Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:02:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_2022/7na7_24267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_2022/7na7_24267.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_2022/7na7_24267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_2022/7na7_24267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_2022/7na7_24267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/12_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} 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: 5.43, 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: 3.40 Conformation dependent library (CDL) restraints added in 1.5 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 34.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 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: 2.69 Time building geometry restraints manager: 3.69 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 1IC L 3 " pdb=" CA 1IC L 3 " pdb=" CB 1IC L 3 " ideal model delta sigma weight residual 110.50 126.38 -15.88 1.50e+00 4.44e-01 1.12e+02 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 ... (remaining 12502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 5155 22.26 - 44.51: 273 44.51 - 66.77: 23 66.77 - 89.03: 5 89.03 - 111.28: 1 Dihedral angle restraints: 5457 sinusoidal: 2154 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 5454 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 -2.48 -1.84 -0.65 2.00e-01 2.50e+01 1.04e+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: 3.630 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: 13.410 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.500 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.060 ------------------------------------------------------------------------------- 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= 0.402 Angle : 1.043 16.282 12507 Z= 0.655 Chirality : 0.218 5.831 1418 Planarity : 0.006 0.071 1566 Dihedral : 12.925 111.283 3316 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 : 1.010 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 241 average time/residue: 0.9669 time to fit residues: 251.7035 Evaluate side-chains 204 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4659 ------------------------------------------------------------------------------- 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 175 GLN B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7710 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9233 Z= 0.244 Angle : 0.768 31.595 12507 Z= 0.356 Chirality : 0.065 1.833 1418 Planarity : 0.004 0.052 1566 Dihedral : 5.089 35.867 1263 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.15 (0.26), residues: 399 sheet: 0.76 (0.28), residues: 303 loop : -0.52 (0.28), residues: 417 *********************** 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 243 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 229 average time/residue: 1.0542 time to fit residues: 259.3238 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 5 average time/residue: 0.1106 time to fit residues: 2.3886 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 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 82 GLN L 9 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3174 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= 0.261 Angle : 0.748 30.410 12507 Z= 0.341 Chirality : 0.065 1.826 1418 Planarity : 0.004 0.050 1566 Dihedral : 4.955 45.226 1263 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 0.59 (0.24), residues: 1119 helix: 1.22 (0.26), residues: 389 sheet: 0.64 (0.28), residues: 299 loop : -0.47 (0.28), residues: 431 *********************** 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 257 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 238 average time/residue: 1.0350 time to fit residues: 265.1696 Evaluate side-chains 219 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.1181 time to fit residues: 2.5806 ------------------------------------------------------------------------------- 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: 0.4980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN B 155 ASN 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: 0.7783 moved from start: 0.3441 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= 0.265 Angle : 0.747 31.302 12507 Z= 0.336 Chirality : 0.064 1.783 1418 Planarity : 0.004 0.054 1566 Dihedral : 5.044 39.065 1263 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.68 (0.24), residues: 1119 helix: 1.40 (0.27), residues: 380 sheet: 0.63 (0.27), residues: 297 loop : -0.44 (0.29), residues: 442 *********************** 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 246 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 205 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 225 average time/residue: 1.0679 time to fit residues: 258.5550 Evaluate side-chains 225 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.3759 time to fit residues: 4.9846 ------------------------------------------------------------------------------- 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: 0.5980 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.0970 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN B 293 ASN G 59 ASN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3620 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= 0.227 Angle : 0.720 30.652 12507 Z= 0.322 Chirality : 0.064 1.841 1418 Planarity : 0.004 0.053 1566 Dihedral : 4.923 34.950 1263 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 3.67 % 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: 0.76 (0.25), residues: 1119 helix: 1.52 (0.26), residues: 381 sheet: 0.63 (0.28), residues: 297 loop : -0.41 (0.29), residues: 441 *********************** 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 237 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 222 average time/residue: 0.9645 time to fit residues: 231.3625 Evaluate side-chains 217 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.5103 time to fit residues: 6.6842 ------------------------------------------------------------------------------- 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: 0.0010 chunk 21 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9233 Z= 0.188 Angle : 0.707 30.581 12507 Z= 0.314 Chirality : 0.064 1.857 1418 Planarity : 0.004 0.053 1566 Dihedral : 4.635 24.480 1263 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.81 (0.25), residues: 1119 helix: 1.61 (0.27), residues: 383 sheet: 0.54 (0.28), residues: 304 loop : -0.37 (0.30), residues: 432 *********************** 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 228 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 213 average time/residue: 0.9944 time to fit residues: 228.9393 Evaluate side-chains 215 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.7511 time to fit residues: 5.5576 ------------------------------------------------------------------------------- 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: 0.6980 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 156 GLN B 239 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 9233 Z= 0.314 Angle : 0.756 30.569 12507 Z= 0.342 Chirality : 0.066 1.860 1418 Planarity : 0.004 0.060 1566 Dihedral : 4.928 24.990 1263 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 3.98 % 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: 0.62 (0.25), residues: 1119 helix: 1.35 (0.27), residues: 382 sheet: 0.49 (0.28), residues: 297 loop : -0.39 (0.29), residues: 440 *********************** 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 235 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 220 average time/residue: 0.9797 time to fit residues: 232.9223 Evaluate side-chains 215 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.5116 time to fit residues: 6.1199 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 103 optimal weight: 0.5980 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 239 ASN B 340 ASN G 59 ASN N 142 GLN N 179 GLN R 186 HIS L 9 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3911 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= 0.147 Angle : 0.693 30.373 12507 Z= 0.306 Chirality : 0.064 1.880 1418 Planarity : 0.003 0.055 1566 Dihedral : 4.526 22.962 1263 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 3.16 % 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: 1.58 (0.27), residues: 379 sheet: 0.52 (0.29), residues: 296 loop : -0.39 (0.30), residues: 444 *********************** 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 230 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.079 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 220 average time/residue: 1.0425 time to fit residues: 248.2791 Evaluate side-chains 210 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.2149 time to fit residues: 2.3041 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.0470 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 156 GLN B 239 ASN G 59 ASN 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: 0.7768 moved from start: 0.3939 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= 0.207 Angle : 0.717 30.391 12507 Z= 0.318 Chirality : 0.065 1.880 1418 Planarity : 0.004 0.059 1566 Dihedral : 4.568 22.411 1263 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.96 % 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: 0.63 (0.25), residues: 1119 helix: 1.43 (0.27), residues: 388 sheet: 0.41 (0.28), residues: 297 loop : -0.41 (0.29), residues: 434 *********************** 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 221 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.054 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 211 average time/residue: 1.0548 time to fit residues: 239.9213 Evaluate side-chains 212 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.3838 time to fit residues: 4.1961 ------------------------------------------------------------------------------- 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: 0.8980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 239 ASN N 82 GLN N 142 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9233 Z= 0.287 Angle : 0.753 30.352 12507 Z= 0.341 Chirality : 0.066 1.886 1418 Planarity : 0.004 0.062 1566 Dihedral : 4.856 24.369 1263 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.24 % 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: 0.50 (0.25), residues: 1119 helix: 1.23 (0.26), residues: 389 sheet: 0.37 (0.29), residues: 293 loop : -0.41 (0.29), residues: 437 ********************** 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 213 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.024 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 205 average time/residue: 1.0221 time to fit residues: 225.7066 Evaluate side-chains 205 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.5996 time to fit residues: 3.0201 ------------------------------------------------------------------------------- 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: 0.7980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109664 restraints weight = 12655.227| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.47 r_work: 0.3346 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9233 Z= 0.253 Angle : 0.737 30.269 12507 Z= 0.333 Chirality : 0.066 1.895 1418 Planarity : 0.004 0.060 1566 Dihedral : 4.849 25.535 1263 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.73 % 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: 0.48 (0.25), residues: 1119 helix: 1.24 (0.26), residues: 386 sheet: 0.35 (0.29), residues: 293 loop : -0.42 (0.29), residues: 440 =============================================================================== Job complete usr+sys time: 4199.78 seconds wall clock time: 75 minutes 1.05 seconds (4501.05 seconds total)