Starting phenix.real_space_refine (version: dev) on Tue Feb 21 18:23:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/02_2023/7tve_26140_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/02_2023/7tve_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_26140/02_2023/7tve_26140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/02_2023/7tve_26140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/02_2023/7tve_26140_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tve_26140/02_2023/7tve_26140_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.17, per 1000 atoms: 0.59 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: 6.25 Conformation dependent library (CDL) restraints added in 2.3 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: 4.90 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: 4.72 Time building geometry restraints manager: 6.71 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: 7992 17.92 - 35.85: 1014 35.85 - 53.77: 371 53.77 - 71.70: 100 71.70 - 89.62: 16 Dihedral angle restraints: 9493 sinusoidal: 4249 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 9490 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 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. 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.230 Process input model: 44.420 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 18.768 89.620 6079 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 % 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 *********************** 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 : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 20 residues processed: 343 average time/residue: 0.2980 time to fit residues: 146.8147 Evaluate side-chains 194 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1992 time to fit residues: 8.8504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 166 GLN D 263 HIS D1009 ASN D1048 GLN E 71 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E1017 ASN E1018 GLN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN G 67 GLN ** G 96 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15803 Z= 0.176 Angle : 0.611 11.689 21502 Z= 0.328 Chirality : 0.042 0.215 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.070 84.682 2462 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.97 % Rotamer Outliers : 3.20 % 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: -3.08 (0.18), residues: 1771 helix: -0.74 (0.18), residues: 772 sheet: -2.14 (0.36), residues: 186 loop : -3.41 (0.18), residues: 813 *********************** 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 271 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 220 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 17 residues processed: 256 average time/residue: 0.2452 time to fit residues: 97.7117 Evaluate side-chains 191 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1503 time to fit residues: 7.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6942 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15803 Z= 0.202 Angle : 0.599 11.251 21502 Z= 0.321 Chirality : 0.042 0.179 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.857 89.052 2462 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.95 % Rotamer Outliers : 3.07 % 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: -2.66 (0.19), residues: 1771 helix: -0.37 (0.19), residues: 771 sheet: -2.05 (0.35), residues: 203 loop : -3.17 (0.19), residues: 797 *********************** 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 249 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 238 average time/residue: 0.2333 time to fit residues: 87.4075 Evaluate side-chains 203 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1421 time to fit residues: 9.1737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** D 255 ASN E 170 ASN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7038 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 15803 Z= 0.282 Angle : 0.663 11.135 21502 Z= 0.349 Chirality : 0.044 0.270 2441 Planarity : 0.004 0.054 2563 Dihedral : 17.759 85.993 2462 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.01 % Favored : 88.93 % Rotamer Outliers : 3.70 % 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: -2.63 (0.19), residues: 1771 helix: -0.42 (0.18), residues: 781 sheet: -1.80 (0.38), residues: 191 loop : -3.17 (0.19), residues: 799 *********************** 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 241 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 182 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 25 residues processed: 223 average time/residue: 0.2399 time to fit residues: 83.7730 Evaluate side-chains 198 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1496 time to fit residues: 9.3529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 137 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: 0.7035 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 15803 Z= 0.258 Angle : 0.641 10.956 21502 Z= 0.338 Chirality : 0.043 0.194 2441 Planarity : 0.004 0.054 2563 Dihedral : 17.602 84.987 2462 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.45 % Favored : 89.50 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.19), residues: 1771 helix: -0.30 (0.19), residues: 784 sheet: -1.72 (0.38), residues: 201 loop : -3.05 (0.20), residues: 786 *********************** 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 228 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 214 average time/residue: 0.2316 time to fit residues: 79.1595 Evaluate side-chains 191 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1457 time to fit residues: 9.2518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15803 Z= 0.230 Angle : 0.627 11.320 21502 Z= 0.328 Chirality : 0.042 0.166 2441 Planarity : 0.003 0.057 2563 Dihedral : 17.503 85.743 2462 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.73 % Favored : 89.22 % Rotamer Outliers : 2.32 % 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: -2.23 (0.20), residues: 1771 helix: -0.14 (0.19), residues: 776 sheet: -1.50 (0.39), residues: 193 loop : -2.91 (0.20), residues: 802 *********************** 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 223 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 212 average time/residue: 0.2326 time to fit residues: 77.4384 Evaluate side-chains 184 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1352 time to fit residues: 6.6669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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** D 963 ASN ** E1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15803 Z= 0.182 Angle : 0.603 11.176 21502 Z= 0.314 Chirality : 0.041 0.183 2441 Planarity : 0.003 0.051 2563 Dihedral : 17.404 86.319 2462 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.03 % Favored : 90.91 % Rotamer Outliers : 1.69 % 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: -2.01 (0.20), residues: 1771 helix: 0.00 (0.19), residues: 779 sheet: -1.43 (0.39), residues: 193 loop : -2.74 (0.20), residues: 799 *********************** 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 206 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 198 average time/residue: 0.2418 time to fit residues: 75.3779 Evaluate side-chains 174 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1517 time to fit residues: 5.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6899 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 15803 Z= 0.152 Angle : 0.599 11.898 21502 Z= 0.307 Chirality : 0.041 0.241 2441 Planarity : 0.003 0.055 2563 Dihedral : 17.309 86.931 2462 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.13 % Favored : 91.81 % Rotamer Outliers : 1.25 % 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: -1.77 (0.20), residues: 1771 helix: 0.21 (0.19), residues: 784 sheet: -1.35 (0.38), residues: 205 loop : -2.65 (0.20), residues: 782 *********************** 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 210 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 202 average time/residue: 0.2402 time to fit residues: 75.7000 Evaluate side-chains 182 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1527 time to fit residues: 5.5610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** 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: 0.6979 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15803 Z= 0.215 Angle : 0.643 11.351 21502 Z= 0.332 Chirality : 0.043 0.290 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.308 87.226 2462 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.77 % Favored : 90.18 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1771 helix: 0.13 (0.19), residues: 786 sheet: -1.34 (0.38), residues: 207 loop : -2.65 (0.21), residues: 778 *********************** 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 184 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 180 average time/residue: 0.2533 time to fit residues: 71.3235 Evaluate side-chains 166 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1441 time to fit residues: 3.9178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 166 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** 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: 0.6936 moved from start: 0.4657 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= 0.181 Angle : 0.641 12.538 21502 Z= 0.326 Chirality : 0.042 0.307 2441 Planarity : 0.003 0.053 2563 Dihedral : 17.188 87.850 2462 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1771 helix: 0.20 (0.19), residues: 785 sheet: -1.23 (0.38), residues: 203 loop : -2.53 (0.21), residues: 783 ********************** 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 172 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.2404 time to fit residues: 64.2983 Evaluate side-chains 161 residues out of total 1607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1660 time to fit residues: 4.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 144 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.166129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.128772 restraints weight = 22886.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130686 restraints weight = 17989.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.131270 restraints weight = 15326.275| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4787 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= 0.176 Angle : 0.631 12.359 21502 Z= 0.322 Chirality : 0.041 0.300 2441 Planarity : 0.003 0.053 2563 Dihedral : 17.088 88.385 2462 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.87 % Favored : 91.08 % Rotamer Outliers : 0.25 % 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: -1.61 (0.20), residues: 1771 helix: 0.28 (0.19), residues: 787 sheet: -1.18 (0.39), residues: 203 loop : -2.51 (0.21), residues: 781 =============================================================================== Job complete usr+sys time: 2840.10 seconds wall clock time: 53 minutes 4.25 seconds (3184.25 seconds total)