Starting phenix.real_space_refine on Wed Feb 14 05:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjj_33229/02_2024/7xjj_33229.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.102 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 57 5.16 5 C 5559 2.51 5 N 1473 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1691 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 121 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "E" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2095 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 4.71, per 1000 atoms: 0.54 Number of scatterers: 8710 At special positions: 0 Unit cell: (88.047, 119.57, 125.005, 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 57 16.00 O 1621 8.00 N 1473 7.00 C 5559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 14 sheets defined 36.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.505A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.955A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'E' and resid 34 through 59 Processing helix chain 'E' and resid 69 through 98 Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 103 through 139 removed outlier: 4.141A pdb=" N ILE E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 173 removed outlier: 3.613A pdb=" N ALA E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Proline residue: E 169 - end of helix Processing helix chain 'E' and resid 193 through 231 removed outlier: 3.714A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 235 through 272 Proline residue: E 262 - end of helix Processing helix chain 'E' and resid 278 through 304 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.710A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.625A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.083A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 5.915A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.612A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.881A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.959A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.869A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.003A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.713A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.676A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.689A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.247A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 148 447 hydrogen bonds defined for protein. 1272 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: 2.43 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1405 1.27 - 1.41: 2326 1.41 - 1.55: 5090 1.55 - 1.69: 3 1.69 - 1.83: 80 Bond restraints: 8904 Sorted by residual: bond pdb=" C LEU A 23 " pdb=" O LEU A 23 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.14e+01 bond pdb=" CA LEU A 23 " pdb=" C LEU A 23 " ideal model delta sigma weight residual 1.523 1.409 0.114 1.30e-02 5.92e+03 7.68e+01 bond pdb=" C ASN A 22 " pdb=" O ASN A 22 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.16e-02 7.43e+03 7.19e+01 bond pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.89e+01 bond pdb=" C ASP A 26 " pdb=" O ASP A 26 " ideal model delta sigma weight residual 1.237 1.155 0.081 1.19e-02 7.06e+03 4.67e+01 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.60: 119 104.60 - 112.07: 4426 112.07 - 119.53: 2995 119.53 - 127.00: 4442 127.00 - 134.47: 108 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N LYS A 35 " pdb=" CA LYS A 35 " pdb=" C LYS A 35 " ideal model delta sigma weight residual 110.36 131.10 -20.74 1.55e+00 4.16e-01 1.79e+02 angle pdb=" N GLY E 157 " pdb=" CA GLY E 157 " pdb=" C GLY E 157 " ideal model delta sigma weight residual 112.83 101.71 11.12 1.22e+00 6.72e-01 8.31e+01 angle pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" CD PRO E 169 " ideal model delta sigma weight residual 112.00 101.15 10.85 1.40e+00 5.10e-01 6.00e+01 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" N ASP A 33 " ideal model delta sigma weight residual 117.30 125.75 -8.45 1.16e+00 7.43e-01 5.31e+01 angle pdb=" CA CYS E 158 " pdb=" CB CYS E 158 " pdb=" SG CYS E 158 " ideal model delta sigma weight residual 114.40 98.13 16.27 2.30e+00 1.89e-01 5.01e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4708 18.00 - 36.00: 425 36.00 - 54.00: 72 54.00 - 72.00: 14 72.00 - 90.00: 4 Dihedral angle restraints: 5223 sinusoidal: 1965 harmonic: 3258 Sorted by residual: dihedral pdb=" C MET E 166 " pdb=" N MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual -122.60 -149.39 26.79 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual 122.80 146.38 -23.58 0 2.50e+00 1.60e-01 8.90e+01 dihedral pdb=" C ILE A 28 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " ideal model delta harmonic sigma weight residual -122.00 -137.24 15.24 0 2.50e+00 1.60e-01 3.72e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1366 0.219 - 0.439: 8 0.439 - 0.658: 3 0.658 - 0.877: 2 0.877 - 1.097: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA MET E 166 " pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CB MET E 166 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" C PRO E 169 " pdb=" CB PRO E 169 " both_signs ideal model delta sigma weight residual False 2.72 1.95 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA LYS A 35 " pdb=" N LYS A 35 " pdb=" C LYS A 35 " pdb=" CB LYS A 35 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1377 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 168 " -0.157 5.00e-02 4.00e+02 2.38e-01 9.05e+01 pdb=" N PRO E 169 " 0.411 5.00e-02 4.00e+02 pdb=" CA PRO E 169 " -0.135 5.00e-02 4.00e+02 pdb=" CD PRO E 169 " -0.119 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 156 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C VAL E 156 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL E 156 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY E 157 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 188 " 0.033 2.00e-02 2.50e+03 3.00e-02 2.24e+01 pdb=" CG TRP E 188 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 188 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 188 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 188 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 188 " 0.001 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 47 2.40 - 3.02: 5273 3.02 - 3.65: 13354 3.65 - 4.27: 19467 4.27 - 4.90: 33595 Nonbonded interactions: 71736 Sorted by model distance: nonbonded pdb=" O LYS A 35 " pdb=" CG LEU A 36 " model vdw 1.771 3.470 nonbonded pdb=" O LYS A 35 " pdb=" CD2 LEU A 36 " model vdw 1.950 3.460 nonbonded pdb=" CE1 TYR E 113 " pdb=" CB ALA E 167 " model vdw 1.990 3.760 nonbonded pdb=" O ASN E 33 " pdb=" OG1 THR E 36 " model vdw 2.139 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.149 2.440 ... (remaining 71731 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: 0.330 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: 1.800 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.007 0.114 8904 Z= 0.456 Angle : 0.879 21.081 12090 Z= 0.529 Chirality : 0.070 1.097 1380 Planarity : 0.008 0.238 1531 Dihedral : 14.108 89.998 3115 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.96 % Allowed : 1.49 % Favored : 97.55 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.26), residues: 1104 helix: 2.09 (0.25), residues: 383 sheet: -0.58 (0.31), residues: 255 loop : -0.74 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP E 188 HIS 0.006 0.001 HIS E 289 PHE 0.018 0.001 PHE E 114 TYR 0.017 0.001 TYR S 101 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 297 TRP cc_start: 0.7247 (m100) cc_final: 0.6894 (m100) REVERT: S 128 MET cc_start: 0.8094 (mmm) cc_final: 0.7627 (mmm) REVERT: S 217 CYS cc_start: 0.5906 (p) cc_final: 0.5491 (p) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.2026 time to fit residues: 50.1019 Evaluate side-chains 146 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 169 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.0040 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN B 156 GLN E 76 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8904 Z= 0.164 Angle : 0.550 6.715 12090 Z= 0.286 Chirality : 0.041 0.167 1380 Planarity : 0.004 0.075 1531 Dihedral : 4.883 65.720 1216 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.06 % Allowed : 10.44 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.26), residues: 1104 helix: 2.06 (0.25), residues: 385 sheet: -0.47 (0.30), residues: 281 loop : -0.88 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 188 HIS 0.005 0.001 HIS E 289 PHE 0.022 0.001 PHE E 177 TYR 0.015 0.001 TYR S 178 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7526 (t0) cc_final: 0.7309 (t0) REVERT: A 230 ASP cc_start: 0.7954 (m-30) cc_final: 0.7671 (m-30) REVERT: B 220 GLN cc_start: 0.7269 (mt0) cc_final: 0.6909 (mp10) REVERT: E 195 ARG cc_start: 0.7262 (tmt170) cc_final: 0.6899 (ttp80) REVERT: S 180 MET cc_start: 0.7042 (ptt) cc_final: 0.6238 (ptt) outliers start: 10 outliers final: 8 residues processed: 164 average time/residue: 0.2098 time to fit residues: 47.1690 Evaluate side-chains 152 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.0020 chunk 82 optimal weight: 0.0980 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN E 92 GLN E 174 GLN ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8904 Z= 0.151 Angle : 0.520 6.426 12090 Z= 0.273 Chirality : 0.041 0.148 1380 Planarity : 0.004 0.062 1531 Dihedral : 4.258 67.274 1207 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.60 % Allowed : 13.10 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.45 (0.26), residues: 1104 helix: 2.21 (0.25), residues: 390 sheet: -0.44 (0.30), residues: 285 loop : -0.95 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 188 HIS 0.003 0.001 HIS E 289 PHE 0.022 0.001 PHE E 177 TYR 0.014 0.001 TYR S 101 ARG 0.004 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8992 (tpp) cc_final: 0.8526 (tpt) REVERT: B 220 GLN cc_start: 0.7218 (mt0) cc_final: 0.6905 (mp10) REVERT: E 195 ARG cc_start: 0.7273 (tmt170) cc_final: 0.6923 (ttp80) REVERT: E 197 LYS cc_start: 0.7593 (tppt) cc_final: 0.6821 (tptm) REVERT: G 38 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5853 (pmm) REVERT: S 34 MET cc_start: 0.8300 (mmm) cc_final: 0.8018 (mmm) REVERT: S 128 MET cc_start: 0.8368 (mmm) cc_final: 0.7554 (mmm) REVERT: S 180 MET cc_start: 0.7296 (ptt) cc_final: 0.6894 (ptt) REVERT: S 219 GLN cc_start: 0.9144 (pp30) cc_final: 0.8641 (pp30) outliers start: 15 outliers final: 9 residues processed: 164 average time/residue: 0.2100 time to fit residues: 47.4056 Evaluate side-chains 157 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN B 156 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8904 Z= 0.268 Angle : 0.576 5.971 12090 Z= 0.301 Chirality : 0.042 0.168 1380 Planarity : 0.004 0.059 1531 Dihedral : 4.495 72.464 1205 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.13 % Allowed : 15.76 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.26), residues: 1104 helix: 2.10 (0.25), residues: 390 sheet: -0.41 (0.31), residues: 280 loop : -0.93 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 188 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE E 177 TYR 0.021 0.001 TYR S 101 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.9020 (tpp) cc_final: 0.8556 (tpt) REVERT: B 220 GLN cc_start: 0.7269 (mt0) cc_final: 0.6894 (mp10) REVERT: E 195 ARG cc_start: 0.7160 (tmt170) cc_final: 0.6836 (ttp80) REVERT: E 197 LYS cc_start: 0.7812 (tppt) cc_final: 0.7016 (tptm) REVERT: E 250 LEU cc_start: 0.8224 (tp) cc_final: 0.8000 (tp) REVERT: G 38 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5929 (pmm) REVERT: S 36 TRP cc_start: 0.7997 (m100) cc_final: 0.7566 (m100) REVERT: S 128 MET cc_start: 0.8197 (mmm) cc_final: 0.7905 (mtp) REVERT: S 180 MET cc_start: 0.7710 (ptt) cc_final: 0.7284 (ptt) REVERT: S 219 GLN cc_start: 0.9214 (pp30) cc_final: 0.8705 (pp30) outliers start: 20 outliers final: 10 residues processed: 163 average time/residue: 0.1976 time to fit residues: 44.7760 Evaluate side-chains 156 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN E 92 GLN E 196 HIS ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8904 Z= 0.210 Angle : 0.546 5.992 12090 Z= 0.285 Chirality : 0.041 0.183 1380 Planarity : 0.004 0.054 1531 Dihedral : 4.396 69.889 1205 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.81 % Allowed : 18.32 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.47 (0.26), residues: 1104 helix: 2.11 (0.25), residues: 390 sheet: -0.38 (0.31), residues: 272 loop : -0.83 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 188 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE E 177 TYR 0.021 0.001 TYR S 101 ARG 0.002 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.9008 (tpp) cc_final: 0.8540 (tpt) REVERT: B 258 ASP cc_start: 0.6451 (t0) cc_final: 0.6230 (t0) REVERT: E 195 ARG cc_start: 0.7164 (tmt170) cc_final: 0.6822 (ttp80) REVERT: E 197 LYS cc_start: 0.7735 (tppt) cc_final: 0.7040 (tptm) REVERT: E 250 LEU cc_start: 0.8227 (tp) cc_final: 0.7997 (tp) REVERT: G 38 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.5896 (pmm) REVERT: S 34 MET cc_start: 0.8402 (mmm) cc_final: 0.8199 (mmm) REVERT: S 36 TRP cc_start: 0.7909 (m100) cc_final: 0.7526 (m100) REVERT: S 180 MET cc_start: 0.7619 (ptt) cc_final: 0.7265 (ptt) REVERT: S 219 GLN cc_start: 0.9201 (pp30) cc_final: 0.8791 (pp30) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.2094 time to fit residues: 46.1689 Evaluate side-chains 159 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8904 Z= 0.186 Angle : 0.538 8.083 12090 Z= 0.278 Chirality : 0.041 0.174 1380 Planarity : 0.003 0.052 1531 Dihedral : 4.346 70.042 1205 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.13 % Allowed : 18.96 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1104 helix: 2.12 (0.25), residues: 391 sheet: -0.36 (0.31), residues: 270 loop : -0.80 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 188 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.001 PHE E 177 TYR 0.020 0.001 TYR S 101 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8981 (tpp) cc_final: 0.8513 (tpt) REVERT: B 219 ARG cc_start: 0.7974 (mmp80) cc_final: 0.7510 (mmp80) REVERT: E 195 ARG cc_start: 0.7351 (tmt170) cc_final: 0.6994 (ttp80) REVERT: E 197 LYS cc_start: 0.7680 (tppt) cc_final: 0.7201 (tptp) REVERT: E 250 LEU cc_start: 0.8296 (tp) cc_final: 0.8066 (tp) REVERT: G 38 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5848 (pmm) REVERT: S 36 TRP cc_start: 0.7910 (m100) cc_final: 0.7595 (m100) REVERT: S 180 MET cc_start: 0.7738 (ptt) cc_final: 0.7504 (ptt) REVERT: S 219 GLN cc_start: 0.9119 (pp30) cc_final: 0.8558 (pp30) outliers start: 20 outliers final: 16 residues processed: 163 average time/residue: 0.1967 time to fit residues: 44.4406 Evaluate side-chains 166 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN E 92 GLN E 190 GLN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8904 Z= 0.169 Angle : 0.540 7.837 12090 Z= 0.277 Chirality : 0.041 0.169 1380 Planarity : 0.003 0.050 1531 Dihedral : 4.258 68.582 1205 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.24 % Allowed : 19.60 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.56 (0.26), residues: 1104 helix: 2.20 (0.26), residues: 392 sheet: -0.36 (0.31), residues: 269 loop : -0.79 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS E 289 PHE 0.018 0.001 PHE E 186 TYR 0.019 0.001 TYR S 60 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7233 (tp) REVERT: A 244 MET cc_start: 0.8974 (tpp) cc_final: 0.8502 (tpt) REVERT: B 217 MET cc_start: 0.7648 (ptp) cc_final: 0.7060 (ptm) REVERT: B 219 ARG cc_start: 0.7981 (mmp80) cc_final: 0.7516 (mmp80) REVERT: B 220 GLN cc_start: 0.7461 (mt0) cc_final: 0.7128 (mt0) REVERT: E 195 ARG cc_start: 0.7438 (tmt170) cc_final: 0.7201 (ttp80) REVERT: E 197 LYS cc_start: 0.7653 (tppt) cc_final: 0.7125 (tptp) REVERT: E 250 LEU cc_start: 0.8290 (tp) cc_final: 0.8084 (tp) REVERT: G 38 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5832 (pmm) REVERT: S 36 TRP cc_start: 0.7936 (m100) cc_final: 0.7647 (m100) REVERT: S 180 MET cc_start: 0.7744 (ptt) cc_final: 0.7530 (ptt) REVERT: S 219 GLN cc_start: 0.9145 (pp30) cc_final: 0.8653 (pp30) REVERT: S 232 LYS cc_start: 0.8520 (tptp) cc_final: 0.8241 (tptt) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.2015 time to fit residues: 45.8411 Evaluate side-chains 162 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN E 92 GLN ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8904 Z= 0.187 Angle : 0.560 10.766 12090 Z= 0.286 Chirality : 0.042 0.196 1380 Planarity : 0.003 0.049 1531 Dihedral : 4.317 69.395 1205 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.56 % Allowed : 20.34 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1104 helix: 2.14 (0.26), residues: 392 sheet: -0.47 (0.31), residues: 270 loop : -0.76 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 164 HIS 0.003 0.001 HIS E 289 PHE 0.016 0.001 PHE E 186 TYR 0.017 0.001 TYR S 101 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7233 (tp) REVERT: A 244 MET cc_start: 0.8978 (tpp) cc_final: 0.8499 (tpt) REVERT: B 217 MET cc_start: 0.7711 (ptp) cc_final: 0.7070 (ptm) REVERT: B 219 ARG cc_start: 0.7986 (mmp80) cc_final: 0.7526 (mmp80) REVERT: B 220 GLN cc_start: 0.7363 (mt0) cc_final: 0.7148 (mt0) REVERT: E 189 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 195 ARG cc_start: 0.7411 (tmt170) cc_final: 0.7168 (ttp80) REVERT: E 197 LYS cc_start: 0.7647 (tppt) cc_final: 0.7100 (tptp) REVERT: E 250 LEU cc_start: 0.8262 (tp) cc_final: 0.8055 (tp) REVERT: G 38 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5839 (pmm) REVERT: S 34 MET cc_start: 0.7968 (mmm) cc_final: 0.7754 (mmp) REVERT: S 36 TRP cc_start: 0.7921 (m100) cc_final: 0.7657 (m100) REVERT: S 180 MET cc_start: 0.7786 (ptt) cc_final: 0.7563 (ptt) REVERT: S 219 GLN cc_start: 0.9197 (pp30) cc_final: 0.8713 (pp30) outliers start: 24 outliers final: 18 residues processed: 159 average time/residue: 0.2098 time to fit residues: 46.1679 Evaluate side-chains 168 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8904 Z= 0.281 Angle : 0.608 7.940 12090 Z= 0.314 Chirality : 0.043 0.201 1380 Planarity : 0.004 0.049 1531 Dihedral : 4.596 71.997 1205 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.66 % Allowed : 20.66 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1104 helix: 1.96 (0.26), residues: 393 sheet: -0.53 (0.31), residues: 270 loop : -0.81 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 188 HIS 0.005 0.001 HIS E 263 PHE 0.015 0.001 PHE B 292 TYR 0.025 0.002 TYR S 101 ARG 0.003 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7313 (tp) REVERT: A 244 MET cc_start: 0.9008 (tpp) cc_final: 0.8532 (tpt) REVERT: B 217 MET cc_start: 0.7649 (ptp) cc_final: 0.7009 (ptm) REVERT: B 219 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7485 (mmp80) REVERT: B 220 GLN cc_start: 0.7386 (mt0) cc_final: 0.7137 (mt0) REVERT: E 189 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 197 LYS cc_start: 0.7711 (tppt) cc_final: 0.7165 (tptp) REVERT: E 250 LEU cc_start: 0.8247 (tp) cc_final: 0.8000 (tp) REVERT: G 38 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5904 (pmm) REVERT: S 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7641 (m100) REVERT: S 101 TYR cc_start: 0.7661 (m-10) cc_final: 0.7451 (m-10) REVERT: S 180 MET cc_start: 0.7741 (ptt) cc_final: 0.7510 (ptt) REVERT: S 219 GLN cc_start: 0.9240 (pp30) cc_final: 0.8758 (pp30) REVERT: S 232 LYS cc_start: 0.8561 (tptp) cc_final: 0.8243 (tptt) outliers start: 25 outliers final: 18 residues processed: 162 average time/residue: 0.2119 time to fit residues: 47.3648 Evaluate side-chains 168 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN E 92 GLN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8904 Z= 0.160 Angle : 0.560 9.236 12090 Z= 0.287 Chirality : 0.042 0.185 1380 Planarity : 0.003 0.049 1531 Dihedral : 4.324 66.704 1205 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.02 % Allowed : 20.87 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.52 (0.26), residues: 1104 helix: 2.21 (0.26), residues: 384 sheet: -0.42 (0.32), residues: 263 loop : -0.76 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS E 289 PHE 0.025 0.001 PHE E 177 TYR 0.014 0.001 TYR S 178 ARG 0.003 0.000 ARG G 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7294 (tp) REVERT: A 244 MET cc_start: 0.8970 (tpp) cc_final: 0.8486 (tpt) REVERT: B 217 MET cc_start: 0.7609 (ptp) cc_final: 0.7377 (ptp) REVERT: B 219 ARG cc_start: 0.7963 (mmp80) cc_final: 0.7594 (mmt-90) REVERT: B 220 GLN cc_start: 0.7274 (mt0) cc_final: 0.7061 (mt0) REVERT: E 195 ARG cc_start: 0.7334 (tmt170) cc_final: 0.7108 (ttp80) REVERT: E 197 LYS cc_start: 0.7645 (tppt) cc_final: 0.7101 (tptp) REVERT: E 250 LEU cc_start: 0.8268 (tp) cc_final: 0.8057 (tp) REVERT: E 275 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7534 (t80) REVERT: G 38 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5791 (pmm) REVERT: S 34 MET cc_start: 0.8218 (mmm) cc_final: 0.7748 (mmp) REVERT: S 36 TRP cc_start: 0.7852 (m100) cc_final: 0.7631 (m100) REVERT: S 38 ARG cc_start: 0.6698 (ptp90) cc_final: 0.6429 (ptp90) REVERT: S 65 LYS cc_start: 0.7933 (mppt) cc_final: 0.7710 (mmtm) REVERT: S 83 MET cc_start: 0.7671 (mtm) cc_final: 0.7174 (mtm) REVERT: S 180 MET cc_start: 0.7739 (ptt) cc_final: 0.7532 (ptt) REVERT: S 232 LYS cc_start: 0.8495 (tptp) cc_final: 0.8191 (tptt) outliers start: 19 outliers final: 12 residues processed: 163 average time/residue: 0.2255 time to fit residues: 50.2810 Evaluate side-chains 163 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 347 ASN E 92 GLN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.196568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153411 restraints weight = 11188.636| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.07 r_work: 0.3652 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8904 Z= 0.231 Angle : 0.580 9.002 12090 Z= 0.299 Chirality : 0.042 0.194 1380 Planarity : 0.004 0.049 1531 Dihedral : 4.471 71.294 1205 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.92 % Allowed : 21.30 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.45 (0.26), residues: 1104 helix: 2.10 (0.26), residues: 386 sheet: -0.50 (0.31), residues: 266 loop : -0.75 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 188 HIS 0.006 0.001 HIS E 289 PHE 0.028 0.001 PHE E 177 TYR 0.020 0.002 TYR S 101 ARG 0.008 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.79 seconds wall clock time: 38 minutes 51.41 seconds (2331.41 seconds total)