Starting phenix.real_space_refine on Sat Feb 17 21:38:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg2_33183/02_2024/7xg2_33183_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 118 5.49 5 S 86 5.16 5 C 12166 2.51 5 N 3531 2.21 5 O 4002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 331": "OD1" <-> "OD2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19904 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1897 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1709 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2488 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2503 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2450 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 1 Chain: "F" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2450 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 1 Chain: "G" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2131 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 17, 'TRANS': 262} Chain breaks: 1 Chain: "H" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "I" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1317 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 13, 'rna3p_pur': 25, 'rna3p_pyr': 11} Link IDs: {'rna2p': 24, 'rna3p': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 798 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 226 SG CYS A 30 44.983 116.255 23.270 1.00 17.43 S ATOM 248 SG CYS A 33 41.619 115.421 22.359 1.00 18.59 S ATOM 526 SG CYS A 69 41.122 115.559 24.311 1.00 22.40 S Time building chain proxies: 11.53, per 1000 atoms: 0.58 Number of scatterers: 19904 At special positions: 0 Unit cell: (107.8, 151.8, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 86 16.00 P 118 15.00 O 4002 8.00 N 3531 7.00 C 12166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 30 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 32 sheets defined 29.5% alpha, 15.5% beta 32 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 8.04 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.867A pdb=" N ASP A 9 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.843A pdb=" N LEU A 81 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.657A pdb=" N ASN A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.588A pdb=" N TYR A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.502A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 160 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 201 through 222 Processing helix chain 'C' and resid 269 through 284 removed outlier: 4.879A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 154 through 160 removed outlier: 5.230A pdb=" N ARG D 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 160 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 222 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 96 through 104 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.603A pdb=" N VAL F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 124 Processing helix chain 'G' and resid 136 through 138 No H-bonds generated for 'chain 'G' and resid 136 through 138' Processing helix chain 'G' and resid 269 through 281 removed outlier: 3.821A pdb=" N LYS G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'H' and resid 141 through 163 removed outlier: 3.843A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.999A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.964A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 56 through 58 Processing sheet with id= E, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= F, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= G, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.383A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.898A pdb=" N ASN C 21 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= J, first strand: chain 'C' and resid 149 through 151 Processing sheet with id= K, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= L, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.192A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.007A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 45 through 50 Processing sheet with id= O, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= P, first strand: chain 'E' and resid 144 through 146 removed outlier: 6.069A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.690A pdb=" N ASN E 21 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= S, first strand: chain 'E' and resid 174 through 181 Processing sheet with id= T, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.166A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= V, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= W, first strand: chain 'F' and resid 45 through 53 removed outlier: 6.905A pdb=" N VAL F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 303 through 305 Processing sheet with id= Y, first strand: chain 'G' and resid 7 through 9 Processing sheet with id= Z, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.669A pdb=" N ASN G 21 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AB, first strand: chain 'G' and resid 174 through 177 Processing sheet with id= AC, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.884A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA H 65 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.918A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 180 through 184 Processing sheet with id= AF, first strand: chain 'H' and resid 211 through 213 removed outlier: 3.627A pdb=" N TRP H 212 " --> pdb=" O ILE H 225 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE H 225 " --> pdb=" O TRP H 212 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF 589 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5315 1.33 - 1.46: 5225 1.46 - 1.58: 9629 1.58 - 1.71: 236 1.71 - 1.83: 162 Bond restraints: 20567 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.604 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.430 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4' 23G I 61 " pdb=" C3' 23G I 61 " ideal model delta sigma weight residual 1.302 1.518 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.426 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" N3 23G I 61 " pdb=" C4 23G I 61 " ideal model delta sigma weight residual 1.502 1.354 0.148 2.00e-02 2.50e+03 5.50e+01 ... (remaining 20562 not shown) Histogram of bond angle deviations from ideal: 93.88 - 102.33: 176 102.33 - 110.79: 7357 110.79 - 119.24: 10358 119.24 - 127.69: 10166 127.69 - 136.15: 373 Bond angle restraints: 28430 Sorted by residual: angle pdb=" C LEU F 149 " pdb=" N TYR F 150 " pdb=" CA TYR F 150 " ideal model delta sigma weight residual 120.94 132.09 -11.15 1.90e+00 2.77e-01 3.45e+01 angle pdb=" O3' DT K 28 " pdb=" C3' DT K 28 " pdb=" C2' DT K 28 " ideal model delta sigma weight residual 111.50 103.65 7.85 1.50e+00 4.44e-01 2.74e+01 angle pdb=" CA ILE F 287 " pdb=" CB ILE F 287 " pdb=" CG1 ILE F 287 " ideal model delta sigma weight residual 110.40 118.97 -8.57 1.70e+00 3.46e-01 2.54e+01 angle pdb=" CA HIS F 291 " pdb=" CB HIS F 291 " pdb=" CG HIS F 291 " ideal model delta sigma weight residual 113.80 118.70 -4.90 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CB GLU G 157 " pdb=" CG GLU G 157 " pdb=" CD GLU G 157 " ideal model delta sigma weight residual 112.60 120.55 -7.95 1.70e+00 3.46e-01 2.19e+01 ... (remaining 28425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 11490 35.43 - 70.86: 687 70.86 - 106.29: 48 106.29 - 141.71: 0 141.71 - 177.14: 6 Dihedral angle restraints: 12231 sinusoidal: 5796 harmonic: 6435 Sorted by residual: dihedral pdb=" O4' C I 20 " pdb=" C1' C I 20 " pdb=" N1 C I 20 " pdb=" C2 C I 20 " ideal model delta sinusoidal sigma weight residual 232.00 68.37 163.63 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" C5' G I 3 " pdb=" C4' G I 3 " pdb=" C3' G I 3 " pdb=" O3' G I 3 " ideal model delta sinusoidal sigma weight residual 147.00 104.88 42.12 1 8.00e+00 1.56e-02 3.87e+01 dihedral pdb=" C5' C I 40 " pdb=" C4' C I 40 " pdb=" C3' C I 40 " pdb=" O3' C I 40 " ideal model delta sinusoidal sigma weight residual 147.00 107.70 39.30 1 8.00e+00 1.56e-02 3.39e+01 ... (remaining 12228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2912 0.108 - 0.216: 271 0.216 - 0.324: 28 0.324 - 0.432: 1 0.432 - 0.540: 3 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CB ILE F 287 " pdb=" CA ILE F 287 " pdb=" CG1 ILE F 287 " pdb=" CG2 ILE F 287 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CB ILE G 64 " pdb=" CA ILE G 64 " pdb=" CG1 ILE G 64 " pdb=" CG2 ILE G 64 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" C3' G I 3 " pdb=" C4' G I 3 " pdb=" O3' G I 3 " pdb=" C2' G I 3 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 3212 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 149 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO A 150 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 9 " -0.022 2.00e-02 2.50e+03 4.65e-02 2.17e+01 pdb=" C ASP A 9 " 0.080 2.00e-02 2.50e+03 pdb=" O ASP A 9 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN A 10 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 110 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 111 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.056 5.00e-02 4.00e+02 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 51 2.32 - 2.97: 9099 2.97 - 3.61: 31524 3.61 - 4.26: 52380 4.26 - 4.90: 83459 Nonbonded interactions: 176513 Sorted by model distance: nonbonded pdb=" N4 C I 48 " pdb=" N2 G I 60 " model vdw 1.681 3.200 nonbonded pdb=" O2' G I 59 " pdb=" OP2 G I 60 " model vdw 1.722 2.440 nonbonded pdb=" O MET G 139 " pdb=" O2' G I 29 " model vdw 1.778 2.440 nonbonded pdb=" O2' A I 16 " pdb=" OP2 C I 17 " model vdw 1.802 2.440 nonbonded pdb=" CG2 THR E 6 " pdb=" NZ LYS E 257 " model vdw 1.809 3.540 ... (remaining 176508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'D' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'E' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'F' and (resid 1 through 217 or resid 240 through 344)) } 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: 0.940 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: 0.030 Extract box with map and model: 4.600 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 62.560 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 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:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 0.270 20567 Z= 0.456 Angle : 1.050 12.120 28430 Z= 0.607 Chirality : 0.065 0.540 3215 Planarity : 0.009 0.132 3275 Dihedral : 20.595 177.143 8121 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.76 % Allowed : 18.17 % Favored : 81.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.16), residues: 2256 helix: -1.54 (0.16), residues: 715 sheet: -0.81 (0.26), residues: 398 loop : -1.47 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 258 HIS 0.020 0.002 HIS F 81 PHE 0.041 0.003 PHE G 341 TYR 0.036 0.003 TYR F 103 ARG 0.015 0.001 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 337 time to evaluate : 2.244 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6925 (tm-30) REVERT: F 45 MET cc_start: 0.6197 (tmm) cc_final: 0.5927 (tmm) REVERT: F 150 TYR cc_start: 0.6755 (m-10) cc_final: 0.6357 (m-10) REVERT: F 253 ILE cc_start: 0.8334 (pt) cc_final: 0.7989 (pp) REVERT: F 340 GLN cc_start: 0.7174 (mp10) cc_final: 0.6885 (mp10) REVERT: G 2 GLN cc_start: 0.6329 (tm-30) cc_final: 0.6114 (tm-30) REVERT: H 77 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.1998 (pp) REVERT: H 131 LYS cc_start: 0.1403 (mptt) cc_final: 0.0568 (mmmt) outliers start: 14 outliers final: 6 residues processed: 343 average time/residue: 1.3422 time to fit residues: 519.7937 Evaluate side-chains 291 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 284 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 137 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 205 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN D 209 GLN D 214 ASN E 81 HIS E 340 GLN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20567 Z= 0.224 Angle : 0.664 11.340 28430 Z= 0.340 Chirality : 0.044 0.268 3215 Planarity : 0.005 0.076 3275 Dihedral : 20.850 179.086 4045 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.84 % Allowed : 19.79 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.17), residues: 2256 helix: -0.43 (0.18), residues: 728 sheet: -0.88 (0.26), residues: 376 loop : -1.25 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 258 HIS 0.007 0.001 HIS F 81 PHE 0.022 0.001 PHE G 341 TYR 0.014 0.001 TYR B 48 ARG 0.003 0.000 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 298 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7579 (m-30) cc_final: 0.7342 (m-30) REVERT: A 157 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6584 (mp) REVERT: F 45 MET cc_start: 0.6409 (tmm) cc_final: 0.5870 (tmm) REVERT: F 253 ILE cc_start: 0.8317 (pt) cc_final: 0.7965 (pp) REVERT: F 340 GLN cc_start: 0.6949 (mp10) cc_final: 0.6628 (mp10) REVERT: G 99 TYR cc_start: 0.5815 (t80) cc_final: 0.5606 (t80) REVERT: H 154 ARG cc_start: 0.2692 (ttp-110) cc_final: 0.2297 (tmm160) outliers start: 71 outliers final: 28 residues processed: 337 average time/residue: 1.2272 time to fit residues: 470.4924 Evaluate side-chains 301 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 272 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 190 optimal weight: 0.0970 chunk 212 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 0.0770 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 88 GLN B 76 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20567 Z= 0.187 Angle : 0.609 10.150 28430 Z= 0.312 Chirality : 0.042 0.187 3215 Planarity : 0.005 0.058 3275 Dihedral : 20.686 179.133 4034 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.76 % Allowed : 20.39 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.17), residues: 2256 helix: 0.17 (0.19), residues: 726 sheet: -0.72 (0.26), residues: 378 loop : -1.09 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 258 HIS 0.011 0.001 HIS F 81 PHE 0.022 0.001 PHE G 341 TYR 0.014 0.001 TYR B 48 ARG 0.004 0.000 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 297 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7578 (m-30) cc_final: 0.7362 (m-30) REVERT: A 157 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6626 (mp) REVERT: A 199 GLU cc_start: 0.7284 (tm-30) cc_final: 0.7024 (tm-30) REVERT: D 1 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6617 (tmt) REVERT: F 253 ILE cc_start: 0.8258 (pt) cc_final: 0.7875 (pp) REVERT: F 340 GLN cc_start: 0.6843 (mp10) cc_final: 0.6573 (mp10) REVERT: G 140 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7945 (mp) REVERT: H 126 MET cc_start: 0.5470 (tpt) cc_final: 0.4982 (tpt) outliers start: 88 outliers final: 32 residues processed: 353 average time/residue: 1.2626 time to fit residues: 506.9629 Evaluate side-chains 314 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 76 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 340 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20567 Z= 0.213 Angle : 0.606 10.287 28430 Z= 0.310 Chirality : 0.042 0.241 3215 Planarity : 0.005 0.053 3275 Dihedral : 20.563 179.056 4034 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.14 % Allowed : 20.71 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.17), residues: 2256 helix: 0.46 (0.20), residues: 724 sheet: -0.72 (0.26), residues: 380 loop : -1.04 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 258 HIS 0.005 0.001 HIS A 220 PHE 0.023 0.001 PHE G 341 TYR 0.016 0.001 TYR B 48 ARG 0.010 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 294 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6881 (mm-40) REVERT: A 41 ASP cc_start: 0.7592 (m-30) cc_final: 0.7385 (m-30) REVERT: A 157 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6622 (mp) REVERT: A 220 HIS cc_start: 0.5430 (p-80) cc_final: 0.5042 (p90) REVERT: B 5 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7308 (tttp) REVERT: B 81 MET cc_start: 0.8078 (mmm) cc_final: 0.7850 (mmt) REVERT: B 99 SER cc_start: 0.7063 (p) cc_final: 0.6859 (t) REVERT: C 25 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6028 (mt) REVERT: D 1 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6651 (tmt) REVERT: E 168 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7249 (mmm) REVERT: F 253 ILE cc_start: 0.8334 (pt) cc_final: 0.7882 (pp) REVERT: G 1 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.4914 (ptp) REVERT: H 126 MET cc_start: 0.5662 (tpt) cc_final: 0.5236 (tpt) REVERT: H 154 ARG cc_start: 0.2801 (ttp-170) cc_final: 0.1824 (tmm160) outliers start: 95 outliers final: 38 residues processed: 357 average time/residue: 1.2242 time to fit residues: 496.9180 Evaluate side-chains 327 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 157 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 76 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN F 81 HIS ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20567 Z= 0.202 Angle : 0.595 12.256 28430 Z= 0.304 Chirality : 0.042 0.257 3215 Planarity : 0.004 0.050 3275 Dihedral : 20.490 178.943 4034 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.65 % Allowed : 21.42 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2256 helix: 0.58 (0.20), residues: 732 sheet: -0.71 (0.26), residues: 380 loop : -0.98 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 258 HIS 0.013 0.001 HIS F 81 PHE 0.011 0.001 PHE G 118 TYR 0.015 0.001 TYR B 48 ARG 0.007 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 296 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6870 (mm-40) REVERT: A 157 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6607 (mp) REVERT: B 5 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7327 (tttp) REVERT: B 81 MET cc_start: 0.8061 (mmm) cc_final: 0.7824 (mmt) REVERT: C 25 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6064 (mt) REVERT: C 168 MET cc_start: 0.7163 (ttm) cc_final: 0.6961 (ttt) REVERT: D 1 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6656 (tmt) REVERT: E 214 ASN cc_start: 0.5840 (m-40) cc_final: 0.5589 (t0) REVERT: F 253 ILE cc_start: 0.8275 (pt) cc_final: 0.7884 (pp) REVERT: G 1 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4827 (ptp) REVERT: H 126 MET cc_start: 0.5622 (tpt) cc_final: 0.5228 (tpt) outliers start: 86 outliers final: 45 residues processed: 355 average time/residue: 1.2872 time to fit residues: 517.0295 Evaluate side-chains 336 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.0570 chunk 204 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN D 166 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 106 ASN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20567 Z= 0.267 Angle : 0.628 11.730 28430 Z= 0.320 Chirality : 0.043 0.301 3215 Planarity : 0.005 0.049 3275 Dihedral : 20.420 178.893 4034 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.19 % Allowed : 21.90 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2256 helix: 0.55 (0.20), residues: 730 sheet: -0.71 (0.26), residues: 382 loop : -0.95 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 258 HIS 0.010 0.001 HIS F 81 PHE 0.013 0.002 PHE E 118 TYR 0.016 0.001 TYR B 48 ARG 0.008 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 289 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6875 (mm-40) REVERT: A 106 THR cc_start: 0.6104 (OUTLIER) cc_final: 0.5789 (t) REVERT: A 157 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 81 MET cc_start: 0.8073 (mmm) cc_final: 0.7865 (mmt) REVERT: C 168 MET cc_start: 0.7307 (ttm) cc_final: 0.7069 (ttt) REVERT: D 1 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6665 (tmt) REVERT: D 333 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8036 (tt) REVERT: F 340 GLN cc_start: 0.6700 (mp10) cc_final: 0.6478 (mp10) REVERT: G 1 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.4755 (ptp) REVERT: G 341 PHE cc_start: 0.8016 (t80) cc_final: 0.7782 (t80) REVERT: H 126 MET cc_start: 0.5653 (tpt) cc_final: 0.5256 (tpt) outliers start: 96 outliers final: 45 residues processed: 350 average time/residue: 1.2162 time to fit residues: 485.4240 Evaluate side-chains 329 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 166 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 126 optimal weight: 0.0670 chunk 226 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 12 ASN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS D 166 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20567 Z= 0.204 Angle : 0.601 12.717 28430 Z= 0.306 Chirality : 0.042 0.350 3215 Planarity : 0.004 0.048 3275 Dihedral : 20.355 179.350 4034 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.71 % Allowed : 23.04 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2256 helix: 0.63 (0.20), residues: 729 sheet: -0.74 (0.26), residues: 378 loop : -0.90 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 258 HIS 0.010 0.001 HIS F 81 PHE 0.014 0.001 PHE G 118 TYR 0.015 0.001 TYR B 48 ARG 0.007 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 292 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6847 (mm-40) REVERT: A 106 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5904 (t) REVERT: A 157 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6681 (mp) REVERT: C 25 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6043 (mt) REVERT: C 168 MET cc_start: 0.7248 (ttm) cc_final: 0.7009 (ttt) REVERT: D 333 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8033 (tt) REVERT: G 1 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4779 (ptp) REVERT: G 341 PHE cc_start: 0.7798 (t80) cc_final: 0.7590 (t80) REVERT: H 126 MET cc_start: 0.5249 (tpt) cc_final: 0.4841 (tpt) REVERT: H 154 ARG cc_start: 0.3459 (ptt90) cc_final: 0.1937 (tmm160) outliers start: 87 outliers final: 45 residues processed: 347 average time/residue: 1.2293 time to fit residues: 484.8381 Evaluate side-chains 330 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 279 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN B 98 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20567 Z= 0.253 Angle : 0.626 12.226 28430 Z= 0.320 Chirality : 0.043 0.300 3215 Planarity : 0.005 0.056 3275 Dihedral : 20.297 179.302 4034 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.43 % Allowed : 23.85 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.18), residues: 2256 helix: 0.61 (0.20), residues: 729 sheet: -0.75 (0.26), residues: 380 loop : -0.90 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 258 HIS 0.009 0.001 HIS F 81 PHE 0.013 0.001 PHE H 222 TYR 0.015 0.001 TYR B 48 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 279 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: A 106 THR cc_start: 0.6088 (OUTLIER) cc_final: 0.5767 (t) REVERT: A 157 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6731 (mp) REVERT: A 165 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6288 (mt-10) REVERT: D 1 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.6871 (tmt) REVERT: D 333 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (tt) REVERT: G 341 PHE cc_start: 0.7829 (t80) cc_final: 0.7603 (t80) REVERT: H 126 MET cc_start: 0.5249 (tpt) cc_final: 0.4840 (tpt) REVERT: H 154 ARG cc_start: 0.3542 (ptt90) cc_final: 0.1861 (tmm160) outliers start: 82 outliers final: 46 residues processed: 332 average time/residue: 1.2837 time to fit residues: 485.7804 Evaluate side-chains 320 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 269 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 197 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 76 GLN B 98 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20567 Z= 0.267 Angle : 0.641 13.410 28430 Z= 0.327 Chirality : 0.043 0.310 3215 Planarity : 0.004 0.052 3275 Dihedral : 20.291 179.373 4034 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.16 % Allowed : 24.23 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2256 helix: 0.59 (0.20), residues: 732 sheet: -0.75 (0.26), residues: 386 loop : -0.92 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 258 HIS 0.007 0.001 HIS F 81 PHE 0.023 0.002 PHE H 2 TYR 0.016 0.001 TYR B 48 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 268 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6863 (mm-40) REVERT: A 106 THR cc_start: 0.6136 (OUTLIER) cc_final: 0.5853 (t) REVERT: A 157 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6728 (mp) REVERT: D 1 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.6784 (tmt) REVERT: D 333 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8073 (tt) REVERT: F 182 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5295 (mpp) REVERT: G 1 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4393 (ppp) REVERT: G 157 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6351 (tp30) REVERT: G 246 PHE cc_start: 0.1771 (OUTLIER) cc_final: 0.1450 (m-80) REVERT: G 341 PHE cc_start: 0.7731 (t80) cc_final: 0.7526 (t80) REVERT: H 154 ARG cc_start: 0.3503 (ptt90) cc_final: 0.1825 (tmm160) outliers start: 77 outliers final: 50 residues processed: 316 average time/residue: 1.2235 time to fit residues: 440.6640 Evaluate side-chains 326 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 155 optimal weight: 0.0050 chunk 234 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 98 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20567 Z= 0.305 Angle : 0.665 12.664 28430 Z= 0.341 Chirality : 0.045 0.320 3215 Planarity : 0.005 0.061 3275 Dihedral : 20.277 179.263 4034 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.11 % Allowed : 24.12 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2256 helix: 0.53 (0.20), residues: 733 sheet: -0.80 (0.25), residues: 386 loop : -0.96 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 258 HIS 0.013 0.002 HIS F 81 PHE 0.013 0.002 PHE C 133 TYR 0.017 0.002 TYR B 48 ARG 0.006 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 277 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6837 (mm-40) REVERT: A 106 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6023 (t) REVERT: A 165 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6312 (mt-10) REVERT: D 333 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8067 (tt) REVERT: F 182 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5220 (mpp) REVERT: G 157 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6331 (tp30) REVERT: G 246 PHE cc_start: 0.1932 (OUTLIER) cc_final: 0.1598 (m-80) REVERT: G 341 PHE cc_start: 0.7738 (t80) cc_final: 0.7519 (t80) REVERT: H 154 ARG cc_start: 0.3497 (ptt90) cc_final: 0.1816 (tmm160) outliers start: 76 outliers final: 48 residues processed: 326 average time/residue: 1.2551 time to fit residues: 464.7600 Evaluate side-chains 320 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 246 PHE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 98 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN C 306 ASN D 214 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129152 restraints weight = 25757.627| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.22 r_work: 0.3412 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20567 Z= 0.328 Angle : 0.693 12.885 28430 Z= 0.355 Chirality : 0.045 0.313 3215 Planarity : 0.005 0.063 3275 Dihedral : 20.301 179.305 4034 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.57 % Allowed : 24.93 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.18), residues: 2256 helix: 0.44 (0.20), residues: 737 sheet: -0.83 (0.25), residues: 388 loop : -1.02 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 258 HIS 0.015 0.002 HIS F 81 PHE 0.013 0.002 PHE C 133 TYR 0.017 0.002 TYR B 48 ARG 0.006 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8032.42 seconds wall clock time: 143 minutes 12.72 seconds (8592.72 seconds total)