Starting phenix.real_space_refine on Sat Feb 17 21:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/02_2024/7xg0_33181_updated.pdb" } resolution = 2.6 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= 0.002 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 12157 2.51 5 N 3537 2.21 5 O 3994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 285": "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" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 19893 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: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2442 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2442 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} 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': 9, 'rna2p_pyr': 12, 'rna3p_pur': 27, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 365 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 71.954 39.770 21.644 1.00 48.83 S ATOM 248 SG CYS A 33 75.711 41.962 22.539 1.00 60.11 S ATOM 495 SG CYS A 66 75.352 38.925 19.938 1.00 61.46 S ATOM 526 SG CYS A 69 75.981 39.246 24.284 1.00 67.58 S Time building chain proxies: 11.31, per 1000 atoms: 0.57 Number of scatterers: 19893 At special positions: 0 Unit cell: (110, 145.2, 178.2, 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 3994 8.00 N 3537 7.00 C 12157 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=0, symmetry=0 Time building additional restraints: 8.96 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 66 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 30 " Number of angles added : 6 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 30 sheets defined 29.7% alpha, 15.7% beta 30 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 9.17 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.933A pdb=" N ILE A 7 " --> pdb=" O PRO A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 150 through 163 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 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 138 through 147 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 89 Processing helix chain 'C' and resid 96 through 104 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 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.800A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (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 280 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 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: 5.097A pdb=" N ARG D 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 160 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 201 through 222 Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'E' and resid 67 through 81 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 201 through 216 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.621A pdb=" N LYS E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) 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 88 Processing helix chain 'F' and resid 96 through 104 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 154 through 160 removed outlier: 4.796A pdb=" N ARG F 158 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU F 160 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' 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 336 through 342 Processing helix chain 'G' and resid 67 through 87 removed outlier: 5.315A pdb=" N GLU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Proline residue: G 85 - end of helix Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 157 through 160 No H-bonds generated for 'chain 'G' and resid 157 through 160' Processing helix chain 'G' and resid 269 through 281 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 38 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 141 through 163 removed outlier: 3.937A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) 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: 3.832A 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: 5.990A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= E, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= F, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.501A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.855A pdb=" N ASN C 21 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= I, first strand: chain 'C' and resid 149 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= K, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.195A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.981A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 45 through 51 Processing sheet with id= N, first strand: chain 'D' and resid 149 through 151 Processing sheet with id= O, first strand: chain 'D' and resid 174 through 181 Processing sheet with id= P, first strand: chain 'E' and resid 144 through 146 removed outlier: 6.255A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= R, first strand: chain 'E' and resid 149 through 151 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: 6.449A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.508A 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 removed outlier: 3.790A pdb=" N ASN F 21 " --> pdb=" O LEU F 40 " (cutoff:3.500A) 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: 7.036A pdb=" N VAL F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 298 through 300 removed outlier: 3.535A pdb=" N LEU G 256 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 45 through 51 removed outlier: 3.702A pdb=" N LEU G 62 " --> pdb=" O MET G 46 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 174 through 177 Processing sheet with id= AA, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.596A pdb=" N GLY H 63 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA H 65 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.843A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 180 through 184 Processing sheet with id= AD, first strand: chain 'H' and resid 211 through 213 removed outlier: 3.502A pdb=" N ILE H 225 " --> pdb=" O TRP H 212 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 9.47 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: 5106 1.33 - 1.46: 5073 1.46 - 1.58: 9985 1.58 - 1.70: 233 1.70 - 1.83: 162 Bond restraints: 20559 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.603 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.431 0.232 2.00e-02 2.50e+03 1.35e+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 1.16e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.427 -0.177 2.00e-02 2.50e+03 7.81e+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 5.46e+01 ... (remaining 20554 not shown) Histogram of bond angle deviations from ideal: 93.72 - 102.20: 154 102.20 - 110.68: 6875 110.68 - 119.16: 10722 119.16 - 127.64: 10294 127.64 - 136.12: 376 Bond angle restraints: 28421 Sorted by residual: angle pdb=" O3' DT K 37 " pdb=" C3' DT K 37 " pdb=" C2' DT K 37 " ideal model delta sigma weight residual 111.50 100.67 10.83 1.50e+00 4.44e-01 5.21e+01 angle pdb=" CA GLU G 328 " pdb=" CB GLU G 328 " pdb=" CG GLU G 328 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" O3' DT K 28 " pdb=" C3' DT K 28 " pdb=" C2' DT K 28 " ideal model delta sigma weight residual 111.50 103.87 7.63 1.50e+00 4.44e-01 2.59e+01 angle pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " ideal model delta sigma weight residual 112.70 126.03 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C GLU G 89 " pdb=" N LYS G 90 " pdb=" CA LYS G 90 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 28416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 11428 35.66 - 71.32: 739 71.32 - 106.98: 49 106.98 - 142.64: 0 142.64 - 178.30: 5 Dihedral angle restraints: 12221 sinusoidal: 5792 harmonic: 6429 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 -128.00 44.66 -172.66 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 17 " pdb=" C1' C I 17 " pdb=" N1 C I 17 " pdb=" C2 C I 17 " ideal model delta sinusoidal sigma weight residual -160.00 -82.52 -77.48 1 1.50e+01 4.44e-03 3.34e+01 dihedral pdb=" O4' C I 46 " pdb=" C2' C I 46 " pdb=" C1' C I 46 " pdb=" C3' C I 46 " ideal model delta sinusoidal sigma weight residual 25.00 -11.25 36.25 1 8.00e+00 1.56e-02 2.90e+01 ... (remaining 12218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2511 0.065 - 0.131: 559 0.131 - 0.196: 117 0.196 - 0.262: 22 0.262 - 0.327: 4 Chirality restraints: 3213 Sorted by residual: chirality pdb=" C3' DT K 37 " pdb=" C4' DT K 37 " pdb=" O3' DT K 37 " pdb=" C2' DT K 37 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' G I 13 " pdb=" C3' G I 13 " pdb=" O2' G I 13 " pdb=" C1' G I 13 " both_signs ideal model delta sigma weight residual False -2.52 -2.24 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB VAL G 310 " pdb=" CA VAL G 310 " pdb=" CG1 VAL G 310 " pdb=" CG2 VAL G 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3210 not shown) Planarity restraints: 3271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 289 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C GLY F 289 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY F 289 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY F 290 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 317 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C THR G 317 " 0.049 2.00e-02 2.50e+03 pdb=" O THR G 317 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY G 318 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 28 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C THR F 28 " -0.048 2.00e-02 2.50e+03 pdb=" O THR F 28 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 29 " 0.016 2.00e-02 2.50e+03 ... (remaining 3268 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 93 2.43 - 3.05: 11155 3.05 - 3.67: 33461 3.67 - 4.28: 50222 4.28 - 4.90: 80040 Nonbonded interactions: 174971 Sorted by model distance: nonbonded pdb=" N4 C I 47 " pdb=" O6 G I 60 " model vdw 1.817 2.520 nonbonded pdb=" OD1 ASP A 6 " pdb=" NH2 ARG A 35 " model vdw 1.866 2.520 nonbonded pdb=" O VAL A 8 " pdb=" O LEU A 12 " model vdw 1.869 3.040 nonbonded pdb=" N3 C I 47 " pdb=" N1 G I 60 " model vdw 1.878 2.600 nonbonded pdb=" CE1 PHE H 60 " pdb=" OP2 G I 37 " model vdw 1.939 3.340 ... (remaining 174966 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 344) selection = (chain 'F' and resid 1 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: 1.840 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: 0.020 Extract box with map and model: 10.230 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 65.260 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 0.269 20559 Z= 0.412 Angle : 0.976 13.332 28421 Z= 0.565 Chirality : 0.059 0.327 3213 Planarity : 0.008 0.079 3271 Dihedral : 20.705 178.295 8115 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.76 % Allowed : 21.98 % Favored : 75.26 % 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: -2.06 (0.15), residues: 2254 helix: -1.50 (0.16), residues: 745 sheet: -0.81 (0.26), residues: 327 loop : -1.38 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 258 HIS 0.009 0.002 HIS B 49 PHE 0.028 0.002 PHE G 118 TYR 0.043 0.003 TYR B 101 ARG 0.020 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 SER cc_start: 0.8772 (m) cc_final: 0.8477 (p) REVERT: C 265 ASP cc_start: 0.7589 (t70) cc_final: 0.7285 (t0) REVERT: D 169 MET cc_start: 0.8066 (tpt) cc_final: 0.7842 (tpt) REVERT: E 182 MET cc_start: 0.8134 (mmm) cc_final: 0.7757 (mpt) REVERT: G 81 HIS cc_start: 0.6790 (m170) cc_final: 0.6551 (m90) REVERT: G 120 GLU cc_start: 0.7338 (pm20) cc_final: 0.6964 (mp0) outliers start: 51 outliers final: 37 residues processed: 371 average time/residue: 1.4355 time to fit residues: 595.5408 Evaluate side-chains 327 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 290 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 99 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 127 GLN B 150 GLN C 2 GLN C 92 ASN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS F 343 GLN G 30 ASN G 280 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20559 Z= 0.301 Angle : 0.642 7.527 28421 Z= 0.332 Chirality : 0.044 0.251 3213 Planarity : 0.005 0.047 3271 Dihedral : 20.752 176.994 4082 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.87 % Allowed : 19.22 % Favored : 75.91 % 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: -1.07 (0.17), residues: 2254 helix: -0.15 (0.18), residues: 748 sheet: -0.74 (0.24), residues: 377 loop : -1.01 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 258 HIS 0.007 0.001 HIS D 153 PHE 0.017 0.002 PHE E 118 TYR 0.015 0.002 TYR A 79 ARG 0.005 0.001 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 302 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6780 (m) REVERT: A 151 GLU cc_start: 0.7849 (tp30) cc_final: 0.7607 (tp30) REVERT: A 230 GLU cc_start: 0.7249 (pp20) cc_final: 0.6764 (pp20) REVERT: B 41 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7898 (t0) REVERT: B 127 GLN cc_start: 0.9083 (tp40) cc_final: 0.8657 (mm-40) REVERT: C 191 SER cc_start: 0.8842 (m) cc_final: 0.8495 (p) REVERT: D 214 ASN cc_start: 0.8178 (m-40) cc_final: 0.7873 (m-40) REVERT: D 320 GLU cc_start: 0.7706 (mp0) cc_final: 0.7506 (mp0) REVERT: E 182 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: F 169 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7636 (mmm) REVERT: F 180 ARG cc_start: 0.7619 (ppp80) cc_final: 0.7395 (ptm-80) REVERT: G 78 MET cc_start: 0.7478 (ptp) cc_final: 0.7211 (ptp) REVERT: G 120 GLU cc_start: 0.7465 (pm20) cc_final: 0.7018 (mp0) outliers start: 90 outliers final: 36 residues processed: 357 average time/residue: 1.4894 time to fit residues: 592.5809 Evaluate side-chains 318 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 278 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 224 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN C 284 ASN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN F 343 GLN G 30 ASN G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20559 Z= 0.299 Angle : 0.614 8.541 28421 Z= 0.319 Chirality : 0.043 0.195 3213 Planarity : 0.004 0.046 3271 Dihedral : 20.552 178.923 4051 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.09 % Allowed : 19.00 % Favored : 75.91 % 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: -0.71 (0.17), residues: 2254 helix: 0.35 (0.19), residues: 759 sheet: -0.73 (0.25), residues: 363 loop : -0.89 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.009 0.001 HIS B 49 PHE 0.018 0.002 PHE E 118 TYR 0.019 0.001 TYR A 79 ARG 0.005 0.001 ARG G 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 283 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7887 (tp30) cc_final: 0.7634 (tp30) REVERT: A 222 LYS cc_start: 0.7898 (pttm) cc_final: 0.7532 (ptpp) REVERT: B 41 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7820 (t0) REVERT: C 191 SER cc_start: 0.8833 (m) cc_final: 0.8588 (p) REVERT: D 214 ASN cc_start: 0.8370 (m-40) cc_final: 0.8069 (m-40) REVERT: E 182 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7573 (mmm) REVERT: E 295 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7987 (m-10) REVERT: F 145 MET cc_start: 0.9274 (mtm) cc_final: 0.9038 (mtp) REVERT: F 157 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: F 180 ARG cc_start: 0.7470 (ppp80) cc_final: 0.7257 (ptm-80) REVERT: G 10 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5521 (pp) REVERT: G 70 MET cc_start: 0.8381 (mmm) cc_final: 0.8057 (mmt) REVERT: G 120 GLU cc_start: 0.7407 (pm20) cc_final: 0.6865 (mp0) REVERT: H 83 ILE cc_start: 0.4700 (OUTLIER) cc_final: 0.4432 (mp) outliers start: 94 outliers final: 43 residues processed: 341 average time/residue: 1.4607 time to fit residues: 557.5461 Evaluate side-chains 326 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 277 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 224 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.5980 chunk 160 optimal weight: 0.0270 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN C 340 GLN D 2 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN F 30 ASN F 343 GLN G 63 GLN ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20559 Z= 0.297 Angle : 0.615 10.459 28421 Z= 0.316 Chirality : 0.043 0.168 3213 Planarity : 0.004 0.045 3271 Dihedral : 20.486 179.239 4047 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.25 % Allowed : 19.27 % Favored : 75.47 % 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: -0.54 (0.17), residues: 2254 helix: 0.64 (0.19), residues: 758 sheet: -0.85 (0.24), residues: 368 loop : -0.82 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.010 0.001 HIS B 49 PHE 0.017 0.002 PHE E 118 TYR 0.016 0.002 TYR A 79 ARG 0.004 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 295 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7898 (tp30) cc_final: 0.7651 (tp30) REVERT: A 222 LYS cc_start: 0.7841 (pttm) cc_final: 0.7554 (ptpp) REVERT: B 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7739 (t0) REVERT: C 92 ASN cc_start: 0.8629 (m110) cc_final: 0.8410 (m110) REVERT: D 214 ASN cc_start: 0.8399 (m-40) cc_final: 0.8102 (m-40) REVERT: D 343 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8196 (tp-100) REVERT: E 182 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: E 281 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8233 (ptpp) REVERT: E 295 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7570 (m-10) REVERT: F 81 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6640 (p-80) REVERT: G 62 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7620 (tt) REVERT: G 70 MET cc_start: 0.8375 (mmm) cc_final: 0.8011 (mmt) REVERT: G 120 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: G 251 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7290 (m) REVERT: H 39 MET cc_start: 0.4060 (mpt) cc_final: 0.3823 (mpt) REVERT: H 83 ILE cc_start: 0.4640 (OUTLIER) cc_final: 0.4387 (mp) outliers start: 97 outliers final: 47 residues processed: 360 average time/residue: 1.3677 time to fit residues: 552.5540 Evaluate side-chains 339 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 282 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.9990 chunk 128 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 193 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 115 optimal weight: 0.1980 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 340 GLN D 2 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN F 30 ASN G 30 ASN G 280 ASN H 134 HIS ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20559 Z= 0.192 Angle : 0.566 7.645 28421 Z= 0.293 Chirality : 0.041 0.160 3213 Planarity : 0.004 0.046 3271 Dihedral : 20.378 179.071 4046 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.76 % Allowed : 19.87 % Favored : 75.37 % 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: -0.36 (0.17), residues: 2254 helix: 0.87 (0.19), residues: 758 sheet: -0.84 (0.24), residues: 354 loop : -0.74 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.008 0.001 HIS B 49 PHE 0.011 0.001 PHE E 118 TYR 0.016 0.001 TYR A 79 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 285 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: A 151 GLU cc_start: 0.7909 (tp30) cc_final: 0.7699 (tp30) REVERT: A 230 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: B 41 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7689 (t0) REVERT: C 92 ASN cc_start: 0.8491 (m110) cc_final: 0.8281 (m110) REVERT: D 214 ASN cc_start: 0.8368 (m-40) cc_final: 0.8077 (m-40) REVERT: E 182 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7513 (mmm) REVERT: E 281 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8132 (ptpp) REVERT: E 295 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: F 81 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6494 (p-80) REVERT: F 157 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: G 120 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: G 256 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7755 (mp) REVERT: H 83 ILE cc_start: 0.4628 (OUTLIER) cc_final: 0.4373 (mp) outliers start: 88 outliers final: 41 residues processed: 341 average time/residue: 1.4156 time to fit residues: 540.9407 Evaluate side-chains 326 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 274 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 224 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 227 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 75 optimal weight: 0.1980 chunk 119 optimal weight: 0.0870 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN D 247 ASN G 30 ASN G 280 ASN G 340 GLN ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20559 Z= 0.179 Angle : 0.562 10.484 28421 Z= 0.289 Chirality : 0.041 0.167 3213 Planarity : 0.004 0.046 3271 Dihedral : 20.303 179.333 4044 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.39 % Allowed : 20.68 % Favored : 74.93 % 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: -0.24 (0.18), residues: 2254 helix: 0.99 (0.19), residues: 762 sheet: -0.83 (0.24), residues: 354 loop : -0.68 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.007 0.001 HIS B 49 PHE 0.010 0.001 PHE E 118 TYR 0.016 0.001 TYR A 79 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 288 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: A 151 GLU cc_start: 0.7908 (tp30) cc_final: 0.7695 (tp30) REVERT: A 179 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8310 (mptt) REVERT: A 230 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: B 41 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7712 (t0) REVERT: B 138 GLN cc_start: 0.8571 (tt0) cc_final: 0.8310 (tt0) REVERT: C 92 ASN cc_start: 0.8393 (m110) cc_final: 0.8187 (m110) REVERT: D 214 ASN cc_start: 0.8370 (m-40) cc_final: 0.8077 (m-40) REVERT: E 281 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8110 (ptpp) REVERT: E 295 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7713 (m-10) REVERT: F 81 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6432 (p-80) REVERT: F 157 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: F 281 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7784 (ptpt) REVERT: F 340 GLN cc_start: 0.8341 (pt0) cc_final: 0.8074 (pt0) REVERT: G 45 MET cc_start: 0.6528 (ppp) cc_final: 0.6285 (ptp) REVERT: G 70 MET cc_start: 0.8340 (mmm) cc_final: 0.8092 (mmm) REVERT: G 120 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: G 256 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7569 (mp) REVERT: G 274 LEU cc_start: 0.8410 (tt) cc_final: 0.8166 (tt) REVERT: H 83 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4369 (mp) outliers start: 81 outliers final: 41 residues processed: 341 average time/residue: 1.4478 time to fit residues: 551.1908 Evaluate side-chains 327 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 224 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 138 optimal weight: 0.0070 chunk 104 optimal weight: 0.9980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 92 ASN C 187 ASN C 284 ASN C 340 GLN D 247 ASN F 175 GLN G 30 ASN G 280 ASN H 224 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20559 Z= 0.264 Angle : 0.594 8.946 28421 Z= 0.306 Chirality : 0.042 0.167 3213 Planarity : 0.004 0.045 3271 Dihedral : 20.319 178.485 4043 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.76 % Allowed : 20.36 % Favored : 74.88 % 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: -0.24 (0.18), residues: 2254 helix: 0.99 (0.19), residues: 758 sheet: -0.88 (0.24), residues: 372 loop : -0.64 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.009 0.001 HIS B 49 PHE 0.015 0.001 PHE E 118 TYR 0.020 0.001 TYR A 79 ARG 0.004 0.000 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 281 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: A 179 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8304 (mptt) REVERT: A 230 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: B 3 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7908 (t0) REVERT: B 4 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7769 (t0) REVERT: B 138 GLN cc_start: 0.8630 (tt0) cc_final: 0.8366 (tt0) REVERT: B 185 ASP cc_start: 0.8692 (p0) cc_final: 0.8491 (p0) REVERT: C 92 ASN cc_start: 0.8475 (m-40) cc_final: 0.8235 (m110) REVERT: D 214 ASN cc_start: 0.8464 (m-40) cc_final: 0.8126 (m-40) REVERT: D 268 THR cc_start: 0.8934 (m) cc_final: 0.8692 (p) REVERT: E 182 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: E 192 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: E 281 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8179 (ptpp) REVERT: E 295 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7678 (m-10) REVERT: F 81 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6633 (p-80) REVERT: F 157 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: F 281 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7920 (ptpt) REVERT: G 70 MET cc_start: 0.8390 (mmm) cc_final: 0.8064 (mmt) REVERT: G 103 TYR cc_start: 0.7606 (m-80) cc_final: 0.6661 (t80) REVERT: G 120 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: G 168 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.2351 (pmm) REVERT: G 266 ARG cc_start: 0.6877 (ttp-110) cc_final: 0.6461 (ttt90) REVERT: H 83 ILE cc_start: 0.4611 (OUTLIER) cc_final: 0.4374 (mp) outliers start: 88 outliers final: 48 residues processed: 339 average time/residue: 1.4438 time to fit residues: 546.6719 Evaluate side-chains 334 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 271 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 168 MET Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 284 ASN C 340 GLN D 247 ASN E 110 ASN G 280 ASN H 224 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20559 Z= 0.263 Angle : 0.602 9.209 28421 Z= 0.309 Chirality : 0.042 0.163 3213 Planarity : 0.004 0.045 3271 Dihedral : 20.306 179.101 4043 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.49 % Allowed : 20.79 % Favored : 74.72 % 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: -0.23 (0.18), residues: 2254 helix: 1.02 (0.19), residues: 758 sheet: -0.87 (0.24), residues: 372 loop : -0.65 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 258 HIS 0.009 0.001 HIS B 49 PHE 0.015 0.001 PHE E 118 TYR 0.020 0.001 TYR A 79 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 276 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: A 179 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8291 (mptt) REVERT: B 41 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 138 GLN cc_start: 0.8606 (tt0) cc_final: 0.8348 (tt0) REVERT: D 214 ASN cc_start: 0.8461 (m-40) cc_final: 0.8121 (m-40) REVERT: D 268 THR cc_start: 0.8890 (m) cc_final: 0.8690 (p) REVERT: D 343 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8195 (tp-100) REVERT: E 182 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: E 192 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: E 281 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8179 (ptpp) REVERT: E 295 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: F 81 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6650 (p-80) REVERT: F 157 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: F 281 LYS cc_start: 0.8249 (ptpt) cc_final: 0.7937 (ptpt) REVERT: F 294 ASP cc_start: 0.7773 (t70) cc_final: 0.7479 (t0) REVERT: G 45 MET cc_start: 0.6665 (ppp) cc_final: 0.6360 (ptp) REVERT: G 70 MET cc_start: 0.8369 (mmm) cc_final: 0.8036 (mmt) REVERT: G 103 TYR cc_start: 0.7565 (m-80) cc_final: 0.6699 (t80) REVERT: G 120 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: G 266 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6469 (ttt90) REVERT: G 337 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: H 83 ILE cc_start: 0.4852 (OUTLIER) cc_final: 0.4598 (mp) outliers start: 83 outliers final: 46 residues processed: 334 average time/residue: 1.4731 time to fit residues: 554.3683 Evaluate side-chains 331 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 272 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN C 340 GLN D 247 ASN F 30 ASN F 175 GLN F 343 GLN G 63 GLN G 280 ASN H 224 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20559 Z= 0.293 Angle : 0.612 8.490 28421 Z= 0.315 Chirality : 0.043 0.167 3213 Planarity : 0.004 0.045 3271 Dihedral : 20.301 178.829 4043 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.22 % Allowed : 20.95 % Favored : 74.82 % 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: -0.27 (0.17), residues: 2254 helix: 0.98 (0.19), residues: 759 sheet: -0.88 (0.24), residues: 372 loop : -0.67 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.010 0.001 HIS B 49 PHE 0.017 0.002 PHE E 118 TYR 0.021 0.002 TYR A 79 ARG 0.003 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 265 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: A 151 GLU cc_start: 0.7994 (tp30) cc_final: 0.7793 (tp30) REVERT: A 179 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8315 (mptt) REVERT: B 3 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7868 (t0) REVERT: B 4 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 41 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7727 (t0) REVERT: B 138 GLN cc_start: 0.8652 (tt0) cc_final: 0.8391 (tt0) REVERT: D 139 MET cc_start: 0.8246 (mtm) cc_final: 0.7935 (mtm) REVERT: D 214 ASN cc_start: 0.8446 (m-40) cc_final: 0.8091 (m-40) REVERT: D 343 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8205 (tp-100) REVERT: E 182 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: E 281 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8234 (ptpp) REVERT: E 295 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: F 81 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6759 (p-80) REVERT: F 157 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: F 281 LYS cc_start: 0.8353 (ptpt) cc_final: 0.7931 (ptpt) REVERT: F 294 ASP cc_start: 0.7778 (t70) cc_final: 0.7473 (t0) REVERT: G 45 MET cc_start: 0.6625 (ppp) cc_final: 0.6315 (ptp) REVERT: G 70 MET cc_start: 0.8375 (mmm) cc_final: 0.8040 (mmt) REVERT: G 103 TYR cc_start: 0.7558 (m-80) cc_final: 0.6728 (t80) REVERT: G 120 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: H 83 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4890 (mp) outliers start: 78 outliers final: 46 residues processed: 319 average time/residue: 1.4626 time to fit residues: 521.4273 Evaluate side-chains 331 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 272 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 0.9980 chunk 223 optimal weight: 0.2980 chunk 136 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN C 284 ASN C 340 GLN C 343 GLN D 2 GLN D 247 ASN F 30 ASN G 280 ASN H 224 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20559 Z= 0.277 Angle : 0.619 9.389 28421 Z= 0.318 Chirality : 0.042 0.168 3213 Planarity : 0.004 0.046 3271 Dihedral : 20.294 179.109 4043 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.95 % Allowed : 21.33 % Favored : 74.72 % 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: -0.27 (0.17), residues: 2254 helix: 0.99 (0.19), residues: 759 sheet: -0.87 (0.24), residues: 379 loop : -0.69 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.009 0.001 HIS B 49 PHE 0.015 0.001 PHE E 118 TYR 0.023 0.001 TYR A 79 ARG 0.003 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 261 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6197 (ptp) cc_final: 0.5933 (ptt) REVERT: A 24 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: A 179 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8314 (mptt) REVERT: B 3 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 4 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 41 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7773 (t0) REVERT: D 214 ASN cc_start: 0.8443 (m-40) cc_final: 0.8089 (m-40) REVERT: D 343 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8204 (tp-100) REVERT: E 182 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7472 (mmm) REVERT: E 281 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8230 (ptpp) REVERT: E 295 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: F 45 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8249 (tmm) REVERT: F 81 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6747 (p-80) REVERT: F 157 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: F 281 LYS cc_start: 0.8321 (ptpt) cc_final: 0.7895 (ptpt) REVERT: F 294 ASP cc_start: 0.7771 (t70) cc_final: 0.7470 (t0) REVERT: G 45 MET cc_start: 0.6583 (ppp) cc_final: 0.6298 (ptp) REVERT: G 70 MET cc_start: 0.8372 (mmm) cc_final: 0.8038 (mmt) REVERT: G 103 TYR cc_start: 0.7553 (m-80) cc_final: 0.6722 (t80) REVERT: G 120 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: G 266 ARG cc_start: 0.6945 (ttp-110) cc_final: 0.6489 (ttt90) REVERT: H 83 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4891 (mp) outliers start: 73 outliers final: 44 residues processed: 312 average time/residue: 1.5045 time to fit residues: 522.6380 Evaluate side-chains 327 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 269 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 295 TYR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 171 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 186 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 191 optimal weight: 0.0170 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN C 284 ASN C 340 GLN D 2 GLN D 247 ASN F 30 ASN F 175 GLN F 306 ASN G 280 ASN H 224 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116651 restraints weight = 23749.426| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.92 r_work: 0.3066 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20559 Z= 0.207 Angle : 0.592 8.628 28421 Z= 0.304 Chirality : 0.041 0.154 3213 Planarity : 0.004 0.046 3271 Dihedral : 20.253 179.850 4043 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.36 % Allowed : 21.93 % Favored : 74.72 % 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: -0.18 (0.18), residues: 2254 helix: 1.07 (0.19), residues: 763 sheet: -0.80 (0.25), residues: 368 loop : -0.66 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.008 0.001 HIS B 49 PHE 0.011 0.001 PHE E 118 TYR 0.024 0.001 TYR A 79 ARG 0.004 0.000 ARG G 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9033.82 seconds wall clock time: 161 minutes 3.60 seconds (9663.60 seconds total)