Starting phenix.real_space_refine (version: dev) on Mon Feb 20 11:35:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2c_14461/02_2023/7z2c_14461_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "K PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "H GLU 417": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12037 Number of models: 1 Model: "" Number of chains: 5 Chain: "K" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5287 Classifications: {'peptide': 347} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 338} Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.74, per 1000 atoms: 0.64 Number of scatterers: 12037 At special positions: 0 Unit cell: (111.3, 109.2, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 65 16.00 P 6 15.00 Mg 2 11.99 O 1833 8.00 N 1637 7.00 C 5940 6.00 H 2554 1.00 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: 7.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 10 sheets defined 46.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'K' and resid 17 through 21 Processing helix chain 'K' and resid 47 through 52 Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 79 through 87 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 116 through 134 removed outlier: 3.559A pdb=" N MET K 120 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE K 134 " --> pdb=" O LYS K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 160 No H-bonds generated for 'chain 'K' and resid 158 through 160' Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.840A pdb=" N ARG K 198 " --> pdb=" O HIS K 194 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN K 199 " --> pdb=" O THR K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 286 Processing helix chain 'K' and resid 296 through 298 No H-bonds generated for 'chain 'K' and resid 296 through 298' Processing helix chain 'K' and resid 300 through 309 removed outlier: 4.794A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 342 removed outlier: 5.814A pdb=" N GLU K 329 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS K 332 " --> pdb=" O GLU K 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.608A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.078A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.588A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.408A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.997A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.602A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.539A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'H' and resid 11 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.294A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.812A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 279 through 281 No H-bonds generated for 'chain 'H' and resid 279 through 281' Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.769A pdb=" N ARG H 390 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 Processing helix chain 'H' and resid 415 through 435 Processing sheet with id= A, first strand: chain 'K' and resid 63 through 65 Processing sheet with id= B, first strand: chain 'K' and resid 56 through 60 removed outlier: 6.609A pdb=" N VAL K 37 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE K 30 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU K 39 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE K 28 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 145 through 148 Processing sheet with id= D, first strand: chain 'K' and resid 165 through 167 Processing sheet with id= E, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.018A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 131 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE A 5 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLN A 133 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 12.392A pdb=" N ILE A 7 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N PHE A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 11.686A pdb=" N VAL A 9 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N VAL A 137 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.633A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 269 through 273 434 hydrogen bonds defined for protein. 1119 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: 4.20 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2548 1.13 - 1.31: 1627 1.31 - 1.48: 3878 1.48 - 1.66: 4066 1.66 - 1.83: 105 Bond restraints: 12224 Sorted by residual: bond pdb=" NE ARG K 297 " pdb=" HE ARG K 297 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" NH1 ARG K 213 " pdb="HH11 ARG K 213 " ideal model delta sigma weight residual 0.860 1.044 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" NE2 HIS K 194 " pdb=" HE2 HIS K 194 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" NE ARG K 53 " pdb=" HE ARG K 53 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" NE ARG K 250 " pdb=" HE ARG K 250 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 12219 not shown) Histogram of bond angle deviations from ideal: 93.65 - 102.43: 68 102.43 - 111.20: 8019 111.20 - 119.97: 6124 119.97 - 128.75: 4646 128.75 - 137.52: 64 Bond angle restraints: 18921 Sorted by residual: angle pdb=" C LYS K 139 " pdb=" N VAL K 140 " pdb=" CA VAL K 140 " ideal model delta sigma weight residual 122.48 113.89 8.59 1.25e+00 6.40e-01 4.73e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.87 126.75 -6.88 1.04e+00 9.25e-01 4.38e+01 angle pdb=" N PRO K 169 " pdb=" CA PRO K 169 " pdb=" C PRO K 169 " ideal model delta sigma weight residual 111.03 100.88 10.15 1.54e+00 4.22e-01 4.35e+01 angle pdb=" C ASN K 157 " pdb=" N PRO K 158 " pdb=" CA PRO K 158 " ideal model delta sigma weight residual 119.82 126.15 -6.33 9.80e-01 1.04e+00 4.18e+01 angle pdb=" N ILE K 152 " pdb=" CA ILE K 152 " pdb=" C ILE K 152 " ideal model delta sigma weight residual 107.80 117.06 -9.26 1.45e+00 4.76e-01 4.08e+01 ... (remaining 18916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.61: 6122 33.61 - 67.21: 122 67.21 - 100.82: 15 100.82 - 134.42: 0 134.42 - 168.03: 3 Dihedral angle restraints: 6262 sinusoidal: 2675 harmonic: 3587 Sorted by residual: dihedral pdb=" CD2 HIS K 332 " pdb=" CG HIS K 332 " pdb=" ND1 HIS K 332 " pdb=" HD1 HIS K 332 " ideal model delta harmonic sigma weight residual -180.00 -136.43 -43.57 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.70 -168.03 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.73 156.33 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 6259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 337 0.158 - 0.237: 96 0.237 - 0.316: 21 0.316 - 0.395: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA HIS A 197 " pdb=" N HIS A 197 " pdb=" C HIS A 197 " pdb=" CB HIS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA THR H 109 " pdb=" N THR H 109 " pdb=" C THR H 109 " pdb=" CB THR H 109 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' G2P H 501 " pdb=" C2' G2P H 501 " pdb=" C4' G2P H 501 " pdb=" O3' G2P H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.38 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1451 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 332 " 0.154 2.00e-02 2.50e+03 1.62e-01 5.92e+02 pdb=" CG HIS K 332 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS K 332 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 HIS K 332 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 HIS K 332 " 0.082 2.00e-02 2.50e+03 pdb=" NE2 HIS K 332 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 HIS K 332 " -0.382 2.00e-02 2.50e+03 pdb=" HD2 HIS K 332 " -0.123 2.00e-02 2.50e+03 pdb=" HE1 HIS K 332 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 4 " -0.072 2.00e-02 2.50e+03 2.82e-02 2.38e+01 pdb=" CG TYR K 4 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR K 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR K 4 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR K 4 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR K 4 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR K 4 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 4 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR K 4 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR K 4 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR K 4 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR K 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 75 " 0.070 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" CG TYR K 75 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 75 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR K 75 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 75 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR K 75 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR K 75 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR K 75 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR K 75 " -0.011 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 32 1.60 - 2.35: 1365 2.35 - 3.10: 21850 3.10 - 3.85: 37271 3.85 - 4.60: 58636 Warning: very small nonbonded interaction distances. Nonbonded interactions: 119154 Sorted by model distance: nonbonded pdb="HG11 VAL K 48 " pdb=" OD1 ASP A 431 " model vdw 0.853 2.620 nonbonded pdb="HD21 ASN K 52 " pdb=" CE LYS A 430 " model vdw 0.973 2.750 nonbonded pdb=" OE1 GLU K 32 " pdb=" HZ3 LYS K 34 " model vdw 1.023 1.850 nonbonded pdb=" HZ1 LYS K 336 " pdb=" CB SER A 419 " model vdw 1.038 2.750 nonbonded pdb="HD21 ASN K 292 " pdb=" CB GLN H 434 " model vdw 1.044 2.750 ... (remaining 119149 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 5940 2.51 5 N 1637 2.21 5 O 1833 1.98 5 H 2554 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.050 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: 0.210 Extract box with map and model: 1.430 Check model and map are aligned: 0.140 Process input model: 38.760 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 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 : 0.012 0.123 9670 Z= 0.777 Angle : 1.591 14.075 13107 Z= 1.078 Chirality : 0.088 0.395 1454 Planarity : 0.008 0.074 1705 Dihedral : 14.559 168.027 3578 Min Nonbonded Distance : 1.174 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.02 % Favored : 96.81 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.04 (0.23), residues: 1193 helix: 0.63 (0.20), residues: 518 sheet: -0.25 (0.36), residues: 209 loop : -0.52 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 349 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 354 average time/residue: 0.3534 time to fit residues: 163.2004 Evaluate side-chains 206 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5963 time to fit residues: 2.2404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 133 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 226 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 139 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9670 Z= 0.199 Angle : 0.564 6.981 13107 Z= 0.311 Chirality : 0.041 0.143 1454 Planarity : 0.004 0.030 1705 Dihedral : 9.565 174.280 1323 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.49 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.54 (0.24), residues: 1193 helix: 1.24 (0.22), residues: 516 sheet: 0.14 (0.33), residues: 226 loop : -0.46 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.3068 time to fit residues: 101.8766 Evaluate side-chains 171 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 ASN K 149 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9670 Z= 0.252 Angle : 0.548 6.620 13107 Z= 0.300 Chirality : 0.041 0.183 1454 Planarity : 0.004 0.034 1705 Dihedral : 8.969 174.495 1323 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 38.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.45 (0.25), residues: 1193 helix: 1.12 (0.23), residues: 517 sheet: 0.11 (0.35), residues: 224 loop : -0.45 (0.30), residues: 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.3074 time to fit residues: 85.4901 Evaluate side-chains 147 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9670 Z= 0.235 Angle : 0.515 6.438 13107 Z= 0.277 Chirality : 0.040 0.152 1454 Planarity : 0.003 0.029 1705 Dihedral : 8.668 172.957 1323 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 46.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.30 (0.24), residues: 1193 helix: 1.02 (0.23), residues: 515 sheet: 0.03 (0.35), residues: 224 loop : -0.55 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3120 time to fit residues: 82.8886 Evaluate side-chains 142 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 215 HIS ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 9670 Z= 0.468 Angle : 0.774 11.585 13107 Z= 0.416 Chirality : 0.045 0.174 1454 Planarity : 0.006 0.058 1705 Dihedral : 8.982 176.355 1323 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 67.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1193 helix: -0.30 (0.21), residues: 513 sheet: -0.35 (0.34), residues: 227 loop : -1.38 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 0.3132 time to fit residues: 73.2870 Evaluate side-chains 128 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1535 time to fit residues: 2.3127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 215 HIS ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.7184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9670 Z= 0.254 Angle : 0.536 8.705 13107 Z= 0.288 Chirality : 0.041 0.148 1454 Planarity : 0.004 0.085 1705 Dihedral : 8.505 176.747 1323 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 55.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.71 (0.24), residues: 1193 helix: 0.27 (0.22), residues: 510 sheet: -0.43 (0.35), residues: 230 loop : -1.23 (0.28), residues: 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3326 time to fit residues: 76.8604 Evaluate side-chains 141 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0070 chunk 12 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 5.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 9670 Z= 0.222 Angle : 0.512 7.817 13107 Z= 0.272 Chirality : 0.040 0.151 1454 Planarity : 0.004 0.036 1705 Dihedral : 8.364 178.432 1323 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 53.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.24), residues: 1193 helix: 0.59 (0.23), residues: 507 sheet: -0.40 (0.35), residues: 229 loop : -1.15 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3191 time to fit residues: 75.7573 Evaluate side-chains 137 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 89 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.7656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9670 Z= 0.224 Angle : 0.506 7.466 13107 Z= 0.269 Chirality : 0.040 0.147 1454 Planarity : 0.003 0.029 1705 Dihedral : 8.310 179.598 1323 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 54.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.42 (0.24), residues: 1193 helix: 0.59 (0.23), residues: 512 sheet: -0.43 (0.35), residues: 225 loop : -1.10 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3173 time to fit residues: 74.8276 Evaluate side-chains 133 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 112 optimal weight: 9.9990 overall best weight: 4.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.7749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9670 Z= 0.170 Angle : 0.470 6.760 13107 Z= 0.249 Chirality : 0.040 0.158 1454 Planarity : 0.003 0.028 1705 Dihedral : 8.119 175.671 1323 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 52.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.15 (0.25), residues: 1193 helix: 0.88 (0.24), residues: 506 sheet: -0.33 (0.35), residues: 225 loop : -0.99 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2937 time to fit residues: 69.9279 Evaluate side-chains 135 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 266 ASN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.7974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9670 Z= 0.230 Angle : 0.514 7.619 13107 Z= 0.274 Chirality : 0.040 0.144 1454 Planarity : 0.003 0.028 1705 Dihedral : 8.128 172.707 1323 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 56.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.24), residues: 1193 helix: 0.76 (0.23), residues: 505 sheet: -0.37 (0.35), residues: 223 loop : -1.11 (0.28), residues: 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3265 time to fit residues: 73.3693 Evaluate side-chains 134 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061043 restraints weight = 58961.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063704 restraints weight = 30934.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065417 restraints weight = 20329.581| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.8143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9670 Z= 0.247 Angle : 0.524 7.914 13107 Z= 0.281 Chirality : 0.040 0.145 1454 Planarity : 0.004 0.034 1705 Dihedral : 8.120 167.946 1323 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 58.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.41 (0.24), residues: 1193 helix: 0.67 (0.23), residues: 505 sheet: -0.30 (0.36), residues: 217 loop : -1.23 (0.28), residues: 471 =============================================================================== Job complete usr+sys time: 2324.51 seconds wall clock time: 43 minutes 35.68 seconds (2615.68 seconds total)