Starting phenix.real_space_refine on Fri Feb 16 22:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as8_15609/02_2024/8as8_15609_trim_updated.pdb" } resolution = 3.0 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= 0.000 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 10424 2.51 5 N 3060 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 821": "OD1" <-> "OD2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A ASP 895": "OD1" <-> "OD2" Residue "A ASP 921": "OD1" <-> "OD2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "B TYR 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B GLU 872": "OE1" <-> "OE2" Residue "B PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 895": "OD1" <-> "OD2" Residue "B ASP 940": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E ASP 399": "OD1" <-> "OD2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 455": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16700 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.22, per 1000 atoms: 0.55 Number of scatterers: 16700 At special positions: 0 Unit cell: (131.261, 137.069, 159.139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 3180 8.00 N 3060 7.00 C 10424 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: 7.15 Conformation dependent library (CDL) restraints added in 3.0 seconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 12 sheets defined 55.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.706A pdb=" N GLY A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 6' Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 153 through 174 removed outlier: 8.383A pdb=" N THR A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 199 through 210 removed outlier: 3.876A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 234 through 282 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 783 through 806 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 819 through 850 Proline residue: A 823 - end of helix removed outlier: 4.183A pdb=" N GLU A 834 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 837 " --> pdb=" O GLU A 834 " (cutoff:3.500A) Proline residue: A 838 - end of helix removed outlier: 4.071A pdb=" N LEU A 848 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 883 removed outlier: 3.712A pdb=" N GLU A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 919 removed outlier: 4.087A pdb=" N PHE A 919 " --> pdb=" O ASN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 948 through 954 Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 986 through 1005 Processing helix chain 'A' and resid 1029 through 1041 removed outlier: 3.678A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1060 removed outlier: 4.065A pdb=" N ASP A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'B' and resid 4 through 10 removed outlier: 5.224A pdb=" N GLY B 9 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.580A pdb=" N LEU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 No H-bonds generated for 'chain 'B' and resid 68 through 71' Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 153 through 174 removed outlier: 8.688A pdb=" N THR B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.894A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 232 through 282 removed outlier: 3.585A pdb=" N ALA B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Proline residue: B 264 - end of helix removed outlier: 3.517A pdb=" N GLN B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 4.381A pdb=" N ALA B 788 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 789 " --> pdb=" O VAL B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 834 Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 836 through 850 Processing helix chain 'B' and resid 857 through 883 Processing helix chain 'B' and resid 902 through 918 Processing helix chain 'B' and resid 925 through 943 Processing helix chain 'B' and resid 948 through 954 Processing helix chain 'B' and resid 956 through 958 No H-bonds generated for 'chain 'B' and resid 956 through 958' Processing helix chain 'B' and resid 987 through 1005 Processing helix chain 'B' and resid 1029 through 1041 removed outlier: 3.737A pdb=" N ARG B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1060 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 77 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 127 through 145 Processing helix chain 'C' and resid 158 through 169 removed outlier: 3.709A pdb=" N LEU C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 3.902A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 77 through 87 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 127 through 147 Processing helix chain 'D' and resid 158 through 169 Proline residue: D 163 - end of helix removed outlier: 3.811A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 208 through 211 Processing helix chain 'D' and resid 216 through 233 Processing helix chain 'E' and resid 3 through 18 removed outlier: 3.962A pdb=" N ARG E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 26 Processing helix chain 'E' and resid 30 through 43 removed outlier: 4.111A pdb=" N LYS E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 77 through 90 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 130 through 143 Processing helix chain 'E' and resid 147 through 169 Processing helix chain 'E' and resid 178 through 219 removed outlier: 3.808A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 231 removed outlier: 5.503A pdb=" N ARG E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.998A pdb=" N ASP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 289 Processing helix chain 'E' and resid 291 through 317 Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.891A pdb=" N LEU E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS E 341 " --> pdb=" O ASN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 399 through 405 Processing helix chain 'E' and resid 410 through 424 Processing helix chain 'E' and resid 430 through 436 Processing helix chain 'E' and resid 442 through 455 removed outlier: 3.901A pdb=" N ALA E 447 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG E 454 " --> pdb=" O GLY E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.284A pdb=" N THR A 113 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 18 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 111 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 20 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY A 109 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1075 through 1081 Processing sheet with id= C, first strand: chain 'A' and resid 892 through 895 Processing sheet with id= D, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.736A pdb=" N THR B 113 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 18 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 111 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 20 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY B 109 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1074 through 1081 removed outlier: 7.059A pdb=" N ALA B 40 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B1068 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 42 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ARG B1070 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B1020 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B1049 " --> pdb=" O LEU B1020 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 893 through 895 removed outlier: 4.014A pdb=" N ALA B 963 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 60 through 62 Processing sheet with id= H, first strand: chain 'C' and resid 155 through 157 Processing sheet with id= I, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.515A pdb=" N TYR D 101 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 155 through 157 Processing sheet with id= K, first strand: chain 'E' and resid 94 through 97 Processing sheet with id= L, first strand: chain 'E' and resid 468 through 471 884 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5684 1.34 - 1.45: 1744 1.45 - 1.57: 9494 1.57 - 1.69: 7 1.69 - 1.81: 57 Bond restraints: 16986 Sorted by residual: bond pdb=" C4 ADP B1101 " pdb=" C5 ADP B1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A1101 " pdb=" C5 ADP A1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP B1101 " pdb=" C6 ADP B1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP A1101 " pdb=" C6 ADP A1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N ASP B1021 " pdb=" CA ASP B1021 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.79e+00 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.35: 178 104.35 - 111.78: 8277 111.78 - 119.22: 5931 119.22 - 126.65: 8342 126.65 - 134.08: 254 Bond angle restraints: 22982 Sorted by residual: angle pdb=" CA PRO A 888 " pdb=" N PRO A 888 " pdb=" CD PRO A 888 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 angle pdb=" C GLU B 95 " pdb=" CA GLU B 95 " pdb=" CB GLU B 95 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.52e+01 angle pdb=" C GLN C 112 " pdb=" CA GLN C 112 " pdb=" CB GLN C 112 " ideal model delta sigma weight residual 117.23 110.98 6.25 1.36e+00 5.41e-01 2.11e+01 angle pdb=" N PRO A 888 " pdb=" CD PRO A 888 " pdb=" CG PRO A 888 " ideal model delta sigma weight residual 103.20 96.92 6.28 1.50e+00 4.44e-01 1.76e+01 angle pdb=" CA ASP B1021 " pdb=" C ASP B1021 " pdb=" O ASP B1021 " ideal model delta sigma weight residual 121.56 117.08 4.48 1.09e+00 8.42e-01 1.69e+01 ... (remaining 22977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.70: 9671 32.70 - 65.39: 601 65.39 - 98.09: 57 98.09 - 130.79: 1 130.79 - 163.48: 2 Dihedral angle restraints: 10332 sinusoidal: 4307 harmonic: 6025 Sorted by residual: dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 136.52 163.48 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1101 " pdb=" O3A ADP A1101 " pdb=" PB ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 166.40 133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" C4' ADP B1101 " pdb=" C5' ADP B1101 " pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " ideal model delta sinusoidal sigma weight residual -180.00 -64.22 -115.78 1 2.00e+01 2.50e-03 3.44e+01 ... (remaining 10329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1929 0.038 - 0.075: 470 0.075 - 0.113: 151 0.113 - 0.150: 18 0.150 - 0.188: 5 Chirality restraints: 2573 Sorted by residual: chirality pdb=" CA ILE B1049 " pdb=" N ILE B1049 " pdb=" C ILE B1049 " pdb=" CB ILE B1049 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" C3' ADP B1101 " pdb=" C2' ADP B1101 " pdb=" C4' ADP B1101 " pdb=" O3' ADP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 2570 not shown) Planarity restraints: 3017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 887 " 0.088 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 888 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 982 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLN A 982 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN A 982 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 983 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1020 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C LEU B1020 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B1020 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B1021 " 0.011 2.00e-02 2.50e+03 ... (remaining 3014 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 170 2.54 - 3.13: 14064 3.13 - 3.72: 27444 3.72 - 4.31: 36513 4.31 - 4.90: 60682 Nonbonded interactions: 138873 Sorted by model distance: nonbonded pdb=" O ASN D 126 " pdb=" OG SER D 130 " model vdw 1.950 2.440 nonbonded pdb=" OG SER A 971 " pdb=" OD1 ASN A 973 " model vdw 1.978 2.440 nonbonded pdb=" O LEU B1058 " pdb=" OG1 THR B1062 " model vdw 1.989 2.440 nonbonded pdb=" OG SER E 44 " pdb=" OD1 ASP E 46 " model vdw 2.003 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OD1 ASP B 218 " model vdw 2.017 2.440 ... (remaining 138868 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.410 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 46.850 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.004 0.131 16986 Z= 0.276 Angle : 0.618 11.617 22982 Z= 0.347 Chirality : 0.038 0.188 2573 Planarity : 0.004 0.128 3017 Dihedral : 19.614 163.482 6422 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 4.10 % Allowed : 36.76 % Favored : 59.13 % 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: 0.90 (0.19), residues: 2068 helix: 1.98 (0.16), residues: 1187 sheet: -0.91 (0.34), residues: 238 loop : -1.50 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 128 HIS 0.004 0.001 HIS E 330 PHE 0.011 0.001 PHE B 919 TYR 0.013 0.001 TYR B 891 ARG 0.010 0.000 ARG E 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 343 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8327 (m) REVERT: A 907 LEU cc_start: 0.9083 (tp) cc_final: 0.8849 (tp) REVERT: B 967 MET cc_start: 0.7760 (mtp) cc_final: 0.7559 (mtp) REVERT: E 51 GLU cc_start: 0.8604 (pm20) cc_final: 0.8293 (mp0) outliers start: 73 outliers final: 55 residues processed: 399 average time/residue: 1.3393 time to fit residues: 596.0916 Evaluate side-chains 380 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 485 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 232 GLN D 68 ASN E 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16986 Z= 0.240 Angle : 0.635 13.054 22982 Z= 0.310 Chirality : 0.040 0.171 2573 Planarity : 0.004 0.059 3017 Dihedral : 9.096 173.651 2423 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 6.24 % Allowed : 31.03 % Favored : 62.73 % 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: 0.83 (0.19), residues: 2068 helix: 1.85 (0.15), residues: 1182 sheet: -0.73 (0.33), residues: 222 loop : -1.39 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 128 HIS 0.006 0.001 HIS B1029 PHE 0.016 0.001 PHE B 886 TYR 0.021 0.001 TYR B 891 ARG 0.007 0.001 ARG E 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 363 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.9185 (ttp) cc_final: 0.8954 (ttm) REVERT: A 792 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8746 (ttp-110) REVERT: A 803 GLU cc_start: 0.8579 (tp30) cc_final: 0.8328 (tp30) REVERT: B 847 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 849 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8030 (t0) REVERT: B 876 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7868 (mm-30) REVERT: B 940 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8294 (p0) REVERT: B 1020 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 1073 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: D 47 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8896 (mmmm) REVERT: D 54 GLU cc_start: 0.8573 (tp30) cc_final: 0.8319 (tp30) REVERT: D 112 GLN cc_start: 0.5593 (OUTLIER) cc_final: 0.5230 (tp40) REVERT: E 51 GLU cc_start: 0.8628 (pm20) cc_final: 0.8340 (mp0) REVERT: E 96 GLU cc_start: 0.7613 (tp30) cc_final: 0.7348 (tp30) REVERT: E 140 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.4956 (mt-10) REVERT: E 142 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6682 (tmt170) REVERT: E 163 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8179 (mtp-110) REVERT: E 167 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: E 327 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8342 (tpt90) outliers start: 111 outliers final: 43 residues processed: 436 average time/residue: 1.3139 time to fit residues: 634.1217 Evaluate side-chains 382 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 328 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1073 GLN Chi-restraints excluded: chain B residue 1075 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 201 optimal weight: 0.0060 chunk 166 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 232 GLN E 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16986 Z= 0.228 Angle : 0.617 12.071 22982 Z= 0.301 Chirality : 0.040 0.152 2573 Planarity : 0.004 0.052 3017 Dihedral : 7.324 157.426 2351 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 5.96 % Allowed : 32.04 % Favored : 62.00 % 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: 0.87 (0.19), residues: 2068 helix: 1.88 (0.15), residues: 1176 sheet: -0.79 (0.33), residues: 222 loop : -1.34 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 128 HIS 0.003 0.001 HIS C 212 PHE 0.018 0.001 PHE A 221 TYR 0.020 0.001 TYR B 891 ARG 0.008 0.001 ARG E 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 358 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9210 (ttp) cc_final: 0.8926 (ttm) REVERT: A 792 ARG cc_start: 0.9065 (mtm110) cc_final: 0.8802 (ttp-110) REVERT: A 803 GLU cc_start: 0.8612 (tp30) cc_final: 0.8211 (tp30) REVERT: A 937 GLN cc_start: 0.8501 (tt0) cc_final: 0.8230 (mt0) REVERT: A 948 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8475 (tm) REVERT: B 171 MET cc_start: 0.8307 (ptm) cc_final: 0.8010 (ptm) REVERT: B 789 GLU cc_start: 0.8317 (tp30) cc_final: 0.8018 (tp30) REVERT: B 847 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: B 849 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 876 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 901 HIS cc_start: 0.8366 (t-90) cc_final: 0.8152 (t-90) REVERT: B 978 ARG cc_start: 0.2612 (OUTLIER) cc_final: 0.0224 (ttt180) REVERT: B 1020 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8668 (pp) REVERT: C 177 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8983 (mtpm) REVERT: D 54 GLU cc_start: 0.8589 (tp30) cc_final: 0.8275 (tp30) REVERT: D 112 GLN cc_start: 0.5749 (OUTLIER) cc_final: 0.5351 (tp40) REVERT: E 96 GLU cc_start: 0.7677 (tp30) cc_final: 0.7395 (tp30) REVERT: E 167 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: E 230 ARG cc_start: 0.7178 (ttp-170) cc_final: 0.6679 (ttp-170) REVERT: E 327 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8370 (tpt90) REVERT: E 455 GLU cc_start: 0.8758 (tp30) cc_final: 0.8442 (tp30) outliers start: 106 outliers final: 52 residues processed: 423 average time/residue: 1.2821 time to fit residues: 603.7235 Evaluate side-chains 387 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 326 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 0.0040 chunk 187 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16986 Z= 0.268 Angle : 0.629 13.525 22982 Z= 0.305 Chirality : 0.040 0.149 2573 Planarity : 0.004 0.055 3017 Dihedral : 6.997 138.950 2343 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.29 % Favored : 93.47 % Rotamer: Outliers : 6.52 % Allowed : 31.70 % Favored : 61.78 % 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: 0.78 (0.19), residues: 2068 helix: 1.81 (0.15), residues: 1181 sheet: -1.09 (0.32), residues: 244 loop : -1.27 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 128 HIS 0.003 0.001 HIS C 76 PHE 0.014 0.001 PHE B 194 TYR 0.020 0.001 TYR B 891 ARG 0.010 0.001 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 344 time to evaluate : 2.184 Fit side-chains revert: symmetry clash REVERT: A 789 GLU cc_start: 0.8676 (tp30) cc_final: 0.8368 (tp30) REVERT: A 792 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8317 (ttp80) REVERT: A 797 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 803 GLU cc_start: 0.8609 (tp30) cc_final: 0.8158 (tp30) REVERT: A 827 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 905 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: A 937 GLN cc_start: 0.8507 (tt0) cc_final: 0.8240 (mt0) REVERT: A 948 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8497 (tm) REVERT: B 37 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8948 (m-30) REVERT: B 171 MET cc_start: 0.8261 (ptm) cc_final: 0.7954 (ptm) REVERT: B 220 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9391 (mp) REVERT: B 250 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: B 847 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: B 849 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8007 (t0) REVERT: B 876 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 901 HIS cc_start: 0.8353 (t-90) cc_final: 0.7966 (t-90) REVERT: B 978 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.0214 (ttt180) REVERT: B 1020 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8685 (pp) REVERT: B 1083 GLU cc_start: 0.8623 (pp20) cc_final: 0.7936 (tm-30) REVERT: C 177 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8991 (mtpm) REVERT: D 47 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8920 (mmmm) REVERT: D 54 GLU cc_start: 0.8612 (tp30) cc_final: 0.8319 (tp30) REVERT: D 112 GLN cc_start: 0.5936 (OUTLIER) cc_final: 0.5422 (tp40) REVERT: E 1 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.3997 (pmm) REVERT: E 140 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.4742 (mt-10) REVERT: E 142 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6795 (tmt170) REVERT: E 143 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7384 (mt) REVERT: E 163 ARG cc_start: 0.8778 (mtp-110) cc_final: 0.8388 (ttm110) REVERT: E 167 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: E 230 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6679 (ttp-170) REVERT: E 327 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8375 (tpt90) REVERT: E 400 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8426 (p0) REVERT: E 455 GLU cc_start: 0.8799 (tp30) cc_final: 0.8492 (tp30) outliers start: 116 outliers final: 59 residues processed: 412 average time/residue: 1.2877 time to fit residues: 589.2636 Evaluate side-chains 395 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 316 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1075 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 169 optimal weight: 0.0270 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16986 Z= 0.206 Angle : 0.618 12.670 22982 Z= 0.299 Chirality : 0.040 0.325 2573 Planarity : 0.004 0.055 3017 Dihedral : 6.655 112.902 2343 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.14 % Favored : 93.67 % Rotamer: Outliers : 6.35 % Allowed : 32.15 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2068 helix: 1.90 (0.15), residues: 1174 sheet: -1.11 (0.32), residues: 244 loop : -1.16 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 128 HIS 0.003 0.001 HIS B 249 PHE 0.013 0.001 PHE A 242 TYR 0.020 0.001 TYR B 891 ARG 0.010 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 341 time to evaluate : 1.841 Fit side-chains revert: symmetry clash REVERT: A 789 GLU cc_start: 0.8656 (tp30) cc_final: 0.8357 (tp30) REVERT: A 792 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8318 (ttp80) REVERT: A 797 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 803 GLU cc_start: 0.8586 (tp30) cc_final: 0.8182 (tp30) REVERT: A 905 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7783 (ptp90) REVERT: A 937 GLN cc_start: 0.8501 (tt0) cc_final: 0.8238 (mt0) REVERT: A 948 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8495 (tm) REVERT: B 171 MET cc_start: 0.8271 (ptm) cc_final: 0.7931 (ptm) REVERT: B 256 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (ttp-110) REVERT: B 847 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 849 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 872 GLU cc_start: 0.8540 (pp20) cc_final: 0.8299 (pp20) REVERT: B 876 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 901 HIS cc_start: 0.8400 (t-90) cc_final: 0.7971 (t-90) REVERT: B 967 MET cc_start: 0.7421 (mtp) cc_final: 0.7120 (mtt) REVERT: B 978 ARG cc_start: 0.2571 (OUTLIER) cc_final: 0.0202 (ttt180) REVERT: B 1083 GLU cc_start: 0.8676 (pp20) cc_final: 0.7982 (tm-30) REVERT: C 164 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: D 54 GLU cc_start: 0.8596 (tp30) cc_final: 0.8336 (tp30) REVERT: D 112 GLN cc_start: 0.5976 (OUTLIER) cc_final: 0.5378 (tp40) REVERT: E 1 MET cc_start: 0.4250 (OUTLIER) cc_final: 0.3937 (pmm) REVERT: E 96 GLU cc_start: 0.7608 (tp30) cc_final: 0.7367 (tp30) REVERT: E 140 GLU cc_start: 0.5153 (OUTLIER) cc_final: 0.4749 (mt-10) REVERT: E 142 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6839 (tmt170) REVERT: E 143 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7433 (mt) REVERT: E 163 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8414 (ttm110) REVERT: E 167 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: E 230 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6656 (ttp-170) REVERT: E 327 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8355 (tpt90) REVERT: E 400 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8417 (p0) outliers start: 113 outliers final: 53 residues processed: 410 average time/residue: 1.3172 time to fit residues: 597.9829 Evaluate side-chains 395 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 325 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16986 Z= 0.369 Angle : 0.678 13.943 22982 Z= 0.328 Chirality : 0.042 0.260 2573 Planarity : 0.004 0.060 3017 Dihedral : 6.455 89.912 2337 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.33 % Favored : 93.47 % Rotamer: Outliers : 6.97 % Allowed : 31.59 % Favored : 61.44 % 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: 0.68 (0.19), residues: 2068 helix: 1.69 (0.15), residues: 1182 sheet: -1.16 (0.32), residues: 244 loop : -1.22 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 128 HIS 0.005 0.001 HIS C 76 PHE 0.029 0.002 PHE B 194 TYR 0.020 0.002 TYR A 891 ARG 0.011 0.001 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 326 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3409 (mm) REVERT: A 272 TYR cc_start: 0.8865 (t80) cc_final: 0.8664 (t80) REVERT: A 789 GLU cc_start: 0.8654 (tp30) cc_final: 0.8314 (tp30) REVERT: A 792 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8264 (ttp80) REVERT: A 797 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 803 GLU cc_start: 0.8571 (tp30) cc_final: 0.8130 (tp30) REVERT: A 905 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7794 (ptp90) REVERT: A 937 GLN cc_start: 0.8527 (tt0) cc_final: 0.8259 (mt0) REVERT: A 948 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8565 (tm) REVERT: B 37 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8959 (m-30) REVERT: B 171 MET cc_start: 0.8289 (ptm) cc_final: 0.8023 (ptm) REVERT: B 256 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8458 (ttp-110) REVERT: B 801 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7676 (mmm) REVERT: B 849 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8045 (t0) REVERT: B 872 GLU cc_start: 0.8563 (pp20) cc_final: 0.8340 (pp20) REVERT: B 876 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7958 (mm-30) REVERT: B 901 HIS cc_start: 0.8471 (t-90) cc_final: 0.7912 (t-90) REVERT: B 913 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8182 (mm110) REVERT: B 978 ARG cc_start: 0.2225 (OUTLIER) cc_final: -0.0065 (ttt180) REVERT: C 164 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: D 112 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.5428 (tp40) REVERT: E 1 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.4120 (pmm) REVERT: E 140 GLU cc_start: 0.5149 (OUTLIER) cc_final: 0.4744 (mt-10) REVERT: E 142 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6786 (tmt170) REVERT: E 143 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7424 (mt) REVERT: E 167 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: E 230 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6489 (ttp-170) REVERT: E 327 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8381 (tpt90) REVERT: E 400 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8425 (p0) REVERT: E 459 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7847 (tm-30) outliers start: 124 outliers final: 59 residues processed: 401 average time/residue: 1.3310 time to fit residues: 590.1393 Evaluate side-chains 389 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 309 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.0020 chunk 22 optimal weight: 0.0770 chunk 113 optimal weight: 0.0980 chunk 144 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 HIS B1029 HIS C 232 GLN E 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16986 Z= 0.190 Angle : 0.638 12.009 22982 Z= 0.308 Chirality : 0.040 0.315 2573 Planarity : 0.004 0.057 3017 Dihedral : 6.086 79.812 2335 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 5.28 % Allowed : 33.67 % Favored : 61.05 % 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: 0.82 (0.19), residues: 2068 helix: 1.85 (0.15), residues: 1173 sheet: -1.14 (0.32), residues: 254 loop : -1.19 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 128 HIS 0.003 0.001 HIS B1029 PHE 0.013 0.001 PHE A 242 TYR 0.020 0.001 TYR B 891 ARG 0.014 0.001 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 349 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3465 (mm) REVERT: A 792 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8764 (ttp-110) REVERT: A 797 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 803 GLU cc_start: 0.8623 (tp30) cc_final: 0.8242 (tp30) REVERT: A 905 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7779 (ptp90) REVERT: A 937 GLN cc_start: 0.8477 (tt0) cc_final: 0.8211 (mt0) REVERT: A 948 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8538 (tm) REVERT: B 220 ILE cc_start: 0.9235 (mp) cc_final: 0.8983 (mp) REVERT: B 847 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 873 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8546 (tpt-90) REVERT: B 901 HIS cc_start: 0.8473 (t-90) cc_final: 0.7894 (t-90) REVERT: B 978 ARG cc_start: 0.2252 (OUTLIER) cc_final: -0.0028 (ttt180) REVERT: B 1083 GLU cc_start: 0.8566 (pp20) cc_final: 0.7917 (tm-30) REVERT: C 164 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: D 54 GLU cc_start: 0.8693 (tp30) cc_final: 0.8414 (tp30) REVERT: D 112 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5387 (tp40) REVERT: E 1 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.4076 (pmm) REVERT: E 51 GLU cc_start: 0.8532 (pm20) cc_final: 0.8230 (mp0) REVERT: E 140 GLU cc_start: 0.5056 (OUTLIER) cc_final: 0.4747 (mt-10) REVERT: E 142 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6821 (tmt170) REVERT: E 163 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8284 (ttm110) REVERT: E 167 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: E 230 ARG cc_start: 0.7127 (ttp-170) cc_final: 0.6609 (ttp-170) REVERT: E 327 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8363 (tpt90) REVERT: E 400 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8449 (p0) REVERT: E 459 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7772 (tm-30) outliers start: 94 outliers final: 47 residues processed: 404 average time/residue: 1.2998 time to fit residues: 582.2477 Evaluate side-chains 381 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 318 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 0.0770 chunk 134 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16986 Z= 0.232 Angle : 0.659 12.093 22982 Z= 0.317 Chirality : 0.041 0.350 2573 Planarity : 0.004 0.057 3017 Dihedral : 5.959 76.320 2333 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 5.34 % Allowed : 34.35 % Favored : 60.31 % 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: 0.81 (0.19), residues: 2068 helix: 1.83 (0.15), residues: 1176 sheet: -1.11 (0.32), residues: 254 loop : -1.19 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 128 HIS 0.003 0.001 HIS C 212 PHE 0.014 0.001 PHE A 242 TYR 0.021 0.001 TYR B 891 ARG 0.010 0.000 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 334 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4031 (OUTLIER) cc_final: 0.3464 (mm) REVERT: A 789 GLU cc_start: 0.8641 (tp30) cc_final: 0.8333 (tp30) REVERT: A 792 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: A 797 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 803 GLU cc_start: 0.8647 (tp30) cc_final: 0.8265 (tp30) REVERT: A 905 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7786 (ptp90) REVERT: A 937 GLN cc_start: 0.8503 (tt0) cc_final: 0.8247 (mt0) REVERT: A 948 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8566 (tm) REVERT: B 37 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8960 (m-30) REVERT: B 220 ILE cc_start: 0.9263 (mp) cc_final: 0.8985 (mp) REVERT: B 792 ARG cc_start: 0.8874 (ttm110) cc_final: 0.8605 (tmm160) REVERT: B 847 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: B 849 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 873 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8519 (mmm-85) REVERT: B 901 HIS cc_start: 0.8476 (t-90) cc_final: 0.7870 (t-90) REVERT: B 913 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8036 (mm110) REVERT: B 978 ARG cc_start: 0.2426 (OUTLIER) cc_final: 0.0044 (ttt180) REVERT: B 1083 GLU cc_start: 0.8593 (pp20) cc_final: 0.7965 (tm-30) REVERT: D 54 GLU cc_start: 0.8704 (tp30) cc_final: 0.8393 (tp30) REVERT: D 112 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5307 (tp40) REVERT: E 1 MET cc_start: 0.4352 (OUTLIER) cc_final: 0.4089 (pmm) REVERT: E 51 GLU cc_start: 0.8503 (pm20) cc_final: 0.8218 (mp0) REVERT: E 97 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7952 (ttp-170) REVERT: E 142 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6770 (tmt170) REVERT: E 163 ARG cc_start: 0.8719 (mtp-110) cc_final: 0.8325 (ttm110) REVERT: E 167 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: E 230 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6613 (ttp-170) REVERT: E 327 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8368 (tpt90) REVERT: E 400 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8451 (p0) REVERT: E 459 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7764 (tm-30) outliers start: 95 outliers final: 55 residues processed: 390 average time/residue: 1.3304 time to fit residues: 573.8431 Evaluate side-chains 390 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 183 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16986 Z= 0.263 Angle : 0.673 12.286 22982 Z= 0.324 Chirality : 0.041 0.326 2573 Planarity : 0.004 0.055 3017 Dihedral : 5.969 75.312 2333 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.76 % Rotamer: Outliers : 5.28 % Allowed : 34.68 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2068 helix: 1.80 (0.15), residues: 1178 sheet: -1.06 (0.32), residues: 240 loop : -1.20 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 128 HIS 0.003 0.001 HIS C 212 PHE 0.030 0.001 PHE A 221 TYR 0.020 0.001 TYR A 891 ARG 0.009 0.000 ARG E 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 325 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4291 (OUTLIER) cc_final: 0.3700 (mm) REVERT: A 789 GLU cc_start: 0.8643 (tp30) cc_final: 0.8332 (tp30) REVERT: A 792 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8368 (ttp80) REVERT: A 797 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 803 GLU cc_start: 0.8652 (tp30) cc_final: 0.8338 (tp30) REVERT: A 905 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7799 (ptp90) REVERT: A 937 GLN cc_start: 0.8509 (tt0) cc_final: 0.8253 (mt0) REVERT: A 948 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8589 (tm) REVERT: B 37 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8958 (m-30) REVERT: B 227 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7758 (p0) REVERT: B 792 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8574 (tmm160) REVERT: B 847 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: B 849 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7949 (t0) REVERT: B 873 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8582 (mmm-85) REVERT: B 901 HIS cc_start: 0.8421 (t-90) cc_final: 0.7796 (t-90) REVERT: B 913 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8084 (mm110) REVERT: B 978 ARG cc_start: 0.2431 (OUTLIER) cc_final: 0.0048 (ttt180) REVERT: B 1083 GLU cc_start: 0.8614 (pp20) cc_final: 0.7974 (tm-30) REVERT: D 54 GLU cc_start: 0.8716 (tp30) cc_final: 0.8388 (tp30) REVERT: D 112 GLN cc_start: 0.5851 (OUTLIER) cc_final: 0.5196 (tp40) REVERT: E 51 GLU cc_start: 0.8505 (pm20) cc_final: 0.8221 (mp0) REVERT: E 96 GLU cc_start: 0.7671 (tp30) cc_final: 0.7433 (tp30) REVERT: E 97 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: E 142 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6859 (tmt170) REVERT: E 163 ARG cc_start: 0.8774 (mtp-110) cc_final: 0.8290 (ttm110) REVERT: E 167 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: E 230 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6613 (ttp-170) REVERT: E 327 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8371 (tpt90) REVERT: E 334 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: E 400 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8430 (p0) REVERT: E 459 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7748 (tm-30) outliers start: 94 outliers final: 56 residues processed: 379 average time/residue: 1.3569 time to fit residues: 569.9444 Evaluate side-chains 394 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 320 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 135 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 0.0770 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 0.2980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN B 794 ASN C 232 GLN E 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16986 Z= 0.203 Angle : 0.661 14.072 22982 Z= 0.318 Chirality : 0.041 0.318 2573 Planarity : 0.004 0.053 3017 Dihedral : 5.849 73.254 2333 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 4.27 % Allowed : 35.81 % Favored : 59.92 % 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: 0.87 (0.19), residues: 2068 helix: 1.87 (0.15), residues: 1174 sheet: -1.13 (0.32), residues: 252 loop : -1.12 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 128 HIS 0.003 0.001 HIS C 212 PHE 0.013 0.001 PHE A 242 TYR 0.019 0.001 TYR A 891 ARG 0.009 0.000 ARG E 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 340 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3685 (mm) REVERT: A 274 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8254 (tptm) REVERT: A 789 GLU cc_start: 0.8646 (tp30) cc_final: 0.8378 (tp30) REVERT: A 792 ARG cc_start: 0.8964 (mtm110) cc_final: 0.8377 (ttp80) REVERT: A 797 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 803 GLU cc_start: 0.8821 (tp30) cc_final: 0.8425 (tp30) REVERT: A 858 GLN cc_start: 0.8076 (mp10) cc_final: 0.7545 (mp10) REVERT: A 905 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7795 (ptp90) REVERT: A 937 GLN cc_start: 0.8480 (tt0) cc_final: 0.8214 (mt0) REVERT: A 948 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8581 (tm) REVERT: B 61 CYS cc_start: 0.8696 (t) cc_final: 0.8377 (t) REVERT: B 227 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7761 (p0) REVERT: B 784 GLU cc_start: 0.7949 (pp20) cc_final: 0.7562 (pp20) REVERT: B 792 ARG cc_start: 0.8807 (ttm110) cc_final: 0.8562 (tmm160) REVERT: B 847 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 901 HIS cc_start: 0.8395 (t-90) cc_final: 0.7782 (t-90) REVERT: B 1083 GLU cc_start: 0.8604 (pp20) cc_final: 0.7975 (tm-30) REVERT: D 54 GLU cc_start: 0.8670 (tp30) cc_final: 0.8369 (tp30) REVERT: D 112 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.4888 (tp40) REVERT: E 51 GLU cc_start: 0.8505 (pm20) cc_final: 0.8225 (mp0) REVERT: E 97 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: E 130 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8477 (p) REVERT: E 163 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8347 (ttm110) REVERT: E 167 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: E 230 ARG cc_start: 0.7064 (ttp-170) cc_final: 0.6528 (ttp-170) REVERT: E 327 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8348 (tpt90) REVERT: E 400 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8471 (p0) outliers start: 76 outliers final: 50 residues processed: 386 average time/residue: 1.3170 time to fit residues: 563.5369 Evaluate side-chains 388 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 327 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN E 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095961 restraints weight = 25398.178| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.84 r_work: 0.2957 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16986 Z= 0.326 Angle : 0.701 14.588 22982 Z= 0.339 Chirality : 0.043 0.318 2573 Planarity : 0.004 0.056 3017 Dihedral : 6.017 75.563 2333 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.09 % Favored : 93.71 % Rotamer: Outliers : 4.50 % Allowed : 35.92 % Favored : 59.58 % 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: 0.73 (0.19), residues: 2068 helix: 1.71 (0.15), residues: 1182 sheet: -1.11 (0.32), residues: 240 loop : -1.16 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 128 HIS 0.004 0.001 HIS C 76 PHE 0.023 0.002 PHE A 221 TYR 0.020 0.001 TYR A 891 ARG 0.010 0.001 ARG B 873 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8429.14 seconds wall clock time: 149 minutes 14.53 seconds (8954.53 seconds total)