Starting phenix.real_space_refine (version: dev) on Fri May 13 00:21:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/05_2022/7na7_24267_updated.pdb" } resolution = 2.7 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= 0.001 sd= 0.023 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "R TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "L GLU 8": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 221, 'PCIS': 1} Chain breaks: 1 Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2339 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 1 Chain: "L" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1IC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 9036 At special positions: 0 Unit cell: (87.75, 120.25, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1662 8.00 N 1526 7.00 C 5786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1IC L 3 " Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 34.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.069A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.699A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.545A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 4.444A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 40 through 70 removed outlier: 4.142A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 77 through 94 Processing helix chain 'R' and resid 96 through 104 Processing helix chain 'R' and resid 113 through 146 removed outlier: 3.713A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 removed outlier: 3.607A pdb=" N VAL R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 178 removed outlier: 3.570A pdb=" N LEU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 163 " --> pdb=" O ARG R 159 " (cutoff:3.500A) Proline residue: R 177 - end of helix Processing helix chain 'R' and resid 192 through 195 No H-bonds generated for 'chain 'R' and resid 192 through 195' Processing helix chain 'R' and resid 202 through 206 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.512A pdb=" N SER R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 219 " --> pdb=" O TRP R 215 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix Processing helix chain 'R' and resid 256 through 289 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 324 removed outlier: 3.629A pdb=" N GLN R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 328 through 337 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.741A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.667A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.718A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.370A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.587A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.793A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 146 through 148 removed outlier: 6.511A pdb=" N LYS N 244 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU N 178 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU N 187 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 155 through 160 397 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.43: 2481 1.43 - 1.56: 5218 1.56 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9233 Sorted by residual: bond pdb=" CA SER N 106 " pdb=" CB SER N 106 " ideal model delta sigma weight residual 1.531 1.449 0.082 1.22e-02 6.72e+03 4.51e+01 bond pdb=" C PRO N 107 " pdb=" O PRO N 107 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.14e-02 7.69e+03 3.17e+01 bond pdb=" CA SER N 105 " pdb=" CB SER N 105 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.61e-02 3.86e+03 2.62e+01 bond pdb=" C LEU N 174 " pdb=" O LEU N 174 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.14e-02 7.69e+03 2.62e+01 bond pdb=" C TYR N 175 " pdb=" O TYR N 175 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.17e-02 7.31e+03 1.71e+01 ... (remaining 9228 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.73: 143 104.73 - 112.10: 4547 112.10 - 119.46: 3234 119.46 - 126.82: 4466 126.82 - 134.18: 117 Bond angle restraints: 12507 Sorted by residual: angle pdb=" C GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta sigma weight residual 110.63 126.91 -16.28 1.85e+00 2.92e-01 7.75e+01 angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 112.92 103.28 9.64 1.23e+00 6.61e-01 6.14e+01 angle pdb=" C ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta sigma weight residual 111.80 122.64 -10.84 1.46e+00 4.69e-01 5.51e+01 angle pdb=" N LEU R 103 " pdb=" CA LEU R 103 " pdb=" C LEU R 103 " ideal model delta sigma weight residual 113.01 105.72 7.29 1.20e+00 6.94e-01 3.69e+01 angle pdb=" N ALA A 7 " pdb=" CA ALA A 7 " pdb=" CB ALA A 7 " ideal model delta sigma weight residual 110.49 100.53 9.96 1.69e+00 3.50e-01 3.48e+01 ... (remaining 12502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.72: 5260 26.72 - 53.44: 174 53.44 - 80.16: 17 80.16 - 106.87: 1 106.87 - 133.59: 2 Dihedral angle restraints: 5454 sinusoidal: 2151 harmonic: 3303 Sorted by residual: dihedral pdb=" C GLN R 302 " pdb=" N GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta harmonic sigma weight residual -122.60 -141.66 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" C ARG N 191 " pdb=" N ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta harmonic sigma weight residual -122.60 -140.00 17.40 0 2.50e+00 1.60e-01 4.84e+01 dihedral pdb=" C ASN R 305 " pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" CB ASN R 305 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.76e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.166: 1416 1.166 - 2.333: 0 2.333 - 3.499: 0 3.499 - 4.665: 0 4.665 - 5.831: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 2.90 -5.83 2.00e-01 2.50e+01 8.50e+02 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 -2.63 5.18 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" CA 1IC L 3 " pdb=" N 1IC L 3 " pdb=" C 1IC L 3 " pdb=" CB 1IC L 3 " both_signs ideal model delta sigma weight residual False -2.61 -1.84 -0.77 2.00e-01 2.50e+01 1.47e+01 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 174 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C LEU N 174 " -0.091 2.00e-02 2.50e+03 pdb=" O LEU N 174 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR N 175 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 6 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 6 " 0.075 2.00e-02 2.50e+03 pdb=" O SER A 6 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 147 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO N 148 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 148 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 148 " -0.039 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 573 2.72 - 3.27: 8769 3.27 - 3.81: 15027 3.81 - 4.36: 19489 4.36 - 4.90: 33272 Nonbonded interactions: 77130 Sorted by model distance: nonbonded pdb=" OG1 THR R 76 " pdb=" OD1 ASN R 79 " model vdw 2.178 2.440 nonbonded pdb=" O GLY R 57 " pdb=" ND2 ASN R 61 " model vdw 2.250 2.520 nonbonded pdb=" O MET G 38 " pdb=" OE1 GLU G 42 " model vdw 2.277 3.040 nonbonded pdb=" O PRO R 192 " pdb=" OD1 ASN R 196 " model vdw 2.284 3.040 nonbonded pdb=" O PHE N 32 " pdb=" NH2 ARG N 72 " model vdw 2.322 2.520 ... (remaining 77125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5786 2.51 5 N 1526 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.130 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 28.510 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.006 0.082 9233 Z= 0.400 Angle : 1.035 16.912 12507 Z= 0.648 Chirality : 0.218 5.831 1418 Planarity : 0.006 0.071 1566 Dihedral : 13.258 133.593 3313 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.23), residues: 1119 helix: 0.86 (0.26), residues: 388 sheet: 0.67 (0.28), residues: 298 loop : -0.62 (0.26), residues: 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 237 time to evaluate : 1.064 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 241 average time/residue: 0.9718 time to fit residues: 252.7544 Evaluate side-chains 203 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN B 295 ASN N 82 GLN N 142 GLN N 179 GLN N 183 GLN R 120 GLN R 302 GLN R 319 ASN L 9 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9233 Z= 0.243 Angle : 0.771 31.829 12507 Z= 0.356 Chirality : 0.065 1.835 1418 Planarity : 0.005 0.111 1566 Dihedral : 6.361 119.215 1260 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.60 (0.24), residues: 1119 helix: 1.12 (0.26), residues: 399 sheet: 0.82 (0.28), residues: 301 loop : -0.54 (0.28), residues: 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 233 average time/residue: 1.0497 time to fit residues: 263.2853 Evaluate side-chains 211 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1368 time to fit residues: 2.0713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 GLN B 175 GLN B 293 ASN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN L 9 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9233 Z= 0.227 Angle : 0.732 30.690 12507 Z= 0.332 Chirality : 0.064 1.807 1418 Planarity : 0.005 0.106 1566 Dihedral : 5.959 97.586 1260 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.69 (0.24), residues: 1119 helix: 1.28 (0.26), residues: 392 sheet: 0.75 (0.27), residues: 299 loop : -0.46 (0.28), residues: 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 232 average time/residue: 1.0625 time to fit residues: 264.8837 Evaluate side-chains 217 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.1185 time to fit residues: 2.5889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 331 ASN B 17 GLN B 156 GLN B 220 GLN B 239 ASN B 295 ASN B 340 ASN G 59 ASN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN R 302 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9233 Z= 0.298 Angle : 0.760 31.986 12507 Z= 0.345 Chirality : 0.064 1.779 1418 Planarity : 0.005 0.090 1566 Dihedral : 5.896 71.089 1260 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1119 helix: 1.35 (0.27), residues: 382 sheet: 0.69 (0.27), residues: 305 loop : -0.41 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 229 average time/residue: 1.0037 time to fit residues: 248.0267 Evaluate side-chains 224 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.1139 time to fit residues: 2.7298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 155 ASN B 156 GLN B 239 ASN B 293 ASN B 295 ASN G 59 ASN N 82 GLN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9233 Z= 0.228 Angle : 0.719 30.513 12507 Z= 0.323 Chirality : 0.065 1.849 1418 Planarity : 0.004 0.084 1566 Dihedral : 5.825 76.652 1260 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.25), residues: 1119 helix: 1.44 (0.27), residues: 382 sheet: 0.68 (0.27), residues: 302 loop : -0.41 (0.29), residues: 435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 220 average time/residue: 1.0133 time to fit residues: 240.3253 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 9 average time/residue: 0.8007 time to fit residues: 9.2828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 44 GLN B 156 GLN B 239 ASN B 340 ASN G 59 ASN N 82 GLN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9233 Z= 0.277 Angle : 0.741 30.631 12507 Z= 0.335 Chirality : 0.066 1.854 1418 Planarity : 0.004 0.079 1566 Dihedral : 5.636 72.557 1260 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.68 (0.25), residues: 1119 helix: 1.38 (0.27), residues: 382 sheet: 0.58 (0.28), residues: 304 loop : -0.40 (0.29), residues: 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 216 average time/residue: 0.9693 time to fit residues: 226.4240 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 10 average time/residue: 0.4679 time to fit residues: 6.9316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 44 GLN B 156 GLN B 239 ASN G 59 ASN N 82 GLN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN R 186 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9233 Z= 0.199 Angle : 0.723 30.487 12507 Z= 0.320 Chirality : 0.065 1.869 1418 Planarity : 0.004 0.078 1566 Dihedral : 5.377 65.638 1260 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.25), residues: 1119 helix: 1.50 (0.27), residues: 381 sheet: 0.61 (0.28), residues: 300 loop : -0.40 (0.29), residues: 438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 214 average time/residue: 0.9359 time to fit residues: 217.1196 Evaluate side-chains 213 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.3493 time to fit residues: 4.2358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 156 GLN B 239 ASN B 340 ASN G 59 ASN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9233 Z= 0.256 Angle : 0.738 30.474 12507 Z= 0.331 Chirality : 0.066 1.872 1418 Planarity : 0.004 0.077 1566 Dihedral : 5.583 71.073 1260 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: 0.66 (0.25), residues: 1119 helix: 1.39 (0.27), residues: 381 sheet: 0.45 (0.28), residues: 304 loop : -0.33 (0.30), residues: 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.065 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 209 average time/residue: 0.9961 time to fit residues: 226.1090 Evaluate side-chains 208 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.7631 time to fit residues: 6.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 0.0030 chunk 66 optimal weight: 0.5980 chunk 106 optimal weight: 0.0870 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 239 ASN G 59 ASN N 82 GLN N 142 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9233 Z= 0.161 Angle : 0.696 30.333 12507 Z= 0.308 Chirality : 0.065 1.886 1418 Planarity : 0.004 0.077 1566 Dihedral : 5.137 57.969 1260 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.55 (0.27), residues: 381 sheet: 0.46 (0.28), residues: 302 loop : -0.36 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 210 average time/residue: 0.9286 time to fit residues: 211.9064 Evaluate side-chains 206 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1899 time to fit residues: 2.2415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.0040 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 239 ASN N 77 ASN N 82 GLN N 142 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9233 Z= 0.182 Angle : 0.712 30.323 12507 Z= 0.315 Chirality : 0.065 1.887 1418 Planarity : 0.004 0.076 1566 Dihedral : 4.984 49.629 1260 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.55 (0.27), residues: 381 sheet: 0.40 (0.28), residues: 302 loop : -0.32 (0.30), residues: 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 207 average time/residue: 0.9775 time to fit residues: 219.1099 Evaluate side-chains 204 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.4367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 17 GLN B 156 GLN B 239 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 142 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112142 restraints weight = 12112.707| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.48 r_work: 0.3452 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work: 0.3423 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.3407 rms_B_bonded: 1.56 restraints_weight: 0.0625 r_work: 0.3388 rms_B_bonded: 1.78 restraints_weight: 0.0312 r_work: 0.3367 rms_B_bonded: 2.06 restraints_weight: 0.0156 r_work: 0.3343 rms_B_bonded: 2.41 restraints_weight: 0.0078 r_work: 0.3315 rms_B_bonded: 2.85 restraints_weight: 0.0039 r_work: 0.3281 rms_B_bonded: 3.39 restraints_weight: 0.0020 r_work: 0.3242 rms_B_bonded: 4.05 restraints_weight: 0.0010 r_work: 0.3194 rms_B_bonded: 4.86 restraints_weight: 0.0005 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9233 Z= 0.231 Angle : 0.728 30.304 12507 Z= 0.327 Chirality : 0.066 1.889 1418 Planarity : 0.004 0.075 1566 Dihedral : 4.892 35.403 1260 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1119 helix: 1.50 (0.27), residues: 381 sheet: 0.36 (0.28), residues: 291 loop : -0.36 (0.29), residues: 447 =============================================================================== Job complete usr+sys time: 3942.22 seconds wall clock time: 70 minutes 38.95 seconds (4238.95 seconds total)