Starting phenix.real_space_refine on Fri Mar 15 17:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/03_2024/7z2a_14459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/03_2024/7z2a_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_14459/03_2024/7z2a_14459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/03_2024/7z2a_14459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/03_2024/7z2a_14459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2a_14459/03_2024/7z2a_14459_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-dev-5265/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: 6.15, per 1000 atoms: 0.50 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: 7.40 Conformation dependent library (CDL) restraints added in 1.7 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: 2.19 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: 4.07 Time building geometry restraints manager: 7.82 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: 6526 33.62 - 67.24: 153 67.24 - 100.86: 17 100.86 - 134.48: 0 134.48 - 168.09: 3 Dihedral angle restraints: 6699 sinusoidal: 3112 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 6696 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: 0.050 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: 0.240 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 37.940 Find NCS groups from input model: 0.310 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- 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 : 14.753 168.095 3606 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 % Allowed : 5.03 % Favored : 94.49 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 21 HIS 0.014 0.002 HIS A 88 PHE 0.033 0.004 PHE K 179 TYR 0.064 0.006 TYR K 4 ARG 0.006 0.001 ARG K 260 *********************** 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 : 1.508 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: A 205 ASP cc_start: 0.5696 (t0) cc_final: 0.5146 (t0) REVERT: A 210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8204 (m-10) REVERT: A 295 CYS cc_start: 0.7822 (m) cc_final: 0.7314 (m) REVERT: A 380 ASN cc_start: 0.6409 (t0) cc_final: 0.5943 (t0) REVERT: H 20 PHE cc_start: 0.7661 (t80) cc_final: 0.7374 (t80) REVERT: H 75 MET cc_start: 0.7827 (mmp) cc_final: 0.7614 (mmp) REVERT: H 156 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8703 (mtmt) REVERT: K 190 MET cc_start: 0.7063 (ttp) cc_final: 0.6439 (tmm) REVERT: K 215 HIS cc_start: 0.5900 (m-70) cc_final: 0.5252 (m-70) outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.3185 time to fit residues: 111.6094 Evaluate side-chains 132 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 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: 7.7990 ------------------------------------------------------------------------------- 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 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: 0.6935 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9667 Z= 0.309 Angle : 0.683 7.863 13103 Z= 0.367 Chirality : 0.042 0.147 1454 Planarity : 0.005 0.080 1703 Dihedral : 10.586 177.646 1350 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 34.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.07 % 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: 0.19 (0.23), residues: 1193 helix: 0.74 (0.21), residues: 522 sheet: 0.17 (0.36), residues: 204 loop : -0.45 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 407 HIS 0.010 0.002 HIS H 139 PHE 0.027 0.002 PHE K 144 TYR 0.019 0.002 TYR K 75 ARG 0.014 0.001 ARG K 297 *********************** 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 153 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.459 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: A 116 ASP cc_start: 0.7910 (p0) cc_final: 0.7505 (p0) REVERT: A 191 THR cc_start: 0.8054 (p) cc_final: 0.7844 (p) REVERT: A 351 PHE cc_start: 0.7026 (m-80) cc_final: 0.6734 (m-80) REVERT: H 160 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7776 (mt-10) REVERT: H 325 MET cc_start: 0.7206 (mmt) cc_final: 0.6828 (tpp) REVERT: H 416 MET cc_start: 0.7816 (ttp) cc_final: 0.7424 (ptm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3011 time to fit residues: 64.3439 Evaluate side-chains 98 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 40.0000 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 193 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9667 Z= 0.227 Angle : 0.534 6.342 13103 Z= 0.289 Chirality : 0.040 0.130 1454 Planarity : 0.004 0.041 1703 Dihedral : 10.060 176.032 1350 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 40.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 0.46 (0.25), residues: 1193 helix: 1.04 (0.23), residues: 528 sheet: -0.07 (0.35), residues: 222 loop : -0.23 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 21 HIS 0.017 0.002 HIS H 37 PHE 0.022 0.002 PHE K 144 TYR 0.018 0.002 TYR K 75 ARG 0.004 0.000 ARG A 390 *********************** 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 133 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 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: A 116 ASP cc_start: 0.7890 (p0) cc_final: 0.7545 (p0) REVERT: A 280 LYS cc_start: 0.4370 (tptp) cc_final: 0.4154 (tptt) REVERT: A 302 MET cc_start: 0.8563 (mmt) cc_final: 0.8312 (mmt) REVERT: A 351 PHE cc_start: 0.7121 (m-80) cc_final: 0.6781 (m-80) REVERT: H 259 MET cc_start: 0.8669 (mmp) cc_final: 0.8432 (mmt) REVERT: H 325 MET cc_start: 0.7305 (mmt) cc_final: 0.7023 (mmm) REVERT: H 416 MET cc_start: 0.7483 (ttp) cc_final: 0.7150 (ptm) REVERT: K 215 HIS cc_start: 0.6582 (m-70) cc_final: 0.6107 (m-70) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2793 time to fit residues: 52.9412 Evaluate side-chains 87 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS H 309 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** 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: 0.7088 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9667 Z= 0.197 Angle : 0.500 5.985 13103 Z= 0.269 Chirality : 0.039 0.130 1454 Planarity : 0.003 0.031 1703 Dihedral : 9.957 179.104 1350 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 43.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 0.55 (0.25), residues: 1193 helix: 1.10 (0.23), residues: 528 sheet: -0.09 (0.36), residues: 217 loop : -0.13 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 21 HIS 0.006 0.001 HIS H 139 PHE 0.026 0.001 PHE K 144 TYR 0.018 0.001 TYR A 224 ARG 0.007 0.000 ARG H 123 *********************** 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 128 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 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: A 116 ASP cc_start: 0.8136 (p0) cc_final: 0.7864 (p0) REVERT: A 339 ARG cc_start: 0.8118 (mmp80) cc_final: 0.7870 (mmp80) REVERT: A 413 MET cc_start: 0.7295 (mmm) cc_final: 0.6617 (mmm) REVERT: H 50 ASN cc_start: 0.7750 (p0) cc_final: 0.7393 (p0) REVERT: H 325 MET cc_start: 0.7190 (mmt) cc_final: 0.6655 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2685 time to fit residues: 49.3157 Evaluate side-chains 87 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9667 Z= 0.261 Angle : 0.540 5.973 13103 Z= 0.286 Chirality : 0.040 0.221 1454 Planarity : 0.004 0.041 1703 Dihedral : 9.836 172.872 1350 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 49.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.35 (0.25), residues: 1193 helix: 0.92 (0.23), residues: 527 sheet: -0.25 (0.36), residues: 217 loop : -0.19 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 407 HIS 0.006 0.001 HIS A 139 PHE 0.025 0.002 PHE K 144 TYR 0.016 0.001 TYR K 75 ARG 0.004 0.001 ARG H 123 *********************** 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 124 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.308 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: A 14 VAL cc_start: 0.8775 (t) cc_final: 0.8553 (p) REVERT: A 116 ASP cc_start: 0.8168 (p0) cc_final: 0.7937 (p0) REVERT: A 118 VAL cc_start: 0.9198 (m) cc_final: 0.8672 (p) REVERT: A 339 ARG cc_start: 0.8220 (mmp80) cc_final: 0.7976 (mmp80) REVERT: H 50 ASN cc_start: 0.7694 (p0) cc_final: 0.7476 (p0) REVERT: H 413 MET cc_start: 0.6965 (mmt) cc_final: 0.6036 (mmt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2929 time to fit residues: 51.7620 Evaluate side-chains 88 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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: 5.9990 chunk 102 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS 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: 0.7226 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9667 Z= 0.244 Angle : 0.522 10.163 13103 Z= 0.275 Chirality : 0.039 0.133 1454 Planarity : 0.003 0.032 1703 Dihedral : 9.827 172.194 1350 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 52.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.24 (0.25), residues: 1193 helix: 0.88 (0.23), residues: 526 sheet: -0.29 (0.36), residues: 217 loop : -0.31 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 407 HIS 0.005 0.001 HIS A 139 PHE 0.026 0.002 PHE K 144 TYR 0.015 0.001 TYR K 75 ARG 0.004 0.000 ARG A 243 *********************** 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 114 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 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: A 14 VAL cc_start: 0.8758 (t) cc_final: 0.8481 (p) REVERT: A 116 ASP cc_start: 0.8208 (p0) cc_final: 0.7958 (p0) REVERT: A 118 VAL cc_start: 0.9235 (m) cc_final: 0.8800 (p) REVERT: H 50 ASN cc_start: 0.7774 (p0) cc_final: 0.7520 (p0) REVERT: H 295 MET cc_start: 0.8027 (ppp) cc_final: 0.7201 (ppp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2583 time to fit residues: 42.7913 Evaluate side-chains 85 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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: 10.0000 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9667 Z= 0.165 Angle : 0.461 6.709 13103 Z= 0.241 Chirality : 0.038 0.131 1454 Planarity : 0.003 0.039 1703 Dihedral : 9.708 173.128 1350 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 49.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.28 (0.24), residues: 520 sheet: -0.22 (0.36), residues: 217 loop : -0.22 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.003 0.001 HIS A 139 PHE 0.027 0.001 PHE K 144 TYR 0.015 0.001 TYR K 4 ARG 0.003 0.000 ARG A 308 *********************** 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 115 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.064 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: A 14 VAL cc_start: 0.8742 (t) cc_final: 0.8500 (p) REVERT: A 77 GLU cc_start: 0.7589 (pt0) cc_final: 0.7279 (pt0) REVERT: A 118 VAL cc_start: 0.9220 (m) cc_final: 0.8733 (p) REVERT: H 50 ASN cc_start: 0.7722 (p0) cc_final: 0.7452 (p0) REVERT: H 295 MET cc_start: 0.7966 (ppp) cc_final: 0.7364 (ppp) REVERT: H 413 MET cc_start: 0.6850 (mmt) cc_final: 0.5946 (mmt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2777 time to fit residues: 45.8224 Evaluate side-chains 88 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 0.7184 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9667 Z= 0.151 Angle : 0.441 5.937 13103 Z= 0.232 Chirality : 0.038 0.132 1454 Planarity : 0.003 0.032 1703 Dihedral : 9.660 175.757 1350 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 49.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.73 (0.26), residues: 1193 helix: 1.42 (0.24), residues: 521 sheet: -0.23 (0.36), residues: 217 loop : -0.12 (0.33), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS H 139 PHE 0.027 0.001 PHE K 144 TYR 0.015 0.001 TYR K 4 ARG 0.008 0.000 ARG A 308 *********************** 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 116 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.241 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: A 14 VAL cc_start: 0.8825 (t) cc_final: 0.8470 (p) REVERT: A 116 ASP cc_start: 0.8183 (p0) cc_final: 0.7959 (p0) REVERT: A 118 VAL cc_start: 0.9220 (m) cc_final: 0.8714 (p) REVERT: H 50 ASN cc_start: 0.7757 (p0) cc_final: 0.7531 (p0) REVERT: H 295 MET cc_start: 0.7964 (ppp) cc_final: 0.7432 (ppp) REVERT: H 413 MET cc_start: 0.6907 (mmt) cc_final: 0.5986 (mmt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2942 time to fit residues: 48.8286 Evaluate side-chains 84 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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: 30.0000 chunk 99 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 46 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 overall best weight: 11.0592 ------------------------------------------------------------------------------- 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9667 Z= 0.338 Angle : 0.612 8.882 13103 Z= 0.327 Chirality : 0.040 0.144 1454 Planarity : 0.004 0.041 1703 Dihedral : 10.058 178.282 1350 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 62.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.07 (0.25), residues: 1193 helix: 0.71 (0.23), residues: 521 sheet: -0.52 (0.36), residues: 218 loop : -0.25 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 407 HIS 0.006 0.002 HIS K 215 PHE 0.025 0.002 PHE K 144 TYR 0.017 0.002 TYR H 224 ARG 0.010 0.001 ARG A 308 *********************** 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 103 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.289 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: A 14 VAL cc_start: 0.8755 (t) cc_final: 0.8476 (p) REVERT: A 116 ASP cc_start: 0.8267 (p0) cc_final: 0.8051 (p0) REVERT: A 118 VAL cc_start: 0.9235 (m) cc_final: 0.8675 (p) REVERT: H 50 ASN cc_start: 0.8079 (p0) cc_final: 0.7727 (p0) REVERT: H 295 MET cc_start: 0.8099 (ppp) cc_final: 0.7607 (ppp) REVERT: H 413 MET cc_start: 0.6552 (mmt) cc_final: 0.6190 (mmp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2835 time to fit residues: 41.4228 Evaluate side-chains 76 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** 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 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 331 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9667 Z= 0.228 Angle : 0.504 6.687 13103 Z= 0.267 Chirality : 0.039 0.138 1454 Planarity : 0.003 0.039 1703 Dihedral : 9.948 176.397 1350 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 57.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.23 (0.26), residues: 1193 helix: 0.92 (0.23), residues: 519 sheet: -0.53 (0.36), residues: 219 loop : -0.22 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 21 HIS 0.005 0.001 HIS A 139 PHE 0.028 0.002 PHE K 144 TYR 0.019 0.002 TYR K 4 ARG 0.007 0.000 ARG A 308 ********************** 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 : 1.215 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: A 14 VAL cc_start: 0.8855 (t) cc_final: 0.8532 (p) REVERT: A 116 ASP cc_start: 0.8280 (p0) cc_final: 0.8054 (p0) REVERT: A 118 VAL cc_start: 0.9272 (m) cc_final: 0.8783 (p) REVERT: H 50 ASN cc_start: 0.8005 (p0) cc_final: 0.7774 (p0) REVERT: H 295 MET cc_start: 0.7872 (ppp) cc_final: 0.7578 (ppp) REVERT: H 413 MET cc_start: 0.6829 (mmt) cc_final: 0.5974 (mmt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2708 time to fit residues: 41.5202 Evaluate side-chains 80 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045710 restraints weight = 73388.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047676 restraints weight = 38376.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049002 restraints weight = 25197.725| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9667 Z= 0.188 Angle : 0.469 6.371 13103 Z= 0.249 Chirality : 0.039 0.139 1454 Planarity : 0.003 0.037 1703 Dihedral : 9.858 175.167 1350 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 56.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.33 (0.26), residues: 1193 helix: 1.06 (0.23), residues: 525 sheet: -0.47 (0.36), residues: 217 loop : -0.27 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 21 HIS 0.004 0.001 HIS H 139 PHE 0.027 0.002 PHE K 144 TYR 0.018 0.001 TYR K 4 ARG 0.007 0.000 ARG A 308 =============================================================================== Job complete usr+sys time: 2239.87 seconds wall clock time: 41 minutes 39.10 seconds (2499.10 seconds total)