Starting phenix.real_space_refine on Thu Mar 14 14:24:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/03_2024/7na7_24267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/03_2024/7na7_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_24267/03_2024/7na7_24267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/03_2024/7na7_24267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/03_2024/7na7_24267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/03_2024/7na7_24267_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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: 5.20, per 1000 atoms: 0.58 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 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: 1.62 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: 2.42 Time building geometry restraints manager: 3.61 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 - 34.69: 5470 34.69 - 69.38: 85 69.38 - 104.07: 7 104.07 - 138.76: 3 138.76 - 173.45: 4 Dihedral angle restraints: 5569 sinusoidal: 2266 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 5566 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 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: 2.810 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: 12.860 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 14.699 173.449 3428 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.61 % Allowed : 3.98 % Favored : 95.41 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 176 HIS 0.008 0.001 HIS B 54 PHE 0.019 0.002 PHE R 179 TYR 0.034 0.003 TYR N 102 ARG 0.009 0.001 ARG B 214 *********************** 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 : 0.959 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7165 (m-30) cc_final: 0.6770 (m-30) REVERT: A 186 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 245 GLU cc_start: 0.6504 (tp30) cc_final: 0.6069 (tp30) REVERT: A 316 THR cc_start: 0.8443 (m) cc_final: 0.8046 (p) REVERT: B 137 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7519 (tpt90) REVERT: N 150 THR cc_start: 0.8011 (t) cc_final: 0.7784 (p) REVERT: R 237 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6751 (ttp80) REVERT: R 283 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6671 (mtt-85) REVERT: R 327 SER cc_start: 0.7871 (t) cc_final: 0.7481 (p) REVERT: L 10 GLN cc_start: 0.5134 (mt0) cc_final: 0.4931 (pm20) outliers start: 6 outliers final: 0 residues processed: 241 average time/residue: 1.0540 time to fit residues: 272.6539 Evaluate side-chains 205 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 L 10 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2078 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= 0.274 Angle : 0.788 32.898 12507 Z= 0.365 Chirality : 0.061 1.573 1418 Planarity : 0.004 0.053 1566 Dihedral : 12.020 178.007 1375 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.45 % Allowed : 13.76 % Favored : 83.79 % Cbeta Deviations : 0.00 % 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: 0.54 (0.24), residues: 1119 helix: 1.07 (0.26), residues: 400 sheet: 0.74 (0.28), residues: 304 loop : -0.54 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.001 HIS B 142 PHE 0.021 0.002 PHE A 189 TYR 0.016 0.002 TYR N 190 ARG 0.006 0.001 ARG A 208 *********************** 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 235 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7191 (m-30) cc_final: 0.6800 (m-30) REVERT: A 29 LYS cc_start: 0.7773 (tttm) cc_final: 0.7473 (tttm) REVERT: A 245 GLU cc_start: 0.6433 (tp30) cc_final: 0.6090 (tp30) REVERT: A 341 ASP cc_start: 0.7546 (t0) cc_final: 0.7259 (t0) REVERT: A 345 LYS cc_start: 0.7595 (mttt) cc_final: 0.7226 (mttt) REVERT: B 111 TYR cc_start: 0.8315 (m-80) cc_final: 0.8069 (m-80) REVERT: B 137 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7655 (tpt90) REVERT: B 146 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8216 (mp) REVERT: R 142 TYR cc_start: 0.7895 (t80) cc_final: 0.7501 (t80) REVERT: R 150 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7068 (ttm170) REVERT: R 237 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6838 (ttp80) REVERT: R 332 VAL cc_start: 0.7803 (p) cc_final: 0.7464 (m) REVERT: L 10 GLN cc_start: 0.5282 (mt0) cc_final: 0.4789 (pp30) outliers start: 24 outliers final: 14 residues processed: 222 average time/residue: 1.0987 time to fit residues: 261.2001 Evaluate side-chains 219 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS 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: 0.5980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 156 GLN B 293 ASN B 295 ASN G 17 GLN N 82 GLN N 142 GLN N 179 GLN R 302 GLN L 9 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2979 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= 0.271 Angle : 0.753 31.486 12507 Z= 0.343 Chirality : 0.063 1.720 1418 Planarity : 0.004 0.051 1566 Dihedral : 11.801 176.093 1375 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.98 % Allowed : 14.68 % Favored : 81.35 % Cbeta Deviations : 0.00 % 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: 0.57 (0.24), residues: 1119 helix: 1.14 (0.26), residues: 393 sheet: 0.70 (0.28), residues: 298 loop : -0.48 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.008 0.001 HIS B 142 PHE 0.019 0.002 PHE A 189 TYR 0.014 0.002 TYR N 190 ARG 0.006 0.001 ARG A 208 *********************** 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 254 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7225 (m-30) cc_final: 0.6826 (m-30) REVERT: A 209 LYS cc_start: 0.8092 (ptmm) cc_final: 0.7891 (ptmm) REVERT: A 245 GLU cc_start: 0.6436 (tp30) cc_final: 0.6149 (tp30) REVERT: A 324 THR cc_start: 0.7341 (m) cc_final: 0.6750 (p) REVERT: A 341 ASP cc_start: 0.7362 (t0) cc_final: 0.6897 (t0) REVERT: A 345 LYS cc_start: 0.7583 (mttt) cc_final: 0.7139 (mttt) REVERT: B 146 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 155 ASN cc_start: 0.8155 (t0) cc_final: 0.7867 (t0) REVERT: B 219 ARG cc_start: 0.7466 (mtp85) cc_final: 0.7217 (mtt-85) REVERT: G 17 GLN cc_start: 0.6704 (pt0) cc_final: 0.6474 (pt0) REVERT: R 142 TYR cc_start: 0.7897 (t80) cc_final: 0.7528 (t80) REVERT: R 150 ARG cc_start: 0.7330 (ttm110) cc_final: 0.7036 (ttm170) REVERT: R 237 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6785 (ttp80) REVERT: R 283 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6339 (mtt-85) REVERT: R 332 VAL cc_start: 0.7807 (p) cc_final: 0.7479 (m) outliers start: 39 outliers final: 17 residues processed: 232 average time/residue: 1.0802 time to fit residues: 269.0485 Evaluate side-chains 223 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 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 156 GLN B 295 ASN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3340 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= 0.246 Angle : 0.732 31.099 12507 Z= 0.329 Chirality : 0.063 1.743 1418 Planarity : 0.004 0.054 1566 Dihedral : 11.968 176.112 1375 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.36 % Allowed : 16.92 % Favored : 79.71 % Cbeta Deviations : 0.00 % 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 (0.24), residues: 1119 helix: 1.28 (0.26), residues: 390 sheet: 0.71 (0.27), residues: 302 loop : -0.49 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.009 0.000 ARG B 42 *********************** 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 241 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7251 (m-30) cc_final: 0.6820 (m-30) REVERT: A 29 LYS cc_start: 0.7797 (tttm) cc_final: 0.7575 (tttm) REVERT: A 209 LYS cc_start: 0.8094 (ptmm) cc_final: 0.7885 (ptmm) REVERT: A 243 MET cc_start: 0.8039 (tpp) cc_final: 0.7767 (tpp) REVERT: A 245 GLU cc_start: 0.6393 (tp30) cc_final: 0.6141 (tp30) REVERT: A 341 ASP cc_start: 0.7310 (t0) cc_final: 0.6922 (t0) REVERT: A 345 LYS cc_start: 0.7538 (mttt) cc_final: 0.7298 (mmtt) REVERT: B 155 ASN cc_start: 0.8204 (t0) cc_final: 0.7859 (t0) REVERT: B 258 ASP cc_start: 0.7442 (t0) cc_final: 0.7148 (t0) REVERT: G 17 GLN cc_start: 0.6680 (pt0) cc_final: 0.6475 (pt0) REVERT: R 75 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7520 (mmt90) REVERT: R 142 TYR cc_start: 0.7892 (t80) cc_final: 0.7512 (t80) REVERT: R 150 ARG cc_start: 0.7315 (ttm110) cc_final: 0.7013 (ttm170) REVERT: R 237 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6773 (ttp80) REVERT: R 283 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5978 (mtt180) REVERT: R 332 VAL cc_start: 0.7765 (p) cc_final: 0.7445 (m) outliers start: 33 outliers final: 18 residues processed: 222 average time/residue: 1.0747 time to fit residues: 256.4005 Evaluate side-chains 223 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 327 SER 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: 0.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 220 GLN B 239 ASN B 293 ASN B 295 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9233 Z= 0.295 Angle : 0.753 31.122 12507 Z= 0.341 Chirality : 0.064 1.744 1418 Planarity : 0.004 0.057 1566 Dihedral : 11.708 172.793 1375 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.08 % Allowed : 17.64 % Favored : 78.29 % Cbeta Deviations : 0.00 % 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 (0.25), residues: 1119 helix: 1.27 (0.27), residues: 383 sheet: 0.56 (0.28), residues: 305 loop : -0.42 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE A 189 TYR 0.013 0.002 TYR R 313 ARG 0.010 0.000 ARG B 42 *********************** 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 239 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7243 (m-30) cc_final: 0.6803 (m-30) REVERT: A 197 LYS cc_start: 0.7784 (mttm) cc_final: 0.7420 (mtpp) REVERT: A 243 MET cc_start: 0.8021 (tpp) cc_final: 0.7731 (tpp) REVERT: A 245 GLU cc_start: 0.6395 (tp30) cc_final: 0.6139 (tp30) REVERT: A 341 ASP cc_start: 0.7256 (t0) cc_final: 0.6887 (t0) REVERT: A 345 LYS cc_start: 0.7524 (mttt) cc_final: 0.7315 (mmtt) REVERT: B 42 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6787 (mmm-85) REVERT: B 249 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 258 ASP cc_start: 0.7499 (t0) cc_final: 0.7174 (t0) REVERT: G 20 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7337 (mtpm) REVERT: N 140 MET cc_start: 0.8398 (mmm) cc_final: 0.8068 (mmt) REVERT: R 90 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6811 (mt) REVERT: R 142 TYR cc_start: 0.7879 (t80) cc_final: 0.7518 (t80) REVERT: R 237 ARG cc_start: 0.7223 (ttp80) cc_final: 0.6836 (ttp80) REVERT: R 270 PHE cc_start: 0.7016 (m-10) cc_final: 0.6577 (m-80) REVERT: R 283 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.5990 (mtt180) REVERT: R 332 VAL cc_start: 0.7749 (p) cc_final: 0.7456 (m) outliers start: 40 outliers final: 24 residues processed: 222 average time/residue: 1.0450 time to fit residues: 249.4160 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9233 Z= 0.225 Angle : 0.724 30.654 12507 Z= 0.324 Chirality : 0.063 1.777 1418 Planarity : 0.004 0.055 1566 Dihedral : 11.557 173.088 1375 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.57 % Allowed : 18.55 % Favored : 77.88 % Cbeta Deviations : 0.00 % 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: 0.64 (0.25), residues: 1119 helix: 1.36 (0.27), residues: 384 sheet: 0.56 (0.28), residues: 304 loop : -0.44 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.007 0.000 ARG B 42 *********************** 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 230 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7241 (m-30) cc_final: 0.6814 (m-30) REVERT: A 53 MET cc_start: 0.4660 (mpt) cc_final: 0.4452 (mpm) REVERT: A 197 LYS cc_start: 0.7788 (mttm) cc_final: 0.7442 (mtpp) REVERT: A 243 MET cc_start: 0.8001 (tpp) cc_final: 0.7715 (tpp) REVERT: A 314 LYS cc_start: 0.8325 (mttp) cc_final: 0.8066 (mttm) REVERT: A 341 ASP cc_start: 0.7258 (t0) cc_final: 0.6891 (t0) REVERT: B 258 ASP cc_start: 0.7485 (t0) cc_final: 0.7181 (t0) REVERT: G 20 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7320 (mtpm) REVERT: R 90 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6812 (mt) REVERT: R 142 TYR cc_start: 0.7885 (t80) cc_final: 0.7571 (t80) REVERT: R 150 ARG cc_start: 0.7326 (ttm110) cc_final: 0.7025 (ttm170) REVERT: R 237 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6858 (ttp80) REVERT: R 283 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6150 (mtt180) REVERT: R 332 VAL cc_start: 0.7746 (p) cc_final: 0.7455 (m) outliers start: 35 outliers final: 21 residues processed: 213 average time/residue: 1.0793 time to fit residues: 246.7320 Evaluate side-chains 216 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 234 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 B 340 ASN G 59 ASN N 82 GLN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN L 9 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3772 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= 0.186 Angle : 0.705 30.580 12507 Z= 0.313 Chirality : 0.063 1.785 1418 Planarity : 0.004 0.057 1566 Dihedral : 11.476 173.482 1375 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.26 % Allowed : 19.37 % Favored : 77.37 % Cbeta Deviations : 0.00 % 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: 0.74 (0.25), residues: 1119 helix: 1.52 (0.27), residues: 384 sheet: 0.59 (0.28), residues: 302 loop : -0.43 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 309 TYR 0.011 0.001 TYR N 190 ARG 0.011 0.000 ARG B 42 *********************** 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 233 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7232 (m-30) cc_final: 0.6830 (m-30) REVERT: A 197 LYS cc_start: 0.7839 (mttm) cc_final: 0.7467 (mtpp) REVERT: A 243 MET cc_start: 0.7980 (tpp) cc_final: 0.7637 (tpp) REVERT: A 245 GLU cc_start: 0.6383 (tp30) cc_final: 0.6128 (tp30) REVERT: A 341 ASP cc_start: 0.7308 (t0) cc_final: 0.7081 (t0) REVERT: B 44 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: B 258 ASP cc_start: 0.7472 (t0) cc_final: 0.7165 (t0) REVERT: G 20 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7301 (mtpm) REVERT: R 138 SER cc_start: 0.7939 (p) cc_final: 0.7727 (p) REVERT: R 142 TYR cc_start: 0.7874 (t80) cc_final: 0.7507 (t80) REVERT: R 150 ARG cc_start: 0.7323 (ttm110) cc_final: 0.7039 (ttm170) REVERT: R 237 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6747 (ttp80) REVERT: R 270 PHE cc_start: 0.7034 (m-10) cc_final: 0.6571 (m-80) REVERT: R 332 VAL cc_start: 0.7753 (p) cc_final: 0.7464 (m) outliers start: 32 outliers final: 17 residues processed: 220 average time/residue: 1.0108 time to fit residues: 239.4607 Evaluate side-chains 212 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 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: 0.6980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9233 Z= 0.203 Angle : 0.718 30.543 12507 Z= 0.317 Chirality : 0.063 1.787 1418 Planarity : 0.004 0.058 1566 Dihedral : 11.460 173.758 1375 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.16 % Allowed : 19.16 % Favored : 77.68 % Cbeta Deviations : 0.00 % 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: 0.67 (0.25), residues: 1119 helix: 1.41 (0.27), residues: 389 sheet: 0.56 (0.28), residues: 302 loop : -0.46 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE A 189 TYR 0.011 0.001 TYR N 190 ARG 0.008 0.000 ARG B 42 *********************** 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 227 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7230 (m-30) cc_final: 0.6821 (m-30) REVERT: A 197 LYS cc_start: 0.7837 (mttm) cc_final: 0.7485 (mtpp) REVERT: A 243 MET cc_start: 0.7977 (tpp) cc_final: 0.7629 (tpp) REVERT: A 245 GLU cc_start: 0.6378 (tp30) cc_final: 0.6125 (tp30) REVERT: A 341 ASP cc_start: 0.7279 (t0) cc_final: 0.7036 (t0) REVERT: B 42 ARG cc_start: 0.7072 (mmm-85) cc_final: 0.6832 (mmm-85) REVERT: B 258 ASP cc_start: 0.7475 (t0) cc_final: 0.7165 (t0) REVERT: G 20 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7305 (mtpm) REVERT: N 140 MET cc_start: 0.8358 (mmm) cc_final: 0.8051 (mmt) REVERT: R 138 SER cc_start: 0.7941 (p) cc_final: 0.7729 (p) REVERT: R 142 TYR cc_start: 0.7871 (t80) cc_final: 0.7506 (t80) REVERT: R 237 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6753 (ttp80) REVERT: R 270 PHE cc_start: 0.7036 (m-10) cc_final: 0.6576 (m-80) REVERT: R 332 VAL cc_start: 0.7755 (p) cc_final: 0.7464 (m) outliers start: 31 outliers final: 20 residues processed: 212 average time/residue: 1.0175 time to fit residues: 232.7609 Evaluate side-chains 217 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 234 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9233 Z= 0.187 Angle : 0.711 30.476 12507 Z= 0.313 Chirality : 0.063 1.790 1418 Planarity : 0.004 0.060 1566 Dihedral : 11.430 174.215 1375 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.85 % Allowed : 19.57 % Favored : 77.57 % Cbeta Deviations : 0.00 % 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: 0.70 (0.25), residues: 1119 helix: 1.49 (0.27), residues: 382 sheet: 0.52 (0.28), residues: 302 loop : -0.43 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 309 TYR 0.011 0.001 TYR N 190 ARG 0.010 0.000 ARG B 42 *********************** 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 227 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7231 (m-30) cc_final: 0.6831 (m-30) REVERT: A 197 LYS cc_start: 0.7839 (mttm) cc_final: 0.7495 (mtpp) REVERT: A 243 MET cc_start: 0.7957 (tpp) cc_final: 0.7624 (tpp) REVERT: A 245 GLU cc_start: 0.6379 (tp30) cc_final: 0.6107 (tp30) REVERT: A 314 LYS cc_start: 0.8374 (mttp) cc_final: 0.8139 (mttm) REVERT: A 341 ASP cc_start: 0.7250 (t0) cc_final: 0.6987 (t0) REVERT: B 258 ASP cc_start: 0.7474 (t0) cc_final: 0.7165 (t0) REVERT: N 140 MET cc_start: 0.8344 (mmm) cc_final: 0.8057 (mmt) REVERT: R 138 SER cc_start: 0.7949 (p) cc_final: 0.7739 (p) REVERT: R 142 TYR cc_start: 0.7864 (t80) cc_final: 0.7507 (t80) REVERT: R 150 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7019 (ttm170) REVERT: R 237 ARG cc_start: 0.7239 (ttp80) cc_final: 0.6723 (ttp80) REVERT: R 270 PHE cc_start: 0.7040 (m-10) cc_final: 0.6578 (m-80) REVERT: R 332 VAL cc_start: 0.7755 (p) cc_final: 0.7475 (m) outliers start: 28 outliers final: 21 residues processed: 212 average time/residue: 1.0240 time to fit residues: 233.5542 Evaluate side-chains 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 234 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS 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: 0.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3963 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= 0.299 Angle : 0.753 30.497 12507 Z= 0.337 Chirality : 0.064 1.787 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.548 174.384 1375 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.65 % Allowed : 20.69 % Favored : 76.66 % Cbeta Deviations : 0.00 % 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: 0.51 (0.25), residues: 1119 helix: 1.28 (0.27), residues: 382 sheet: 0.36 (0.28), residues: 306 loop : -0.43 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE A 189 TYR 0.013 0.001 TYR R 313 ARG 0.004 0.000 ARG N 202 ********************** 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 212 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7237 (m-30) cc_final: 0.6823 (m-30) REVERT: A 243 MET cc_start: 0.7963 (tpp) cc_final: 0.7627 (tpp) REVERT: A 245 GLU cc_start: 0.6389 (tp30) cc_final: 0.6115 (tp30) REVERT: A 314 LYS cc_start: 0.8380 (mttp) cc_final: 0.8147 (mttm) REVERT: A 341 ASP cc_start: 0.7234 (t0) cc_final: 0.6965 (t0) REVERT: B 258 ASP cc_start: 0.7476 (t0) cc_final: 0.7175 (t0) REVERT: N 82 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (mm-40) REVERT: N 140 MET cc_start: 0.8378 (mmm) cc_final: 0.8048 (mmt) REVERT: R 138 SER cc_start: 0.7923 (p) cc_final: 0.7714 (p) REVERT: R 142 TYR cc_start: 0.7865 (t80) cc_final: 0.7543 (t80) REVERT: R 150 ARG cc_start: 0.7320 (ttm110) cc_final: 0.7020 (ttm170) REVERT: R 237 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6739 (ttp80) outliers start: 26 outliers final: 21 residues processed: 202 average time/residue: 1.0759 time to fit residues: 233.4709 Evaluate side-chains 205 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 234 GLU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 328 LYS 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: 0.5980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108696 restraints weight = 12714.499| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.47 r_work: 0.3333 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3961 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= 0.257 Angle : 0.741 30.456 12507 Z= 0.331 Chirality : 0.064 1.789 1418 Planarity : 0.004 0.063 1566 Dihedral : 11.531 174.469 1375 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.65 % Allowed : 20.69 % Favored : 76.66 % Cbeta Deviations : 0.00 % 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: 1.28 (0.27), residues: 382 sheet: 0.33 (0.28), residues: 306 loop : -0.41 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR R 313 ARG 0.003 0.000 ARG N 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.77 seconds wall clock time: 75 minutes 29.22 seconds (4529.22 seconds total)