Starting phenix.real_space_refine on Sat Mar 16 19:02:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/03_2024/7tve_26140_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 59 5.16 5 C 9572 2.51 5 N 2692 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 945": "OE1" <-> "OE2" Residue "D GLU 1002": "OE1" <-> "OE2" Residue "D GLU 1023": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E GLU 874": "OE1" <-> "OE2" Residue "E GLU 876": "OE1" <-> "OE2" Residue "E GLU 884": "OE1" <-> "OE2" Residue "E GLU 963": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 256": "NH1" <-> "NH2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2489 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3512 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3661 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2150 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 1 Chain: "G" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2506 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.57, per 1000 atoms: 0.55 Number of scatterers: 15456 At special positions: 0 Unit cell: (98.348, 148.591, 169.971, 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 59 16.00 P 57 15.00 O 3076 8.00 N 2692 7.00 C 9572 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: 6.21 Conformation dependent library (CDL) restraints added in 2.6 seconds 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 11 sheets defined 40.9% alpha, 6.9% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'C' and resid 14 through 27 removed outlier: 4.182A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 47 removed outlier: 3.949A pdb=" N LEU C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 78 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 152 through 170 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 213 through 218 removed outlier: 4.011A pdb=" N GLN C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.659A pdb=" N GLN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 4.341A pdb=" N THR D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 246 removed outlier: 4.043A pdb=" N TYR D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 294 removed outlier: 4.268A pdb=" N THR D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'D' and resid 904 through 915 Processing helix chain 'D' and resid 922 through 985 removed outlier: 4.068A pdb=" N LYS D 941 " --> pdb=" O LYS D 937 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D 963 " --> pdb=" O ALA D 959 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1025 through 1034 removed outlier: 3.914A pdb=" N ALA D1030 " --> pdb=" O PHE D1026 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D1034 " --> pdb=" O ALA D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1071 removed outlier: 3.657A pdb=" N LYS D1059 " --> pdb=" O GLN D1055 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D1060 " --> pdb=" O VAL D1056 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS D1067 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D1070 " --> pdb=" O VAL D1066 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D1071 " --> pdb=" O LYS D1067 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 99 through 102 removed outlier: 4.220A pdb=" N PHE E 102 " --> pdb=" O VAL E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 159 through 168 Processing helix chain 'E' and resid 182 through 187 removed outlier: 4.170A pdb=" N VAL E 185 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU E 186 " --> pdb=" O GLU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 207 through 261 removed outlier: 3.580A pdb=" N SER E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 877 Processing helix chain 'E' and resid 904 through 944 removed outlier: 3.978A pdb=" N VAL E 924 " --> pdb=" O GLU E 920 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 925 " --> pdb=" O ASP E 921 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 926 " --> pdb=" O HIS E 922 " (cutoff:3.500A) Proline residue: E 927 - end of helix removed outlier: 3.832A pdb=" N VAL E 933 " --> pdb=" O LEU E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 1001 removed outlier: 3.639A pdb=" N MET E 999 " --> pdb=" O THR E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1023 through 1036 removed outlier: 3.715A pdb=" N ILE E1027 " --> pdb=" O ARG E1023 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL E1028 " --> pdb=" O ASN E1024 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET E1032 " --> pdb=" O VAL E1028 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN E1035 " --> pdb=" O ALA E1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 Processing helix chain 'F' and resid 29 through 35 removed outlier: 4.154A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 69 through 82 removed outlier: 4.371A pdb=" N MET F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 150 removed outlier: 6.702A pdb=" N PHE F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR F 146 " --> pdb=" O GLN F 142 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU F 149 " --> pdb=" O HIS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 208 Processing helix chain 'F' and resid 228 through 236 Processing helix chain 'F' and resid 261 through 264 No H-bonds generated for 'chain 'F' and resid 261 through 264' Processing helix chain 'F' and resid 268 through 278 removed outlier: 4.501A pdb=" N LYS F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.054A pdb=" N LYS F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER F 288 " --> pdb=" O GLN F 285 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS F 290 " --> pdb=" O LYS F 287 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS F 295 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 70 removed outlier: 4.424A pdb=" N HIS G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 89 removed outlier: 3.797A pdb=" N ASP G 79 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN G 80 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN G 82 " --> pdb=" O ASP G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 120 removed outlier: 3.812A pdb=" N ASN G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 150 removed outlier: 4.549A pdb=" N ASN G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER G 138 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU G 146 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 240 through 245 removed outlier: 3.580A pdb=" N LEU G 244 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 245 " --> pdb=" O MET G 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 245' Processing helix chain 'G' and resid 290 through 299 removed outlier: 3.910A pdb=" N LYS G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.740A pdb=" N ASN G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 372 Processing helix chain 'G' and resid 385 through 387 No H-bonds generated for 'chain 'G' and resid 385 through 387' Processing sheet with id= A, first strand: chain 'C' and resid 80 through 86 removed outlier: 3.533A pdb=" N VAL C 134 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 85 " --> pdb=" O PHE C 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.928A pdb=" N TYR C 334 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 333 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 283 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 335 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C 281 " --> pdb=" O VAL C 335 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 95 through 99 removed outlier: 3.555A pdb=" N PHE D 96 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 98 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 85 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 84 " --> pdb=" O HIS D 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 6.251A pdb=" N PHE D 106 " --> pdb=" O HIS D1099 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 990 through 993 removed outlier: 3.517A pdb=" N TYR D1004 " --> pdb=" O ASN D 991 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 993 " --> pdb=" O GLU D1002 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU D1002 " --> pdb=" O SER D 993 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 55 through 57 removed outlier: 3.533A pdb=" N ILE E 112 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 139 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 114 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 1061 through 1063 removed outlier: 6.538A pdb=" N LEU E 64 " --> pdb=" O ARG E1062 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR E1044 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 67 " --> pdb=" O TYR E1044 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU E1046 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E1047 " --> pdb=" O VAL E1013 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 951 through 956 Processing sheet with id= I, first strand: chain 'F' and resid 45 through 47 Processing sheet with id= J, first strand: chain 'F' and resid 240 through 242 Processing sheet with id= K, first strand: chain 'G' and resid 337 through 339 510 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 6.70 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: 4958 1.34 - 1.46: 3515 1.46 - 1.58: 7122 1.58 - 1.70: 111 1.70 - 1.83: 97 Bond restraints: 15803 Sorted by residual: bond pdb=" C4 ATP E1101 " pdb=" C5 ATP E1101 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP E1101 " pdb=" C6 ATP E1101 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP E1101 " pdb=" N7 ATP E1101 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP E1101 " pdb=" N7 ATP E1101 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.80e+01 bond pdb=" C4 ATP E1101 " pdb=" N9 ATP E1101 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 15798 not shown) Histogram of bond angle deviations from ideal: 99.88 - 107.13: 648 107.13 - 114.39: 9407 114.39 - 121.64: 7826 121.64 - 128.90: 3497 128.90 - 136.15: 124 Bond angle restraints: 21502 Sorted by residual: angle pdb=" PB ATP E1101 " pdb=" O3B ATP E1101 " pdb=" PG ATP E1101 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP E1101 " pdb=" O3A ATP E1101 " pdb=" PB ATP E1101 " ideal model delta sigma weight residual 136.83 120.36 16.47 1.00e+00 1.00e+00 2.71e+02 angle pdb=" C5 ATP E1101 " pdb=" C4 ATP E1101 " pdb=" N3 ATP E1101 " ideal model delta sigma weight residual 126.80 118.72 8.08 1.00e+00 1.00e+00 6.53e+01 angle pdb=" N3 ATP E1101 " pdb=" C4 ATP E1101 " pdb=" N9 ATP E1101 " ideal model delta sigma weight residual 127.04 134.94 -7.90 1.15e+00 7.59e-01 4.74e+01 angle pdb=" N1 ATP E1101 " pdb=" C2 ATP E1101 " pdb=" N3 ATP E1101 " ideal model delta sigma weight residual 128.69 123.73 4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 21497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8029 17.92 - 35.85: 1092 35.85 - 53.77: 393 53.77 - 71.70: 100 71.70 - 89.62: 18 Dihedral angle restraints: 9632 sinusoidal: 4388 harmonic: 5244 Sorted by residual: dihedral pdb=" CA ASN G 376 " pdb=" C ASN G 376 " pdb=" N HIS G 377 " pdb=" CA HIS G 377 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ALA G 373 " pdb=" C ALA G 373 " pdb=" N HIS G 374 " pdb=" CA HIS G 374 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS G 392 " pdb=" C LYS G 392 " pdb=" N LYS G 393 " pdb=" CA LYS G 393 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 9629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1830 0.051 - 0.103: 515 0.103 - 0.154: 76 0.154 - 0.205: 18 0.205 - 0.257: 2 Chirality restraints: 2441 Sorted by residual: chirality pdb=" CA SER E 193 " pdb=" N SER E 193 " pdb=" C SER E 193 " pdb=" CB SER E 193 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE G 153 " pdb=" CA ILE G 153 " pdb=" CG1 ILE G 153 " pdb=" CG2 ILE G 153 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE E 263 " pdb=" CA ILE E 263 " pdb=" CG1 ILE E 263 " pdb=" CG2 ILE E 263 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2438 not shown) Planarity restraints: 2563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 239 " 0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP C 239 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 239 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 239 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 239 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 239 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 239 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 239 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 239 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 239 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 957 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO E 958 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 958 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 958 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 192 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C LYS E 192 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS E 192 " -0.011 2.00e-02 2.50e+03 pdb=" N SER E 193 " -0.010 2.00e-02 2.50e+03 ... (remaining 2560 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2187 2.75 - 3.29: 15507 3.29 - 3.83: 25184 3.83 - 4.36: 29101 4.36 - 4.90: 47740 Nonbonded interactions: 119719 Sorted by model distance: nonbonded pdb=" OE1 GLN E1003 " pdb=" OH TYR E1044 " model vdw 2.213 2.440 nonbonded pdb=" NZ LYS E 971 " pdb=" O ALA E 976 " model vdw 2.215 2.520 nonbonded pdb=" OG1 THR C 270 " pdb=" O LYS C 276 " model vdw 2.221 2.440 nonbonded pdb=" O ARG G 65 " pdb=" OG1 THR G 69 " model vdw 2.229 2.440 nonbonded pdb=" ND2 ASN G 134 " pdb=" O ARG G 202 " model vdw 2.242 2.520 ... (remaining 119714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.370 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.850 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.005 0.082 15803 Z= 0.343 Angle : 0.861 19.438 21502 Z= 0.535 Chirality : 0.048 0.257 2441 Planarity : 0.004 0.056 2563 Dihedral : 19.049 89.620 6218 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.44 % Favored : 86.28 % Rotamer: Outliers : 3.26 % Allowed : 11.97 % Favored : 84.76 % 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: -4.24 (0.16), residues: 1771 helix: -1.83 (0.16), residues: 777 sheet: -2.76 (0.34), residues: 172 loop : -3.89 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 239 HIS 0.008 0.001 HIS G 377 PHE 0.025 0.002 PHE E 50 TYR 0.020 0.002 TYR F 181 ARG 0.007 0.001 ARG G 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.6480 (ttp80) cc_final: 0.5935 (ttt180) REVERT: C 151 ASN cc_start: 0.7802 (t0) cc_final: 0.7467 (t0) REVERT: D 205 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 1023 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6018 (pm20) REVERT: E 50 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: E 75 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6604 (pttm) REVERT: E 91 GLU cc_start: 0.8511 (pt0) cc_final: 0.8139 (pm20) REVERT: E 101 ASP cc_start: 0.7432 (m-30) cc_final: 0.6912 (t0) REVERT: E 155 TYR cc_start: 0.5281 (m-80) cc_final: 0.3911 (m-80) REVERT: E 230 ASP cc_start: 0.7739 (m-30) cc_final: 0.7418 (m-30) REVERT: E 875 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7785 (p) REVERT: F 50 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7618 (tppt) REVERT: F 166 SER cc_start: 0.7824 (m) cc_final: 0.7430 (p) REVERT: F 207 PHE cc_start: 0.7781 (t80) cc_final: 0.7568 (t80) REVERT: F 252 GLU cc_start: 0.6792 (mp0) cc_final: 0.6464 (mp0) REVERT: G 290 LYS cc_start: 0.8425 (mppt) cc_final: 0.8171 (mmtp) REVERT: G 393 LYS cc_start: 0.6599 (tptm) cc_final: 0.6057 (tptm) outliers start: 52 outliers final: 20 residues processed: 343 average time/residue: 0.2867 time to fit residues: 140.5434 Evaluate side-chains 205 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 884 GLU Chi-restraints excluded: chain E residue 891 ASP Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 165 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: C 35 ASN C 52 ASN C 87 HIS C 188 ASN C 215 ASN C 267 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 166 GLN D 255 ASN D 263 HIS D1009 ASN D1048 GLN E 71 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E 882 HIS E1017 ASN E1018 GLN ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN G 67 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 ASN G 260 ASN G 353 GLN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15803 Z= 0.193 Angle : 0.615 10.807 21502 Z= 0.332 Chirality : 0.042 0.232 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.526 84.711 2656 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.20 % Favored : 90.74 % Rotamer: Outliers : 3.82 % Allowed : 18.37 % Favored : 77.81 % 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: -3.12 (0.18), residues: 1771 helix: -0.75 (0.18), residues: 771 sheet: -2.21 (0.35), residues: 196 loop : -3.46 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 160 HIS 0.009 0.001 HIS G 62 PHE 0.021 0.001 PHE E 78 TYR 0.016 0.001 TYR F 84 ARG 0.007 0.000 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6766 (mm-30) REVERT: C 151 ASN cc_start: 0.7612 (t0) cc_final: 0.7367 (t0) REVERT: D 205 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 1009 ASN cc_start: 0.6197 (OUTLIER) cc_final: 0.5747 (p0) REVERT: D 1023 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: E 50 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: E 91 GLU cc_start: 0.8257 (pt0) cc_final: 0.7918 (mp0) REVERT: E 101 ASP cc_start: 0.7376 (m-30) cc_final: 0.6834 (t0) REVERT: E 155 TYR cc_start: 0.5013 (m-80) cc_final: 0.3743 (m-80) REVERT: E 180 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6627 (pp) REVERT: E 230 ASP cc_start: 0.7759 (m-30) cc_final: 0.7451 (m-30) REVERT: E 877 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8288 (tp) REVERT: E 969 MET cc_start: 0.6454 (mtm) cc_final: 0.6079 (mtm) REVERT: E 1061 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7244 (ptp) REVERT: F 166 SER cc_start: 0.8599 (m) cc_final: 0.7967 (p) REVERT: F 266 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5124 (tt) REVERT: G 54 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.5933 (m-80) REVERT: G 290 LYS cc_start: 0.8304 (mppt) cc_final: 0.8020 (mmtp) REVERT: G 393 LYS cc_start: 0.6450 (tptm) cc_final: 0.6131 (tptp) outliers start: 61 outliers final: 26 residues processed: 262 average time/residue: 0.2577 time to fit residues: 103.3492 Evaluate side-chains 204 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1009 ASN Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1025 SER Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 877 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 999 MET Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 132 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15803 Z= 0.165 Angle : 0.571 11.532 21502 Z= 0.306 Chirality : 0.040 0.159 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.233 88.598 2621 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.20 % Favored : 90.74 % Rotamer: Outliers : 4.08 % Allowed : 20.94 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.19), residues: 1771 helix: -0.31 (0.19), residues: 767 sheet: -1.71 (0.37), residues: 194 loop : -3.18 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 160 HIS 0.010 0.001 HIS G 62 PHE 0.032 0.001 PHE E 256 TYR 0.016 0.001 TYR E 961 ARG 0.009 0.000 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 204 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ASN cc_start: 0.7549 (t0) cc_final: 0.7289 (t0) REVERT: D 205 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 211 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: D 1009 ASN cc_start: 0.6315 (OUTLIER) cc_final: 0.5919 (m-40) REVERT: E 50 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6603 (m-10) REVERT: E 91 GLU cc_start: 0.8142 (pt0) cc_final: 0.7809 (mp0) REVERT: E 101 ASP cc_start: 0.7273 (m-30) cc_final: 0.6786 (t0) REVERT: E 155 TYR cc_start: 0.5230 (m-80) cc_final: 0.4076 (m-80) REVERT: E 876 GLU cc_start: 0.7686 (pp20) cc_final: 0.7102 (tm-30) REVERT: E 1061 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7165 (ptp) REVERT: F 166 SER cc_start: 0.8566 (m) cc_final: 0.7914 (p) REVERT: G 290 LYS cc_start: 0.8284 (mppt) cc_final: 0.7993 (mmtp) outliers start: 65 outliers final: 36 residues processed: 250 average time/residue: 0.2311 time to fit residues: 90.7191 Evaluate side-chains 220 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1009 ASN Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15803 Z= 0.191 Angle : 0.586 11.536 21502 Z= 0.310 Chirality : 0.041 0.215 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.056 86.951 2618 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 5.39 % Allowed : 21.07 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1771 helix: -0.20 (0.19), residues: 784 sheet: -1.67 (0.38), residues: 196 loop : -3.02 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 160 HIS 0.010 0.001 HIS G 62 PHE 0.025 0.001 PHE E 256 TYR 0.021 0.001 TYR D 161 ARG 0.004 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 187 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ASN cc_start: 0.7523 (t0) cc_final: 0.6866 (t0) REVERT: D 144 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6934 (ttt180) REVERT: D 205 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7413 (tm-30) REVERT: E 50 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: E 91 GLU cc_start: 0.8149 (pt0) cc_final: 0.7816 (mp0) REVERT: E 101 ASP cc_start: 0.7352 (m-30) cc_final: 0.6760 (t0) REVERT: E 155 TYR cc_start: 0.5379 (m-80) cc_final: 0.4113 (m-80) REVERT: E 180 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6404 (pp) REVERT: E 230 ASP cc_start: 0.7533 (m-30) cc_final: 0.7200 (m-30) REVERT: E 876 GLU cc_start: 0.7617 (pp20) cc_final: 0.7282 (tm-30) REVERT: F 166 SER cc_start: 0.8573 (m) cc_final: 0.8141 (p) REVERT: G 290 LYS cc_start: 0.8279 (mppt) cc_final: 0.7983 (mmtp) outliers start: 86 outliers final: 54 residues processed: 246 average time/residue: 0.2292 time to fit residues: 87.6735 Evaluate side-chains 235 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1009 ASN Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15803 Z= 0.257 Angle : 0.622 11.244 21502 Z= 0.330 Chirality : 0.043 0.193 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.001 84.498 2616 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.27 % Rotamer: Outliers : 5.45 % Allowed : 22.82 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1771 helix: -0.21 (0.19), residues: 783 sheet: -1.55 (0.37), residues: 215 loop : -3.05 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 PHE 0.018 0.002 PHE G 209 TYR 0.025 0.002 TYR C 261 ARG 0.005 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 183 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6879 (ttt180) REVERT: D 205 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7404 (tm-30) REVERT: E 91 GLU cc_start: 0.8329 (pt0) cc_final: 0.7806 (mp0) REVERT: E 101 ASP cc_start: 0.7357 (m-30) cc_final: 0.6858 (t0) REVERT: E 155 TYR cc_start: 0.5568 (m-80) cc_final: 0.4277 (m-80) REVERT: E 180 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6745 (pp) REVERT: F 166 SER cc_start: 0.8663 (m) cc_final: 0.8229 (p) REVERT: F 207 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7430 (t80) REVERT: F 285 GLN cc_start: 0.7661 (pm20) cc_final: 0.7349 (pm20) REVERT: G 54 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: G 290 LYS cc_start: 0.8399 (mppt) cc_final: 0.8103 (mmtp) REVERT: G 330 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.6115 (m-10) REVERT: G 393 LYS cc_start: 0.6454 (tptm) cc_final: 0.6141 (tptp) outliers start: 87 outliers final: 66 residues processed: 247 average time/residue: 0.2211 time to fit residues: 85.3900 Evaluate side-chains 243 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 172 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 177 CYS Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 0.0060 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1028 GLN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15803 Z= 0.195 Angle : 0.592 11.303 21502 Z= 0.310 Chirality : 0.041 0.215 2441 Planarity : 0.003 0.055 2563 Dihedral : 17.877 85.375 2616 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.87 % Favored : 91.08 % Rotamer: Outliers : 4.95 % Allowed : 24.20 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1771 helix: -0.03 (0.19), residues: 787 sheet: -1.42 (0.37), residues: 215 loop : -2.89 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 PHE 0.036 0.002 PHE E 256 TYR 0.036 0.001 TYR C 261 ARG 0.004 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 189 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.6967 (tt) REVERT: D 86 ILE cc_start: 0.6058 (mt) cc_final: 0.5305 (mt) REVERT: D 144 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6991 (ttt180) REVERT: D 205 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7339 (tm-30) REVERT: D 245 LYS cc_start: 0.8491 (ttpt) cc_final: 0.7935 (tttm) REVERT: E 91 GLU cc_start: 0.8318 (pt0) cc_final: 0.7843 (mp0) REVERT: E 101 ASP cc_start: 0.7379 (m-30) cc_final: 0.6860 (t0) REVERT: E 155 TYR cc_start: 0.5733 (m-80) cc_final: 0.4369 (m-80) REVERT: E 180 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6517 (pp) REVERT: E 254 ARG cc_start: 0.7849 (tpt-90) cc_final: 0.7567 (tpp80) REVERT: F 166 SER cc_start: 0.8630 (m) cc_final: 0.8213 (p) outliers start: 79 outliers final: 52 residues processed: 245 average time/residue: 0.2418 time to fit residues: 93.7970 Evaluate side-chains 227 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN C 164 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15803 Z= 0.232 Angle : 0.622 11.691 21502 Z= 0.325 Chirality : 0.042 0.163 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.863 85.824 2616 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.67 % Favored : 89.27 % Rotamer: Outliers : 5.39 % Allowed : 24.89 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1771 helix: -0.10 (0.19), residues: 788 sheet: -1.40 (0.37), residues: 215 loop : -2.89 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 160 HIS 0.012 0.001 HIS G 62 PHE 0.032 0.002 PHE E 256 TYR 0.038 0.002 TYR C 261 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 184 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7006 (tt) REVERT: C 251 ASP cc_start: 0.7315 (t0) cc_final: 0.6957 (t0) REVERT: D 144 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7073 (ttt180) REVERT: D 205 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7523 (tm-30) REVERT: E 91 GLU cc_start: 0.8345 (pt0) cc_final: 0.7802 (mp0) REVERT: E 101 ASP cc_start: 0.7387 (m-30) cc_final: 0.6826 (t0) REVERT: E 155 TYR cc_start: 0.5817 (m-80) cc_final: 0.4461 (m-80) REVERT: E 180 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6791 (pp) REVERT: F 166 SER cc_start: 0.8682 (m) cc_final: 0.8303 (p) REVERT: G 367 ARG cc_start: 0.6331 (mtt180) cc_final: 0.6078 (ptm160) outliers start: 86 outliers final: 65 residues processed: 247 average time/residue: 0.2358 time to fit residues: 90.3677 Evaluate side-chains 236 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15803 Z= 0.209 Angle : 0.610 11.359 21502 Z= 0.317 Chirality : 0.042 0.204 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.798 86.473 2616 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.43 % Favored : 90.51 % Rotamer: Outliers : 4.89 % Allowed : 25.83 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1771 helix: 0.00 (0.19), residues: 781 sheet: -1.34 (0.38), residues: 215 loop : -2.81 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 160 HIS 0.012 0.001 HIS G 62 PHE 0.018 0.002 PHE G 209 TYR 0.014 0.001 TYR D 161 ARG 0.004 0.000 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 181 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7265 (tt) REVERT: D 144 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7101 (ttt180) REVERT: D 205 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7515 (tm-30) REVERT: D 245 LYS cc_start: 0.8568 (ttpt) cc_final: 0.7946 (tttm) REVERT: D 293 GLU cc_start: 0.7723 (pt0) cc_final: 0.7404 (pt0) REVERT: D 296 GLN cc_start: 0.6289 (pm20) cc_final: 0.5773 (pm20) REVERT: E 91 GLU cc_start: 0.8329 (pt0) cc_final: 0.7783 (mp0) REVERT: E 101 ASP cc_start: 0.7385 (m-30) cc_final: 0.6816 (t0) REVERT: E 155 TYR cc_start: 0.5718 (m-80) cc_final: 0.4396 (m-80) REVERT: E 180 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6717 (pp) REVERT: F 166 SER cc_start: 0.8654 (m) cc_final: 0.8274 (p) REVERT: G 49 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7785 (mmtp) REVERT: G 201 MET cc_start: 0.7027 (mmm) cc_final: 0.6815 (mmp) outliers start: 78 outliers final: 66 residues processed: 238 average time/residue: 0.2385 time to fit residues: 87.8147 Evaluate side-chains 239 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 170 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1088 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 128 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 162 optimal weight: 0.0770 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN E 907 GLN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15803 Z= 0.148 Angle : 0.584 12.370 21502 Z= 0.299 Chirality : 0.041 0.306 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.635 87.319 2616 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.09 % Rotamer: Outliers : 3.95 % Allowed : 27.34 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1771 helix: 0.20 (0.19), residues: 791 sheet: -1.15 (0.38), residues: 211 loop : -2.69 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 PHE 0.016 0.001 PHE G 209 TYR 0.026 0.001 TYR C 261 ARG 0.003 0.000 ARG D 933 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.5351 (ttp80) REVERT: C 230 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7120 (tt) REVERT: D 144 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7034 (ttt180) REVERT: D 205 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 245 LYS cc_start: 0.8440 (ttpt) cc_final: 0.7813 (tttp) REVERT: D 275 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7160 (tp30) REVERT: D 1069 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6828 (mm) REVERT: E 91 GLU cc_start: 0.8172 (pt0) cc_final: 0.7721 (mp0) REVERT: E 101 ASP cc_start: 0.7329 (m-30) cc_final: 0.6751 (t0) REVERT: E 155 TYR cc_start: 0.5468 (m-80) cc_final: 0.4245 (m-80) REVERT: F 166 SER cc_start: 0.8587 (m) cc_final: 0.8243 (p) REVERT: G 327 TYR cc_start: 0.7929 (m-10) cc_final: 0.7612 (m-80) REVERT: G 367 ARG cc_start: 0.6268 (mtt180) cc_final: 0.5996 (ptm160) outliers start: 63 outliers final: 48 residues processed: 236 average time/residue: 0.2248 time to fit residues: 82.8978 Evaluate side-chains 224 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 0.0370 chunk 120 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15803 Z= 0.170 Angle : 0.606 13.234 21502 Z= 0.310 Chirality : 0.041 0.382 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.562 87.458 2614 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 3.39 % Allowed : 28.03 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1771 helix: 0.26 (0.19), residues: 793 sheet: -1.11 (0.38), residues: 213 loop : -2.65 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 160 HIS 0.012 0.001 HIS G 62 PHE 0.031 0.001 PHE C 310 TYR 0.023 0.001 TYR C 261 ARG 0.002 0.000 ARG D 933 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7280 (tt) REVERT: D 144 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7066 (ttt180) REVERT: D 205 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 245 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7800 (tttm) REVERT: D 275 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7197 (tp30) REVERT: E 91 GLU cc_start: 0.8181 (pt0) cc_final: 0.7708 (mp0) REVERT: E 101 ASP cc_start: 0.7396 (m-30) cc_final: 0.6739 (t0) REVERT: E 155 TYR cc_start: 0.5523 (m-80) cc_final: 0.4201 (m-80) REVERT: E 1016 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6695 (pp) REVERT: F 166 SER cc_start: 0.8628 (m) cc_final: 0.8253 (p) outliers start: 54 outliers final: 49 residues processed: 215 average time/residue: 0.2528 time to fit residues: 83.4658 Evaluate side-chains 225 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 144 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.164107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.127630 restraints weight = 23044.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128998 restraints weight = 18510.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129573 restraints weight = 17831.989| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15803 Z= 0.166 Angle : 0.611 13.601 21502 Z= 0.311 Chirality : 0.041 0.352 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.469 88.043 2614 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer: Outliers : 3.64 % Allowed : 28.46 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.20), residues: 1771 helix: 0.24 (0.19), residues: 800 sheet: -1.09 (0.38), residues: 213 loop : -2.60 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 60 HIS 0.012 0.001 HIS G 62 PHE 0.027 0.001 PHE C 310 TYR 0.030 0.001 TYR C 261 ARG 0.003 0.000 ARG G 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.35 seconds wall clock time: 56 minutes 23.39 seconds (3383.39 seconds total)