Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 11:02:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/04_2023/7z2a_14459_updated.pdb" } resolution = 4.3 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= 0.004 sd= 0.012 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 5937 2.51 5 N 1635 2.21 5 O 1834 1.98 5 H 2765 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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" Residue "K PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 5 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: "K" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5494 Classifications: {'peptide': 347} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 337} 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: 6.48, per 1000 atoms: 0.53 Number of scatterers: 12244 At special positions: 0 Unit cell: (112.05, 105.3, 85.05, 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 1834 8.00 N 1635 7.00 C 5937 6.00 H 2765 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: 8.33 Conformation dependent library (CDL) restraints added in 1.5 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: 1.06 Creating SS restraints... 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: 3.609A 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: 3.587A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.957A 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: 4.407A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.261A 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: 3.601A 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: 3.995A 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: 3.603A 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: 3.811A 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: 5.739A 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: 3.770A 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 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: 3.937A pdb=" N ALA 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: 5.812A pdb=" N GLU K 329 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS K 332 " --> pdb=" O GLU K 329 " (cutoff:3.500A) Processing sheet with id= A, 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: 6.249A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 131 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 8.316A 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: 9.417A pdb=" N PHE A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL A 9 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N VAL A 137 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.949A 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: 8.044A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, 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= D, 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: 6.173A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.722A 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: 7.534A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.348A 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: 4.828A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.458A 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: 8.222A 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: 7.575A 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: 6.708A 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= E, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'K' and resid 63 through 65 Processing sheet with id= H, 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: 6.348A pdb=" N ILE K 28 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 145 through 148 Processing sheet with id= J, first strand: chain 'K' and resid 165 through 167 434 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: 4.16 Time building geometry restraints manager: 8.63 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: 2758 1.13 - 1.31: 1625 1.31 - 1.48: 3888 1.48 - 1.66: 4056 1.66 - 1.83: 105 Bond restraints: 12432 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 58 " pdb="HH11 ARG K 58 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.54e+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 8.44e+01 bond pdb=" NH2 ARG K 58 " pdb="HH21 ARG K 58 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 7.97e+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 7.83e+01 ... (remaining 12427 not shown) Histogram of bond angle deviations from ideal: 93.65 - 102.43: 70 102.43 - 111.20: 8450 111.20 - 119.97: 6155 119.97 - 128.75: 4645 128.75 - 137.52: 64 Bond angle restraints: 19384 Sorted by residual: angle pdb=" C LYS K 139 " pdb=" N ILE K 140 " pdb=" CA ILE K 140 " ideal model delta sigma weight residual 122.48 113.87 8.61 1.25e+00 6.40e-01 4.75e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.87 126.71 -6.84 1.04e+00 9.25e-01 4.33e+01 angle pdb=" N PRO K 169 " pdb=" CA PRO K 169 " pdb=" C PRO K 169 " ideal model delta sigma weight residual 111.03 100.91 10.12 1.54e+00 4.22e-01 4.32e+01 angle pdb=" C ASN K 157 " pdb=" N PRO K 158 " pdb=" CA PRO K 158 " ideal model delta sigma weight residual 119.82 126.20 -6.38 9.80e-01 1.04e+00 4.23e+01 angle pdb=" N ILE K 152 " pdb=" CA ILE K 152 " pdb=" C ILE K 152 " ideal model delta sigma weight residual 107.80 117.01 -9.21 1.45e+00 4.76e-01 4.03e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 6162 33.62 - 67.24: 124 67.24 - 100.86: 15 100.86 - 134.48: 0 134.48 - 168.09: 3 Dihedral angle restraints: 6304 sinusoidal: 2717 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 -136.41 -43.59 0 5.00e+00 4.00e-02 7.60e+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 -122.64 -168.09 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 -51.70 156.29 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 6301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 989 0.079 - 0.159: 343 0.159 - 0.238: 97 0.238 - 0.317: 22 0.317 - 0.396: 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 2.11 0.40 2.00e-01 2.50e+01 3.92e+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 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 2.69e+00 ... (remaining 1451 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 332 " 0.153 2.00e-02 2.50e+03 1.62e-01 5.90e+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 " -0.041 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 " -0.381 2.00e-02 2.50e+03 pdb=" HD2 HIS K 332 " -0.123 2.00e-02 2.50e+03 pdb=" HE1 HIS K 332 " 0.121 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 2.85e-02 2.44e+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 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR K 4 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR K 4 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR K 4 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 4 " -0.048 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 2.34e+01 pdb=" CG TYR K 75 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.028 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 " 0.038 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 2037 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.13: 9 1.13 - 2.00: 285 2.00 - 2.87: 15681 2.87 - 3.73: 39239 3.73 - 4.60: 69535 Warning: very small nonbonded interaction distances. Nonbonded interactions: 124749 Sorted by model distance: nonbonded pdb=" OD1 ASP A 431 " pdb="HG11 VAL K 48 " model vdw 0.268 2.620 nonbonded pdb=" CG GLU A 415 " pdb="HH12 ARG K 340 " model vdw 0.813 2.750 nonbonded pdb=" OD1 ASP A 431 " pdb=" CG1 VAL K 48 " model vdw 0.925 3.100 nonbonded pdb=" OE1 GLU A 434 " pdb=" OE1 GLN K 51 " model vdw 0.946 2.800 nonbonded pdb=" OE2 GLU H 431 " pdb=" HD2 PHE K 293 " model vdw 1.011 2.450 ... (remaining 124744 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 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: 0.040 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: 0.280 Extract box with map and model: 1.500 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 38.690 Find NCS groups from input model: 0.300 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 0.124 9667 Z= 0.792 Angle : 1.594 14.069 13103 Z= 1.079 Chirality : 0.089 0.396 1454 Planarity : 0.008 0.074 1703 Dihedral : 14.601 168.095 3578 Min Nonbonded Distance : 0.925 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.85 % Favored : 96.98 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.08 % 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: -0.00 (0.23), residues: 1193 helix: 0.65 (0.20), residues: 518 sheet: -0.23 (0.36), residues: 209 loop : -0.49 (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 **************************** Evaluate side-chains 259 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 254 time to evaluate : 1.296 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: 5 outliers final: 0 residues processed: 258 average time/residue: 0.3187 time to fit residues: 111.7319 Evaluate side-chains 127 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6194 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 101 ASN A 300 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN H 406 HIS H 433 GLN K 5 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 9667 Z= 0.329 Angle : 0.700 8.600 13103 Z= 0.375 Chirality : 0.042 0.144 1454 Planarity : 0.006 0.082 1703 Dihedral : 9.836 177.817 1322 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 35.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.09 (0.23), residues: 1193 helix: 0.59 (0.21), residues: 528 sheet: 0.15 (0.37), residues: 202 loop : -0.45 (0.29), residues: 463 *********************** 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 **************************** Evaluate side-chains 154 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.358 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 outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.3381 time to fit residues: 71.1067 Evaluate side-chains 100 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7381 ------------------------------------------------------------------------------- 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: 30.0000 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 15 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** 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: 0.7036 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9667 Z= 0.213 Angle : 0.527 6.150 13103 Z= 0.286 Chirality : 0.040 0.162 1454 Planarity : 0.004 0.040 1703 Dihedral : 9.400 175.705 1322 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 40.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.44 (0.25), residues: 1193 helix: 1.03 (0.23), residues: 526 sheet: -0.09 (0.35), residues: 222 loop : -0.25 (0.31), residues: 445 *********************** 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 **************************** Evaluate side-chains 137 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.424 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 outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3038 time to fit residues: 58.8023 Evaluate side-chains 89 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7002 ------------------------------------------------------------------------------- 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: 50.0000 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN H 197 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 9667 Z= 0.313 Angle : 0.617 8.062 13103 Z= 0.331 Chirality : 0.040 0.134 1454 Planarity : 0.004 0.046 1703 Dihedral : 9.617 174.250 1322 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 50.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1193 helix: 0.60 (0.23), residues: 527 sheet: -0.32 (0.36), residues: 217 loop : -0.39 (0.31), residues: 449 *********************** 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 **************************** Evaluate side-chains 125 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.423 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 outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.3338 time to fit residues: 60.1479 Evaluate side-chains 91 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1234 time to fit residues: 1.9433 ------------------------------------------------------------------------------- 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: 50.0000 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9667 Z= 0.208 Angle : 0.497 7.315 13103 Z= 0.264 Chirality : 0.039 0.180 1454 Planarity : 0.003 0.044 1703 Dihedral : 9.471 171.139 1322 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 49.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.25), residues: 1193 helix: 0.97 (0.23), residues: 525 sheet: -0.31 (0.37), residues: 219 loop : -0.30 (0.32), residues: 449 *********************** 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 **************************** Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.376 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 outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2783 time to fit residues: 49.2611 Evaluate side-chains 88 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5928 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 9667 Z= 0.181 Angle : 0.468 5.962 13103 Z= 0.249 Chirality : 0.039 0.130 1454 Planarity : 0.003 0.031 1703 Dihedral : 9.445 173.027 1322 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 49.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.38 (0.25), residues: 1193 helix: 1.04 (0.23), residues: 526 sheet: -0.20 (0.36), residues: 217 loop : -0.31 (0.32), residues: 450 *********************** 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 **************************** Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 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 outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2928 time to fit residues: 46.8832 Evaluate side-chains 89 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8383 ------------------------------------------------------------------------------- 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: 20.0000 chunk 12 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 40.0000 chunk 63 optimal weight: 0.0670 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9667 Z= 0.183 Angle : 0.468 7.138 13103 Z= 0.247 Chirality : 0.039 0.132 1454 Planarity : 0.003 0.031 1703 Dihedral : 9.441 172.879 1322 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 50.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.51 (0.26), residues: 1193 helix: 1.16 (0.24), residues: 526 sheet: -0.19 (0.36), residues: 217 loop : -0.23 (0.32), residues: 450 *********************** 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 **************************** Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.348 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 outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2904 time to fit residues: 46.9621 Evaluate side-chains 84 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7600 ------------------------------------------------------------------------------- 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: 20.0000 chunk 45 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 9667 Z= 0.144 Angle : 0.442 6.496 13103 Z= 0.236 Chirality : 0.038 0.132 1454 Planarity : 0.003 0.029 1703 Dihedral : 9.426 177.728 1322 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 48.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.72 (0.26), residues: 1193 helix: 1.40 (0.24), residues: 526 sheet: -0.12 (0.36), residues: 217 loop : -0.19 (0.32), residues: 450 *********************** 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 **************************** Evaluate side-chains 110 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.208 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 outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2939 time to fit residues: 46.3347 Evaluate side-chains 85 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8311 ------------------------------------------------------------------------------- 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: 50.0000 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 424 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9667 Z= 0.236 Angle : 0.513 7.373 13103 Z= 0.273 Chirality : 0.039 0.138 1454 Planarity : 0.003 0.033 1703 Dihedral : 9.557 178.166 1322 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 55.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.58 (0.26), residues: 1193 helix: 1.23 (0.24), residues: 520 sheet: -0.17 (0.37), residues: 215 loop : -0.18 (0.32), residues: 458 *********************** 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 **************************** Evaluate side-chains 107 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.318 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 outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2980 time to fit residues: 45.8841 Evaluate side-chains 82 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7217 ------------------------------------------------------------------------------- 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: 0.0970 chunk 117 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9667 Z= 0.188 Angle : 0.473 8.279 13103 Z= 0.253 Chirality : 0.039 0.137 1454 Planarity : 0.003 0.031 1703 Dihedral : 9.454 173.883 1322 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 53.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.67 (0.26), residues: 1193 helix: 1.35 (0.24), residues: 518 sheet: -0.15 (0.37), residues: 218 loop : -0.17 (0.32), residues: 457 ********************** 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 **************************** Evaluate side-chains 106 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.448 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 outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3266 time to fit residues: 49.2657 Evaluate side-chains 81 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8089 ------------------------------------------------------------------------------- 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: 0.0010 chunk 86 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 4.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.066588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046449 restraints weight = 72213.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048507 restraints weight = 38011.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049862 restraints weight = 24841.798| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9667 Z= 0.179 Angle : 0.466 8.152 13103 Z= 0.248 Chirality : 0.038 0.137 1454 Planarity : 0.003 0.030 1703 Dihedral : 9.409 175.746 1322 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 54.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.72 (0.26), residues: 1193 helix: 1.44 (0.24), residues: 515 sheet: -0.15 (0.37), residues: 218 loop : -0.19 (0.32), residues: 460 =============================================================================== Job complete usr+sys time: 2217.21 seconds wall clock time: 41 minutes 23.00 seconds (2483.00 seconds total)