmt) REVERT: A 216 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 252 SER cc_start: 0.7926 (m) cc_final: 0.7650 (p) REVERT: A 341 ASP cc_start: 0.7386 (t0) cc_final: 0.6791 (m-30) REVERT: B 129 ARG cc_start: 0.7454 (mtp-110) cc_final: 0.7253 (mtm180) REVERT: B 150 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7301 (mmt-90) REVERT: B 234 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: B 250 CYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6515 (m) REVERT: B 312 ASP cc_start: 0.7463 (p0) cc_final: 0.7248 (p0) REVERT: H 83 MET cc_start: 0.6686 (mtm) cc_final: 0.6307 (mtm) REVERT: H 186 GLN cc_start: 0.6899 (tt0) cc_final: 0.6273 (tm-30) REVERT: H 230 MET cc_start: 0.7501 (ttp) cc_final: 0.7033 (ttp) REVERT: R 17 ASN cc_start: 0.5492 (m-40) cc_final: 0.5019 (m110) REVERT: R 36 LEU cc_start: 0.5598 (pp) cc_final: 0.5211 (mt) REVERT: R 52 PHE cc_start: 0.5923 (t80) cc_final: 0.4951 (m-80) REVERT: R 106 MET cc_start: 0.4899 (mmp) cc_final: 0.4068 (ttt) REVERT: R 195 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5441 (mp) REVERT: R 258 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5912 (mt) REVERT: R 264 GLN cc_start: 0.5146 (pp30) cc_final: 0.4525 (mp10) REVERT: R 287 SER cc_start: 0.6940 (OUTLIER) cc_final: 0.6660 (p) outliers start: 31 outliers final: 20 residues processed: 161 average time/residue: 0.2358 time to fit residues: 51.1788 Evaluate side-chains 148 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9035 Z= 0.199 Angle : 0.573 8.960 12241 Z= 0.296 Chirality : 0.042 0.177 1387 Planarity : 0.004 0.047 1545 Dihedral : 4.221 23.619 1220 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 4.14 % Allowed : 20.70 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.25), residues: 1120 helix: 1.32 (0.27), residues: 367 sheet: 0.21 (0.30), residues: 281 loop : -0.72 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS B 54 PHE 0.043 0.002 PHE R 255 TYR 0.011 0.001 TYR B 59 ARG 0.007 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7380 (mmtm) cc_final: 0.7010 (ttmt) REVERT: A 32 ARG cc_start: 0.7540 (mtm180) cc_final: 0.6324 (mpt180) REVERT: A 252 SER cc_start: 0.7980 (m) cc_final: 0.7692 (p) REVERT: A 341 ASP cc_start: 0.7455 (t0) cc_final: 0.7095 (m-30) REVERT: B 234 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: B 250 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6703 (m) REVERT: B 336 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7549 (tt) REVERT: H 83 MET cc_start: 0.6846 (mtm) cc_final: 0.6494 (mtm) REVERT: H 159 CYS cc_start: 0.6427 (m) cc_final: 0.6092 (t) REVERT: R 12 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6137 (mp0) REVERT: R 17 ASN cc_start: 0.5810 (m-40) cc_final: 0.5464 (m110) REVERT: R 36 LEU cc_start: 0.5597 (pp) cc_final: 0.5213 (mt) REVERT: R 195 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5486 (mp) REVERT: R 213 TRP cc_start: 0.5526 (t60) cc_final: 0.5138 (t60) REVERT: R 264 GLN cc_start: 0.5286 (pp30) cc_final: 0.4675 (mp10) outliers start: 39 outliers final: 26 residues processed: 157 average time/residue: 0.2285 time to fit residues: 48.8297 Evaluate side-chains 152 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN H 194 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.155 Angle : 0.526 7.376 12241 Z= 0.273 Chirality : 0.041 0.192 1387 Planarity : 0.003 0.044 1545 Dihedral : 4.053 21.474 1220 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 3.82 % Allowed : 21.76 % Favored : 74.42 % 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: 0.31 (0.25), residues: 1120 helix: 1.38 (0.27), residues: 363 sheet: 0.21 (0.30), residues: 283 loop : -0.67 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 161 PHE 0.045 0.001 PHE R 255 TYR 0.012 0.001 TYR R 269 ARG 0.007 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7385 (mmtm) cc_final: 0.6985 (ttmt) REVERT: A 32 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6277 (mpt180) REVERT: A 252 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7729 (p) REVERT: A 341 ASP cc_start: 0.7471 (t0) cc_final: 0.7177 (m-30) REVERT: B 150 ARG cc_start: 0.7879 (tpp-160) cc_final: 0.7557 (mmt-90) REVERT: B 169 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7981 (m100) REVERT: B 220 GLN cc_start: 0.7347 (mm110) cc_final: 0.6507 (mt0) REVERT: B 234 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: B 250 CYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6809 (m) REVERT: H 83 MET cc_start: 0.6977 (mtm) cc_final: 0.6653 (mtm) REVERT: H 159 CYS cc_start: 0.6474 (m) cc_final: 0.6151 (t) REVERT: R 12 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6143 (mp0) REVERT: R 17 ASN cc_start: 0.5649 (m-40) cc_final: 0.5288 (m110) REVERT: R 36 LEU cc_start: 0.5619 (pp) cc_final: 0.5364 (mt) REVERT: R 101 ARG cc_start: 0.4967 (mmt180) cc_final: 0.4155 (mmt180) REVERT: R 109 MET cc_start: 0.6038 (ttp) cc_final: 0.5453 (ttp) REVERT: R 142 ARG cc_start: 0.5143 (tmm160) cc_final: 0.4102 (ptt180) REVERT: R 195 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5428 (mp) REVERT: R 213 TRP cc_start: 0.5596 (t60) cc_final: 0.5180 (t60) REVERT: R 264 GLN cc_start: 0.5286 (pp30) cc_final: 0.4652 (mp10) outliers start: 36 outliers final: 25 residues processed: 154 average time/residue: 0.2353 time to fit residues: 49.1981 Evaluate side-chains 150 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 293 ASN B 295 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.231 Angle : 0.599 11.198 12241 Z= 0.307 Chirality : 0.043 0.198 1387 Planarity : 0.004 0.046 1545 Dihedral : 4.444 23.051 1220 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.20 % Favored : 95.62 % Rotamer: Outliers : 4.99 % Allowed : 21.13 % Favored : 73.89 % 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: 0.12 (0.25), residues: 1120 helix: 1.28 (0.27), residues: 366 sheet: 0.02 (0.29), residues: 289 loop : -0.78 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 188 PHE 0.044 0.002 PHE R 255 TYR 0.015 0.001 TYR R 269 ARG 0.006 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7060 (ttmt) REVERT: A 32 ARG cc_start: 0.7464 (mtm180) cc_final: 0.6325 (mpt180) REVERT: A 252 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 269 ASN cc_start: 0.8091 (m110) cc_final: 0.7742 (m-40) REVERT: A 341 ASP cc_start: 0.7467 (t0) cc_final: 0.7153 (m-30) REVERT: B 30 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4503 (mp) REVERT: B 234 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: B 259 GLN cc_start: 0.6521 (mm-40) cc_final: 0.6097 (mm-40) REVERT: B 336 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7464 (tt) REVERT: H 83 MET cc_start: 0.6930 (mtm) cc_final: 0.6631 (mtm) REVERT: H 138 ILE cc_start: 0.5630 (mm) cc_final: 0.5425 (mm) REVERT: H 184 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (m) REVERT: R 12 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6022 (mp0) REVERT: R 36 LEU cc_start: 0.5481 (pp) cc_final: 0.5215 (mt) REVERT: R 63 ARG cc_start: 0.6938 (mmt90) cc_final: 0.6289 (mtm-85) REVERT: R 101 ARG cc_start: 0.4937 (mmt180) cc_final: 0.4144 (mmt180) REVERT: R 109 MET cc_start: 0.6097 (ttp) cc_final: 0.5404 (ttp) REVERT: R 140 SER cc_start: 0.6442 (m) cc_final: 0.5899 (t) REVERT: R 142 ARG cc_start: 0.5221 (tmm160) cc_final: 0.4072 (ptt180) REVERT: R 195 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5469 (mp) REVERT: R 213 TRP cc_start: 0.5741 (t60) cc_final: 0.5272 (t60) REVERT: R 258 LEU cc_start: 0.6610 (tp) cc_final: 0.6381 (tt) REVERT: R 264 GLN cc_start: 0.5294 (pp30) cc_final: 0.4612 (mp10) outliers start: 47 outliers final: 31 residues processed: 159 average time/residue: 0.2333 time to fit residues: 49.9413 Evaluate side-chains 152 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.0060 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN R 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9035 Z= 0.160 Angle : 0.542 8.336 12241 Z= 0.279 Chirality : 0.042 0.208 1387 Planarity : 0.003 0.043 1545 Dihedral : 4.178 20.817 1220 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 4.67 % Allowed : 21.87 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1120 helix: 1.34 (0.28), residues: 363 sheet: 0.05 (0.29), residues: 289 loop : -0.70 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS R 161 PHE 0.040 0.001 PHE R 255 TYR 0.011 0.001 TYR R 269 ARG 0.006 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7111 (ttmt) REVERT: A 32 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6195 (mpt180) REVERT: A 252 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 341 ASP cc_start: 0.7396 (t0) cc_final: 0.7126 (m-30) REVERT: B 30 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4555 (mp) REVERT: B 150 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7514 (mmt-90) REVERT: B 220 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: B 234 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: B 336 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7551 (tt) REVERT: H 83 MET cc_start: 0.7024 (mtm) cc_final: 0.6703 (mtm) REVERT: H 184 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7559 (m) REVERT: H 230 MET cc_start: 0.7508 (ttp) cc_final: 0.7140 (ttp) REVERT: R 12 GLU cc_start: 0.6731 (mt-10) cc_final: 0.5969 (mp0) REVERT: R 36 LEU cc_start: 0.5556 (pp) cc_final: 0.5305 (mt) REVERT: R 63 ARG cc_start: 0.6967 (mmt90) cc_final: 0.6311 (mtm-85) REVERT: R 101 ARG cc_start: 0.5053 (mmt180) cc_final: 0.4262 (mmt180) REVERT: R 140 SER cc_start: 0.6404 (m) cc_final: 0.5916 (t) REVERT: R 142 ARG cc_start: 0.5132 (tmm160) cc_final: 0.4114 (ptt180) REVERT: R 195 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5424 (mp) REVERT: R 213 TRP cc_start: 0.5702 (t60) cc_final: 0.5273 (t60) REVERT: R 258 LEU cc_start: 0.6657 (tp) cc_final: 0.6416 (tt) REVERT: R 264 GLN cc_start: 0.5350 (pp30) cc_final: 0.4627 (mp10) outliers start: 44 outliers final: 32 residues processed: 154 average time/residue: 0.2512 time to fit residues: 53.1555 Evaluate side-chains 152 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.163 Angle : 0.545 7.774 12241 Z= 0.280 Chirality : 0.042 0.225 1387 Planarity : 0.004 0.043 1545 Dihedral : 4.132 21.939 1220 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 4.56 % Allowed : 21.76 % Favored : 73.67 % 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: 0.21 (0.25), residues: 1120 helix: 1.36 (0.28), residues: 363 sheet: 0.07 (0.29), residues: 287 loop : -0.71 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS R 161 PHE 0.040 0.001 PHE R 255 TYR 0.010 0.001 TYR R 269 ARG 0.007 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7536 (mmtm) cc_final: 0.7135 (ttmt) REVERT: A 32 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6202 (mpt180) REVERT: A 252 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7734 (p) REVERT: A 341 ASP cc_start: 0.7402 (t0) cc_final: 0.7121 (m-30) REVERT: B 30 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.4491 (mp) REVERT: B 220 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6707 (mt0) REVERT: B 234 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: B 336 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (tt) REVERT: H 83 MET cc_start: 0.7009 (mtm) cc_final: 0.6715 (mtm) REVERT: H 184 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7607 (m) REVERT: H 230 MET cc_start: 0.7477 (ttp) cc_final: 0.7105 (ttp) REVERT: R 12 GLU cc_start: 0.6599 (mt-10) cc_final: 0.5907 (mp0) REVERT: R 36 LEU cc_start: 0.5532 (pp) cc_final: 0.5269 (mt) REVERT: R 49 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4801 (mm) REVERT: R 63 ARG cc_start: 0.6944 (mmt90) cc_final: 0.6367 (mtm-85) REVERT: R 140 SER cc_start: 0.6486 (m) cc_final: 0.6003 (t) REVERT: R 142 ARG cc_start: 0.5139 (tmm160) cc_final: 0.4115 (ptt180) REVERT: R 195 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5420 (mp) REVERT: R 213 TRP cc_start: 0.5613 (t60) cc_final: 0.5173 (t60) REVERT: R 258 LEU cc_start: 0.6731 (tp) cc_final: 0.6490 (tt) REVERT: R 264 GLN cc_start: 0.5235 (pp30) cc_final: 0.4572 (mp10) outliers start: 43 outliers final: 33 residues processed: 148 average time/residue: 0.2271 time to fit residues: 45.5700 Evaluate side-chains 155 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 114 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN R 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.162 Angle : 0.542 7.650 12241 Z= 0.280 Chirality : 0.042 0.207 1387 Planarity : 0.003 0.042 1545 Dihedral : 4.105 22.286 1220 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 4.67 % Allowed : 21.55 % Favored : 73.78 % 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: 0.20 (0.25), residues: 1120 helix: 1.33 (0.28), residues: 363 sheet: 0.07 (0.29), residues: 287 loop : -0.70 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS R 161 PHE 0.018 0.001 PHE R 296 TYR 0.010 0.001 TYR R 269 ARG 0.007 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7526 (mmtm) cc_final: 0.7125 (ttmt) REVERT: A 32 ARG cc_start: 0.7220 (mtm180) cc_final: 0.6181 (mpt180) REVERT: A 252 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7749 (p) REVERT: A 341 ASP cc_start: 0.7371 (t0) cc_final: 0.7111 (m-30) REVERT: B 220 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6710 (mt0) REVERT: B 234 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: B 336 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7560 (tt) REVERT: H 83 MET cc_start: 0.7000 (mtm) cc_final: 0.6712 (mtm) REVERT: H 184 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7690 (m) REVERT: R 12 GLU cc_start: 0.6598 (mt-10) cc_final: 0.5904 (mp0) REVERT: R 36 LEU cc_start: 0.5529 (pp) cc_final: 0.5269 (mt) REVERT: R 49 LEU cc_start: 0.5144 (OUTLIER) cc_final: 0.4801 (mm) REVERT: R 63 ARG cc_start: 0.6918 (mmt90) cc_final: 0.6324 (mtm-85) REVERT: R 140 SER cc_start: 0.6516 (m) cc_final: 0.6021 (t) REVERT: R 142 ARG cc_start: 0.5162 (tmm160) cc_final: 0.4114 (ptt180) REVERT: R 195 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5434 (mp) REVERT: R 213 TRP cc_start: 0.5661 (t60) cc_final: 0.5226 (t60) REVERT: R 264 GLN cc_start: 0.5366 (pp30) cc_final: 0.4699 (mp10) outliers start: 44 outliers final: 35 residues processed: 149 average time/residue: 0.2268 time to fit residues: 45.9772 Evaluate side-chains 151 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9035 Z= 0.171 Angle : 0.558 9.342 12241 Z= 0.287 Chirality : 0.043 0.335 1387 Planarity : 0.004 0.043 1545 Dihedral : 4.130 22.918 1220 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 4.46 % Allowed : 22.40 % Favored : 73.14 % 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: 0.13 (0.25), residues: 1120 helix: 1.25 (0.28), residues: 366 sheet: 0.05 (0.29), residues: 287 loop : -0.76 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS R 161 PHE 0.018 0.001 PHE R 296 TYR 0.010 0.001 TYR R 269 ARG 0.008 0.000 ARG R 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7524 (mmtm) cc_final: 0.7124 (ttmt) REVERT: A 32 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6190 (mpt180) REVERT: A 252 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7748 (p) REVERT: A 341 ASP cc_start: 0.7373 (t0) cc_final: 0.7119 (m-30) REVERT: B 220 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: B 234 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: B 336 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7577 (tt) REVERT: H 83 MET cc_start: 0.7006 (mtm) cc_final: 0.6719 (mtm) REVERT: H 184 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7789 (m) REVERT: R 12 GLU cc_start: 0.6563 (mt-10) cc_final: 0.5871 (mp0) REVERT: R 36 LEU cc_start: 0.5659 (pp) cc_final: 0.5384 (mt) REVERT: R 49 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4810 (mm) REVERT: R 63 ARG cc_start: 0.6919 (mmt90) cc_final: 0.6278 (mtm-85) REVERT: R 140 SER cc_start: 0.6598 (m) cc_final: 0.6098 (t) REVERT: R 142 ARG cc_start: 0.5142 (tmm160) cc_final: 0.4105 (ptt180) REVERT: R 195 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5412 (mp) REVERT: R 213 TRP cc_start: 0.5630 (t60) cc_final: 0.5210 (t60) REVERT: R 264 GLN cc_start: 0.5449 (pp30) cc_final: 0.4856 (mp10) outliers start: 42 outliers final: 34 residues processed: 144 average time/residue: 0.2339 time to fit residues: 45.3063 Evaluate side-chains 151 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 125 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN R 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.197632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.161465 restraints weight = 10458.874| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.33 r_work: 0.3680 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9035 Z= 0.228 Angle : 0.609 9.082 12241 Z= 0.313 Chirality : 0.044 0.309 1387 Planarity : 0.004 0.043 1545 Dihedral : 4.544 30.070 1220 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 4.67 % Allowed : 22.72 % 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: -0.01 (0.25), residues: 1120 helix: 1.12 (0.28), residues: 359 sheet: -0.01 (0.29), residues: 283 loop : -0.80 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.010 0.001 HIS R 161 PHE 0.017 0.002 PHE R 54 TYR 0.014 0.001 TYR R 269 ARG 0.007 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.63 seconds wall clock time: 43 minutes 3.40 seconds (2583.40 seconds total)