Starting phenix.real_space_refine on Thu Mar 5 18:50:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.map" model { file = "/net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sit_54931/03_2026/9sit_54931.cif" } resolution = 1.75 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 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= 0.002 sd= 0.031 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 110 5.49 5 S 117 5.16 5 C 14969 2.51 5 N 4046 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24078 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2714 Classifications: {'peptide': 340} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1438 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "E" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2639 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "F" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2628 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "G" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2637 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "H" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2436 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 810 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 32} Time building chain proxies: 5.13, per 1000 atoms: 0.21 Number of scatterers: 24078 At special positions: 0 Unit cell: (113.825, 145.725, 156.6, 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 117 16.00 P 110 15.00 O 4836 8.00 N 4046 7.00 C 14969 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 - 3.00 Amino acid : True - 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 36 sheets defined 34.2% alpha, 10.5% beta 38 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.726A pdb=" N ALA A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.532A pdb=" N SER A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.748A pdb=" N TYR A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.873A pdb=" N GLN A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.530A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.023A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.293A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.502A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.713A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.062A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.731A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 238 Processing helix chain 'I' and resid 15 through 23 Processing helix chain 'I' and resid 24 through 35 removed outlier: 3.564A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 31 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 72 removed outlier: 3.834A pdb=" N CYS I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 78 Processing helix chain 'I' and resid 79 through 81 No H-bonds generated for 'chain 'I' and resid 79 through 81' Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.504A pdb=" N ARG I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 141 removed outlier: 3.877A pdb=" N HIS I 141 " --> pdb=" O GLN I 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.983A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.609A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 70 removed outlier: 4.026A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.509A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.526A pdb=" N TYR E 271 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.127A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.778A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.744A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.213A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.507A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.334A pdb=" N GLU G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.525A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.679A pdb=" N ILE G 324 " --> pdb=" O MET G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.517A pdb=" N ILE H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.649A pdb=" N LEU H 148 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.514A pdb=" N HIS H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 319 " --> pdb=" O ASP H 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.748A pdb=" N ASP A 78 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 153 removed outlier: 4.280A pdb=" N ASP B 214 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 removed outlier: 8.425A pdb=" N VAL B 24 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 212 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 17 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 141 current: chain 'B' and resid 218 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 218 through 229 current: chain 'B' and resid 249 through 253 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'I' and resid 39 through 42 removed outlier: 3.652A pdb=" N LEU I 61 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER I 3 " --> pdb=" O GLU I 89 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU I 89 " --> pdb=" O SER I 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'I' and resid 143 through 147 Processing sheet with id=AB2, first strand: chain 'I' and resid 168 through 169 removed outlier: 4.110A pdb=" N SER I 168 " --> pdb=" O ARG I 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.529A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.365A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB7, first strand: chain 'E' and resid 106 through 109 Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 57 removed outlier: 4.255A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AC2, first strand: chain 'E' and resid 282 through 283 removed outlier: 3.564A pdb=" N ILE E 288 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.740A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 50 through 57 Processing sheet with id=AC6, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC7, first strand: chain 'F' and resid 282 through 283 removed outlier: 3.610A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.694A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 172 through 173 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.101A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AD3, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 168 current: chain 'G' and resid 246 through 249 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 50 through 57 removed outlier: 4.094A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD7, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.511A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 172 through 173 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 260 through 262 644 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6646 1.33 - 1.46: 5367 1.46 - 1.58: 12413 1.58 - 1.70: 219 1.70 - 1.82: 187 Bond restraints: 24832 Sorted by residual: bond pdb=" N TYR A 232 " pdb=" CA TYR A 232 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.90e+00 bond pdb=" N GLU A 96 " pdb=" CA GLU A 96 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.28e+00 bond pdb=" N THR A 102 " pdb=" CA THR A 102 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.26e+00 bond pdb=" N ASP C 166 " pdb=" CA ASP C 166 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.15e+00 bond pdb=" N LEU A 233 " pdb=" CA LEU A 233 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.33e-02 5.65e+03 7.15e+00 ... (remaining 24827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 33516 2.23 - 4.47: 459 4.47 - 6.70: 51 6.70 - 8.93: 14 8.93 - 11.17: 3 Bond angle restraints: 34043 Sorted by residual: angle pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" C LEU A 228 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.21e+00 6.83e-01 2.41e+01 angle pdb=" C GLU F 165 " pdb=" N ASP F 166 " pdb=" CA ASP F 166 " ideal model delta sigma weight residual 125.66 133.83 -8.17 1.85e+00 2.92e-01 1.95e+01 angle pdb=" N ASP A 229 " pdb=" CA ASP A 229 " pdb=" C ASP A 229 " ideal model delta sigma weight residual 111.03 106.55 4.48 1.11e+00 8.12e-01 1.63e+01 angle pdb=" N ILE H 261 " pdb=" CA ILE H 261 " pdb=" C ILE H 261 " ideal model delta sigma weight residual 113.20 109.38 3.82 9.60e-01 1.09e+00 1.58e+01 angle pdb=" C ILE E 164 " pdb=" N GLU E 165 " pdb=" CA GLU E 165 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 ... (remaining 34038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 13966 33.78 - 67.57: 951 67.57 - 101.35: 80 101.35 - 135.14: 0 135.14 - 168.92: 1 Dihedral angle restraints: 14998 sinusoidal: 7086 harmonic: 7912 Sorted by residual: dihedral pdb=" O4' U J 44 " pdb=" C1' U J 44 " pdb=" N1 U J 44 " pdb=" C2 U J 44 " ideal model delta sinusoidal sigma weight residual -128.00 -47.54 -80.46 1 1.70e+01 3.46e-03 2.77e+01 dihedral pdb=" CA ARG F 325 " pdb=" C ARG F 325 " pdb=" N GLY F 326 " pdb=" CA GLY F 326 " ideal model delta harmonic sigma weight residual 180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU C 148 " pdb=" C LEU C 148 " pdb=" N TRP C 149 " pdb=" CA TRP C 149 " ideal model delta harmonic sigma weight residual -180.00 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 14995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3711 0.118 - 0.237: 52 0.237 - 0.355: 0 0.355 - 0.473: 0 0.473 - 0.591: 7 Chirality restraints: 3770 Sorted by residual: chirality pdb=" P DA K 12 " pdb=" OP1 DA K 12 " pdb=" OP2 DA K 12 " pdb=" O5' DA K 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.74e+00 chirality pdb=" P DG K 16 " pdb=" OP1 DG K 16 " pdb=" OP2 DG K 16 " pdb=" O5' DG K 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" P DA L 12 " pdb=" OP1 DA L 12 " pdb=" OP2 DA L 12 " pdb=" O5' DA L 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 3767 not shown) Planarity restraints: 3967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A J 40 " 0.030 2.00e-02 2.50e+03 1.44e-02 5.74e+00 pdb=" N9 A J 40 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A J 40 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A J 40 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A J 40 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A J 40 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A J 40 " 0.003 2.00e-02 2.50e+03 pdb=" N1 A J 40 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A J 40 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A J 40 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A J 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A J 4 " 0.029 2.00e-02 2.50e+03 1.31e-02 4.69e+00 pdb=" N9 A J 4 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A J 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A J 4 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A J 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A J 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A J 4 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A J 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A J 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A J 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A J 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 95 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C MET A 95 " -0.035 2.00e-02 2.50e+03 pdb=" O MET A 95 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 96 " 0.012 2.00e-02 2.50e+03 ... (remaining 3964 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1400 2.72 - 3.26: 24182 3.26 - 3.81: 42405 3.81 - 4.35: 55512 4.35 - 4.90: 88814 Nonbonded interactions: 212313 Sorted by model distance: nonbonded pdb=" O2' A J 40 " pdb=" O5' G J 41 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP G 293 " pdb=" OG1 THR G 294 " model vdw 2.200 3.040 nonbonded pdb=" O GLU E 278 " pdb=" OH TYR E 318 " model vdw 2.217 3.040 nonbonded pdb=" O GLU G 278 " pdb=" OH TYR G 318 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR H 265 " pdb=" O PHE H 273 " model vdw 2.220 3.040 ... (remaining 212308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 12 through 52 or resid 79 through 333)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 333)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 333)) selection = (chain 'F' and (resid 12 through 52 or resid 79 through 333)) selection = (chain 'G' and (resid 12 through 52 or resid 79 through 333)) selection = (chain 'H' and resid 12 through 333) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.980 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.470 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: 0.000 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 0.054 24832 Z= 0.243 Angle : 0.666 11.168 34043 Z= 0.366 Chirality : 0.049 0.591 3770 Planarity : 0.004 0.048 3967 Dihedral : 20.297 168.919 9888 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 0.46 % Allowed : 24.82 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2664 helix: 0.40 (0.19), residues: 764 sheet: 0.28 (0.26), residues: 466 loop : -0.79 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 204 TYR 0.016 0.002 TYR G 265 PHE 0.032 0.002 PHE A 339 TRP 0.009 0.001 TRP F 149 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd covalent geometry : bond 0.00536 (24832) covalent geometry : angle 0.66626 (34043) hydrogen bonds : bond 0.22009 ( 736) hydrogen bonds : angle 8.35196 ( 2003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 641 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8088 (t0) cc_final: 0.7446 (t160) REVERT: A 76 GLU cc_start: 0.7590 (pm20) cc_final: 0.7341 (pm20) REVERT: A 104 MET cc_start: 0.1115 (mmp) cc_final: -0.1020 (mtt) REVERT: A 113 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: A 218 LYS cc_start: 0.7848 (tptm) cc_final: 0.7595 (tptm) REVERT: A 223 ASN cc_start: 0.7815 (p0) cc_final: 0.7549 (p0) REVERT: A 226 LYS cc_start: 0.8229 (mttp) cc_final: 0.7914 (mtpp) REVERT: B 21 ASN cc_start: 0.7508 (t0) cc_final: 0.7254 (t0) REVERT: B 40 GLU cc_start: 0.7421 (tt0) cc_final: 0.7057 (tt0) REVERT: B 42 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7536 (mmmm) REVERT: B 60 HIS cc_start: 0.8324 (m-70) cc_final: 0.8104 (m90) REVERT: B 68 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7770 (mtpp) REVERT: B 119 MET cc_start: 0.5931 (tpp) cc_final: 0.5522 (pmm) REVERT: B 144 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7260 (mmmt) REVERT: B 177 ASP cc_start: 0.6648 (m-30) cc_final: 0.6356 (m-30) REVERT: B 206 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 219 GLU cc_start: 0.7824 (pt0) cc_final: 0.7618 (pt0) REVERT: B 251 LEU cc_start: 0.7687 (mp) cc_final: 0.7474 (mm) REVERT: I 57 ILE cc_start: 0.6074 (mt) cc_final: 0.5300 (tt) REVERT: D 68 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7740 (tm-30) REVERT: D 111 ASP cc_start: 0.7924 (t0) cc_final: 0.7688 (t70) REVERT: D 331 LYS cc_start: 0.7698 (tttp) cc_final: 0.7486 (tttp) REVERT: E 72 MET cc_start: 0.8033 (mmm) cc_final: 0.7669 (mtm) REVERT: F 123 ASP cc_start: 0.7096 (m-30) cc_final: 0.6888 (m-30) REVERT: F 132 LEU cc_start: 0.7979 (tp) cc_final: 0.7707 (tm) REVERT: F 210 TYR cc_start: 0.8461 (m-80) cc_final: 0.8198 (m-80) REVERT: C 23 ARG cc_start: 0.8300 (ptp90) cc_final: 0.8099 (ptp90) REVERT: C 29 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 112 TYR cc_start: 0.7150 (t80) cc_final: 0.6818 (t80) REVERT: C 172 PHE cc_start: 0.8627 (m-80) cc_final: 0.8332 (m-80) REVERT: C 241 PHE cc_start: 0.8038 (t80) cc_final: 0.7808 (t80) REVERT: C 331 LYS cc_start: 0.8382 (pttt) cc_final: 0.8062 (pttp) REVERT: G 72 MET cc_start: 0.5265 (mmm) cc_final: 0.5032 (mmm) REVERT: G 186 ASN cc_start: 0.7801 (t0) cc_final: 0.7218 (t0) REVERT: G 230 THR cc_start: 0.8221 (p) cc_final: 0.7960 (p) REVERT: G 278 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7154 (mm-30) REVERT: H 29 GLU cc_start: 0.8239 (mp0) cc_final: 0.7965 (mp0) REVERT: H 132 LEU cc_start: 0.8038 (tp) cc_final: 0.7658 (tp) REVERT: H 242 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7980 (mtpp) REVERT: H 270 THR cc_start: 0.7461 (p) cc_final: 0.7240 (t) outliers start: 11 outliers final: 4 residues processed: 647 average time/residue: 0.6797 time to fit residues: 500.8700 Evaluate side-chains 574 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 569 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain C residue 167 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 105 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS D 18 ASN D 77 GLN E 18 ASN C 195 GLN C 227 GLN G 227 GLN H 26 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.169720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.139968 restraints weight = 33207.472| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.69 r_work: 0.4060 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24832 Z= 0.168 Angle : 0.591 7.952 34043 Z= 0.317 Chirality : 0.042 0.210 3770 Planarity : 0.005 0.064 3967 Dihedral : 18.546 175.844 4421 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.77 % Allowed : 27.00 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2664 helix: 0.76 (0.18), residues: 796 sheet: 0.30 (0.24), residues: 507 loop : -0.92 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 204 TYR 0.017 0.002 TYR F 271 PHE 0.015 0.001 PHE C 273 TRP 0.008 0.001 TRP A 341 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00379 (24832) covalent geometry : angle 0.59052 (34043) hydrogen bonds : bond 0.05188 ( 736) hydrogen bonds : angle 5.89923 ( 2003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 592 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8073 (t0) cc_final: 0.7653 (t0) REVERT: A 255 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6409 (tp) REVERT: A 261 ASP cc_start: 0.7556 (m-30) cc_final: 0.7351 (m-30) REVERT: B 37 ARG cc_start: 0.7597 (tpp80) cc_final: 0.7335 (ttm110) REVERT: B 113 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: B 119 MET cc_start: 0.6534 (tpp) cc_final: 0.6075 (pmm) REVERT: B 129 MET cc_start: 0.8568 (mmm) cc_final: 0.8367 (mmt) REVERT: B 177 ASP cc_start: 0.7148 (m-30) cc_final: 0.6924 (m-30) REVERT: I 74 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6386 (tm-30) REVERT: D 29 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: D 68 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 322 ILE cc_start: 0.7800 (mm) cc_final: 0.7576 (mp) REVERT: E 72 MET cc_start: 0.7835 (mmm) cc_final: 0.7601 (mtm) REVERT: F 210 TYR cc_start: 0.8184 (m-80) cc_final: 0.7982 (m-80) REVERT: C 29 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 112 TYR cc_start: 0.6952 (t80) cc_final: 0.6740 (t80) REVERT: C 172 PHE cc_start: 0.8589 (m-80) cc_final: 0.8356 (m-80) REVERT: G 72 MET cc_start: 0.5127 (mmm) cc_final: 0.4857 (mmm) REVERT: G 119 TYR cc_start: 0.8127 (m-10) cc_final: 0.7919 (m-10) REVERT: H 44 LYS cc_start: 0.7574 (ptpt) cc_final: 0.7236 (ptpt) REVERT: H 206 TYR cc_start: 0.8162 (p90) cc_final: 0.7733 (p90) outliers start: 90 outliers final: 34 residues processed: 648 average time/residue: 0.6448 time to fit residues: 479.0971 Evaluate side-chains 597 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 559 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 274 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 152 optimal weight: 1.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS B 21 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN E 18 ASN F 195 GLN C 26 ASN G 195 GLN G 227 GLN G 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.168132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.138106 restraints weight = 32593.886| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.42 r_work: 0.4046 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24832 Z= 0.253 Angle : 0.621 8.428 34043 Z= 0.332 Chirality : 0.045 0.244 3770 Planarity : 0.005 0.050 3967 Dihedral : 18.355 175.716 4410 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.94 % Allowed : 26.71 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2664 helix: 0.65 (0.18), residues: 797 sheet: 0.36 (0.25), residues: 479 loop : -1.06 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 40 TYR 0.018 0.002 TYR H 125 PHE 0.019 0.002 PHE D 231 TRP 0.012 0.002 TRP G 33 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00592 (24832) covalent geometry : angle 0.62117 (34043) hydrogen bonds : bond 0.05021 ( 736) hydrogen bonds : angle 5.77820 ( 2003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 584 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8139 (t0) cc_final: 0.7809 (t0) REVERT: A 113 GLU cc_start: 0.6810 (mp0) cc_final: 0.6579 (pm20) REVERT: A 176 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7447 (mmm-85) REVERT: A 255 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6444 (tp) REVERT: A 261 ASP cc_start: 0.7552 (m-30) cc_final: 0.7306 (m-30) REVERT: B 37 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7413 (ttm-80) REVERT: B 53 ASN cc_start: 0.7465 (m110) cc_final: 0.7078 (m-40) REVERT: B 113 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: B 119 MET cc_start: 0.6651 (tpp) cc_final: 0.6173 (pmm) REVERT: B 177 ASP cc_start: 0.7155 (m-30) cc_final: 0.6860 (m-30) REVERT: B 231 LYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5493 (mppt) REVERT: I 57 ILE cc_start: 0.7003 (mt) cc_final: 0.6781 (mm) REVERT: D 29 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: D 284 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7350 (ttm110) REVERT: D 315 ASP cc_start: 0.7182 (m-30) cc_final: 0.6972 (m-30) REVERT: E 152 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7865 (ttt-90) REVERT: F 314 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: F 328 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7062 (ttp) REVERT: C 23 ARG cc_start: 0.8282 (ptp90) cc_final: 0.8070 (ttp-110) REVERT: C 29 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 112 TYR cc_start: 0.6914 (t80) cc_final: 0.6710 (t80) REVERT: G 72 MET cc_start: 0.5134 (mmm) cc_final: 0.4843 (mmm) REVERT: G 103 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8188 (mtmm) REVERT: H 44 LYS cc_start: 0.7533 (ptpt) cc_final: 0.7204 (ptpt) REVERT: H 206 TYR cc_start: 0.8130 (p90) cc_final: 0.7760 (p90) outliers start: 118 outliers final: 48 residues processed: 653 average time/residue: 0.6606 time to fit residues: 493.8194 Evaluate side-chains 621 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 565 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 35 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 154 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 99 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN F 140 ASN C 26 ASN C 77 GLN G 195 GLN G 227 GLN H 140 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.140273 restraints weight = 32526.339| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.42 r_work: 0.4073 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24832 Z= 0.163 Angle : 0.566 7.220 34043 Z= 0.303 Chirality : 0.042 0.217 3770 Planarity : 0.005 0.048 3967 Dihedral : 18.297 174.935 4410 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.06 % Allowed : 27.21 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2664 helix: 0.78 (0.18), residues: 801 sheet: 0.37 (0.25), residues: 482 loop : -1.04 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 204 TYR 0.019 0.001 TYR H 125 PHE 0.012 0.001 PHE E 37 TRP 0.007 0.001 TRP G 33 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00376 (24832) covalent geometry : angle 0.56625 (34043) hydrogen bonds : bond 0.04324 ( 736) hydrogen bonds : angle 5.46571 ( 2003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 580 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.1088 (mmp) cc_final: -0.1063 (mmt) REVERT: A 113 GLU cc_start: 0.6763 (mp0) cc_final: 0.6493 (pm20) REVERT: A 176 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7430 (mmm-85) REVERT: A 255 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6456 (tp) REVERT: A 261 ASP cc_start: 0.7550 (m-30) cc_final: 0.7280 (m-30) REVERT: A 320 MET cc_start: 0.6672 (ptp) cc_final: 0.6324 (ptp) REVERT: B 37 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7355 (ttm-80) REVERT: B 53 ASN cc_start: 0.7472 (m110) cc_final: 0.7123 (m-40) REVERT: B 113 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: B 119 MET cc_start: 0.6673 (tpp) cc_final: 0.6282 (pmm) REVERT: B 129 MET cc_start: 0.8483 (mmm) cc_final: 0.8281 (mmt) REVERT: B 177 ASP cc_start: 0.7219 (m-30) cc_final: 0.6947 (m-30) REVERT: I 57 ILE cc_start: 0.7077 (mt) cc_final: 0.6264 (tt) REVERT: D 29 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7311 (mm-30) REVERT: D 284 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7387 (ttm110) REVERT: E 72 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7279 (mtm) REVERT: F 314 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: C 29 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7024 (mm-30) REVERT: G 72 MET cc_start: 0.5107 (mmm) cc_final: 0.4812 (mmm) REVERT: G 103 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (mtmm) REVERT: H 44 LYS cc_start: 0.7527 (ptpt) cc_final: 0.7220 (ptpt) REVERT: H 206 TYR cc_start: 0.8120 (p90) cc_final: 0.7824 (p90) REVERT: H 229 MET cc_start: 0.7692 (tmm) cc_final: 0.7195 (tmm) REVERT: H 307 LYS cc_start: 0.7735 (mptt) cc_final: 0.7503 (mptt) outliers start: 97 outliers final: 52 residues processed: 640 average time/residue: 0.6434 time to fit residues: 472.3821 Evaluate side-chains 613 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 555 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 250 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 231 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 51 ASN A 193 ASN B 21 ASN B 99 GLN B 105 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN F 140 ASN C 77 GLN G 195 GLN G 227 GLN H 18 ASN H 140 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.169241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.139424 restraints weight = 32320.977| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.41 r_work: 0.4061 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24832 Z= 0.203 Angle : 0.578 7.302 34043 Z= 0.310 Chirality : 0.043 0.224 3770 Planarity : 0.005 0.050 3967 Dihedral : 18.209 175.128 4406 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.65 % Allowed : 27.12 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2664 helix: 0.77 (0.18), residues: 803 sheet: 0.38 (0.24), residues: 486 loop : -1.10 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 204 TYR 0.023 0.002 TYR H 125 PHE 0.015 0.001 PHE E 37 TRP 0.010 0.001 TRP G 33 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00475 (24832) covalent geometry : angle 0.57795 (34043) hydrogen bonds : bond 0.04423 ( 736) hydrogen bonds : angle 5.44138 ( 2003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 565 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8276 (mtmm) cc_final: 0.8056 (mtmp) REVERT: A 113 GLU cc_start: 0.6772 (mp0) cc_final: 0.6495 (pm20) REVERT: A 207 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7912 (pttp) REVERT: A 255 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 261 ASP cc_start: 0.7560 (m-30) cc_final: 0.7262 (m-30) REVERT: A 320 MET cc_start: 0.6632 (ptp) cc_final: 0.6269 (ptp) REVERT: B 37 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7135 (ttm-80) REVERT: B 113 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: B 119 MET cc_start: 0.6713 (tpp) cc_final: 0.6291 (pmm) REVERT: I 18 ILE cc_start: 0.7371 (mt) cc_final: 0.7033 (mp) REVERT: I 57 ILE cc_start: 0.7093 (mt) cc_final: 0.6793 (mm) REVERT: D 29 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: D 107 TYR cc_start: 0.7942 (t80) cc_final: 0.7688 (t80) REVERT: D 152 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7735 (ttp80) REVERT: E 72 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7209 (mtm) REVERT: F 314 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: C 29 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7026 (mm-30) REVERT: G 72 MET cc_start: 0.5159 (mmm) cc_final: 0.4839 (mmm) REVERT: G 103 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: H 44 LYS cc_start: 0.7532 (ptpt) cc_final: 0.7225 (ptpt) REVERT: H 206 TYR cc_start: 0.8110 (p90) cc_final: 0.7837 (p90) REVERT: H 229 MET cc_start: 0.7771 (tmm) cc_final: 0.7278 (tmm) REVERT: H 278 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: H 307 LYS cc_start: 0.7746 (mptt) cc_final: 0.7506 (mptt) outliers start: 111 outliers final: 60 residues processed: 634 average time/residue: 0.6361 time to fit residues: 464.1430 Evaluate side-chains 611 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 542 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 278 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 181 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 178 optimal weight: 0.0970 chunk 106 optimal weight: 0.0970 chunk 133 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 51 ASN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 168 ASN B 208 GLN I 29 HIS D 18 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN F 140 ASN C 77 GLN G 227 GLN H 18 ASN H 140 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.171651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.142386 restraints weight = 32965.503| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.42 r_work: 0.4090 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24832 Z= 0.125 Angle : 0.542 8.169 34043 Z= 0.290 Chirality : 0.041 0.198 3770 Planarity : 0.004 0.050 3967 Dihedral : 18.119 173.869 4406 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.77 % Allowed : 27.63 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2664 helix: 0.93 (0.18), residues: 812 sheet: 0.53 (0.25), residues: 475 loop : -1.07 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 204 TYR 0.025 0.001 TYR H 125 PHE 0.012 0.001 PHE C 273 TRP 0.007 0.001 TRP H 149 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00281 (24832) covalent geometry : angle 0.54155 (34043) hydrogen bonds : bond 0.04013 ( 736) hydrogen bonds : angle 5.16076 ( 2003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 560 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6793 (mp0) cc_final: 0.6480 (pm20) REVERT: A 176 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7688 (mmm-85) REVERT: A 255 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6529 (tp) REVERT: A 261 ASP cc_start: 0.7551 (m-30) cc_final: 0.7335 (m-30) REVERT: A 320 MET cc_start: 0.6722 (ptp) cc_final: 0.6338 (ptp) REVERT: B 73 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: B 113 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: B 119 MET cc_start: 0.6624 (tpp) cc_final: 0.6211 (pmm) REVERT: I 18 ILE cc_start: 0.7315 (mt) cc_final: 0.7006 (mp) REVERT: I 54 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7220 (mm) REVERT: I 57 ILE cc_start: 0.6989 (mt) cc_final: 0.6181 (tt) REVERT: D 29 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: D 107 TYR cc_start: 0.7961 (t80) cc_final: 0.7687 (t80) REVERT: D 152 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: E 72 MET cc_start: 0.7882 (mmm) cc_final: 0.7342 (mtm) REVERT: C 29 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7104 (mm-30) REVERT: G 72 MET cc_start: 0.5169 (mmm) cc_final: 0.4847 (mmm) REVERT: H 44 LYS cc_start: 0.7471 (ptpt) cc_final: 0.7200 (ptpt) REVERT: H 206 TYR cc_start: 0.8157 (p90) cc_final: 0.7885 (p90) REVERT: H 229 MET cc_start: 0.7803 (tmm) cc_final: 0.7235 (tmm) REVERT: H 307 LYS cc_start: 0.7667 (mptt) cc_final: 0.7440 (mptt) outliers start: 90 outliers final: 48 residues processed: 617 average time/residue: 0.6219 time to fit residues: 439.3041 Evaluate side-chains 594 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 540 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 308 ASN Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 32 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 184 optimal weight: 0.0040 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN B 208 GLN D 18 ASN D 77 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN E 227 GLN F 140 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN H 140 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.170835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.141586 restraints weight = 32919.232| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.41 r_work: 0.4082 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24832 Z= 0.155 Angle : 0.557 9.795 34043 Z= 0.298 Chirality : 0.041 0.198 3770 Planarity : 0.005 0.050 3967 Dihedral : 18.041 174.001 4406 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.98 % Allowed : 28.05 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2664 helix: 0.94 (0.18), residues: 811 sheet: 0.44 (0.24), residues: 489 loop : -1.06 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 204 TYR 0.028 0.001 TYR H 125 PHE 0.019 0.001 PHE I 158 TRP 0.006 0.001 TRP G 33 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00360 (24832) covalent geometry : angle 0.55680 (34043) hydrogen bonds : bond 0.04069 ( 736) hydrogen bonds : angle 5.15977 ( 2003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 534 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7926 (mtmp) REVERT: A 113 GLU cc_start: 0.6802 (mp0) cc_final: 0.6443 (mp0) REVERT: A 207 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7926 (pttp) REVERT: A 255 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6523 (tp) REVERT: A 261 ASP cc_start: 0.7601 (m-30) cc_final: 0.7367 (m-30) REVERT: A 302 GLU cc_start: 0.5192 (mp0) cc_final: 0.4852 (mp0) REVERT: A 320 MET cc_start: 0.6697 (ptp) cc_final: 0.6307 (ptp) REVERT: B 73 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: B 119 MET cc_start: 0.6676 (tpp) cc_final: 0.6216 (pmm) REVERT: I 54 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7266 (mm) REVERT: D 29 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: D 107 TYR cc_start: 0.7954 (t80) cc_final: 0.7739 (t80) REVERT: D 152 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7412 (ttp80) REVERT: E 72 MET cc_start: 0.7892 (mmm) cc_final: 0.7352 (mtm) REVERT: C 29 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7137 (mm-30) REVERT: G 72 MET cc_start: 0.5201 (mmm) cc_final: 0.4858 (mmm) REVERT: H 44 LYS cc_start: 0.7517 (ptpt) cc_final: 0.7201 (ptpt) REVERT: H 206 TYR cc_start: 0.8187 (p90) cc_final: 0.7913 (p90) REVERT: H 229 MET cc_start: 0.7774 (tmm) cc_final: 0.7219 (tmm) REVERT: H 307 LYS cc_start: 0.7680 (mptt) cc_final: 0.7452 (mptt) outliers start: 95 outliers final: 58 residues processed: 595 average time/residue: 0.6317 time to fit residues: 432.5439 Evaluate side-chains 590 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 526 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 250 optimal weight: 0.0000 chunk 239 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 211 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 99 GLN D 18 ASN D 77 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN E 227 GLN F 140 ASN C 77 GLN C 252 GLN G 77 GLN G 227 GLN H 18 ASN H 140 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.171352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.141945 restraints weight = 32822.761| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.69 r_work: 0.4074 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24832 Z= 0.141 Angle : 0.551 9.142 34043 Z= 0.296 Chirality : 0.041 0.193 3770 Planarity : 0.004 0.053 3967 Dihedral : 17.988 173.665 4406 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.64 % Allowed : 28.71 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2664 helix: 0.99 (0.18), residues: 812 sheet: 0.49 (0.25), residues: 480 loop : -1.04 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 204 TYR 0.026 0.001 TYR H 125 PHE 0.015 0.001 PHE I 158 TRP 0.007 0.001 TRP F 264 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00324 (24832) covalent geometry : angle 0.55143 (34043) hydrogen bonds : bond 0.03981 ( 736) hydrogen bonds : angle 5.08602 ( 2003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 540 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6870 (mp0) cc_final: 0.6528 (pm20) REVERT: A 207 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7933 (pttp) REVERT: A 255 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6575 (tp) REVERT: A 261 ASP cc_start: 0.7637 (m-30) cc_final: 0.7386 (m-30) REVERT: A 302 GLU cc_start: 0.5195 (mp0) cc_final: 0.4799 (mp0) REVERT: A 320 MET cc_start: 0.6742 (ptp) cc_final: 0.6341 (ptp) REVERT: B 73 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: B 119 MET cc_start: 0.6674 (tpp) cc_final: 0.6177 (pmm) REVERT: I 54 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7266 (mm) REVERT: D 29 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: D 107 TYR cc_start: 0.7986 (t80) cc_final: 0.7671 (t80) REVERT: D 152 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7379 (ttp80) REVERT: E 72 MET cc_start: 0.7968 (mmm) cc_final: 0.7461 (mtm) REVERT: C 29 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7211 (mm-30) REVERT: G 72 MET cc_start: 0.5255 (mmm) cc_final: 0.4919 (mmm) REVERT: G 103 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: H 44 LYS cc_start: 0.7525 (ptpt) cc_final: 0.7200 (ptpt) REVERT: H 121 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7963 (mptm) REVERT: H 206 TYR cc_start: 0.8290 (p90) cc_final: 0.8052 (p90) REVERT: H 229 MET cc_start: 0.7802 (tmm) cc_final: 0.7332 (tmm) REVERT: H 307 LYS cc_start: 0.7674 (mptt) cc_final: 0.7413 (mptt) outliers start: 87 outliers final: 55 residues processed: 596 average time/residue: 0.6439 time to fit residues: 441.0088 Evaluate side-chains 595 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 533 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 93 optimal weight: 0.3980 chunk 156 optimal weight: 0.2980 chunk 142 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 138 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 18 ASN D 77 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN F 140 ASN C 77 GLN C 252 GLN G 77 GLN H 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.171792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.142425 restraints weight = 32672.491| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.44 r_work: 0.4091 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24832 Z= 0.144 Angle : 0.562 10.005 34043 Z= 0.299 Chirality : 0.041 0.193 3770 Planarity : 0.005 0.060 3967 Dihedral : 17.942 173.494 4406 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.64 % Allowed : 29.38 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2664 helix: 1.04 (0.18), residues: 812 sheet: 0.47 (0.25), residues: 485 loop : -1.04 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 204 TYR 0.028 0.001 TYR H 125 PHE 0.014 0.001 PHE H 290 TRP 0.005 0.001 TRP H 33 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00335 (24832) covalent geometry : angle 0.56202 (34043) hydrogen bonds : bond 0.03944 ( 736) hydrogen bonds : angle 5.05650 ( 2003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 532 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6809 (mp0) cc_final: 0.6518 (pm20) REVERT: A 207 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (pttp) REVERT: A 255 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6601 (tp) REVERT: A 261 ASP cc_start: 0.7657 (m-30) cc_final: 0.7387 (m-30) REVERT: A 302 GLU cc_start: 0.5248 (mp0) cc_final: 0.4804 (mp0) REVERT: B 73 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: B 119 MET cc_start: 0.6718 (tpp) cc_final: 0.6233 (pmm) REVERT: I 54 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7227 (mm) REVERT: D 107 TYR cc_start: 0.7927 (t80) cc_final: 0.7689 (t80) REVERT: D 152 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7314 (ttp80) REVERT: E 72 MET cc_start: 0.7869 (mmm) cc_final: 0.7355 (mtm) REVERT: C 29 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7137 (mm-30) REVERT: C 320 MET cc_start: 0.7780 (mpp) cc_final: 0.7580 (mmt) REVERT: G 72 MET cc_start: 0.5239 (mmm) cc_final: 0.4896 (mmm) REVERT: G 103 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8199 (mtmm) REVERT: H 44 LYS cc_start: 0.7482 (ptpt) cc_final: 0.7190 (ptpt) REVERT: H 121 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7828 (mptt) REVERT: H 206 TYR cc_start: 0.8241 (p90) cc_final: 0.8010 (p90) REVERT: H 229 MET cc_start: 0.7779 (tmm) cc_final: 0.7328 (tmm) REVERT: H 307 LYS cc_start: 0.7650 (mptt) cc_final: 0.7405 (mptt) outliers start: 87 outliers final: 57 residues processed: 588 average time/residue: 0.6285 time to fit residues: 425.8496 Evaluate side-chains 597 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 534 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 221 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 255 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 99 GLN B 208 GLN D 18 ASN D 77 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN F 140 ASN C 77 GLN C 252 GLN G 77 GLN H 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.171266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.141835 restraints weight = 32637.784| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.44 r_work: 0.4083 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24832 Z= 0.164 Angle : 0.574 9.828 34043 Z= 0.305 Chirality : 0.042 0.220 3770 Planarity : 0.005 0.059 3967 Dihedral : 17.919 173.539 4406 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 29.89 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2664 helix: 1.00 (0.18), residues: 812 sheet: 0.42 (0.25), residues: 487 loop : -1.07 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 152 TYR 0.036 0.001 TYR H 125 PHE 0.024 0.001 PHE G 273 TRP 0.007 0.001 TRP H 33 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00384 (24832) covalent geometry : angle 0.57391 (34043) hydrogen bonds : bond 0.04041 ( 736) hydrogen bonds : angle 5.10128 ( 2003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 538 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.6761 (mp0) cc_final: 0.6465 (pm20) REVERT: A 207 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7916 (pttp) REVERT: A 255 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6618 (tp) REVERT: A 261 ASP cc_start: 0.7653 (m-30) cc_final: 0.7381 (m-30) REVERT: A 281 LYS cc_start: 0.7329 (ttpp) cc_final: 0.6961 (ttpp) REVERT: A 302 GLU cc_start: 0.5281 (mp0) cc_final: 0.4840 (mp0) REVERT: A 320 MET cc_start: 0.6700 (ptp) cc_final: 0.6331 (ptp) REVERT: B 73 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: B 119 MET cc_start: 0.6749 (tpp) cc_final: 0.6298 (pmm) REVERT: I 54 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7195 (mm) REVERT: D 29 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: D 152 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7318 (ttp80) REVERT: E 72 MET cc_start: 0.7875 (mmm) cc_final: 0.7347 (mtm) REVERT: C 29 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7133 (mm-30) REVERT: G 72 MET cc_start: 0.5271 (mmm) cc_final: 0.4927 (mmm) REVERT: G 103 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: H 44 LYS cc_start: 0.7517 (ptpt) cc_final: 0.7216 (ptpt) REVERT: H 206 TYR cc_start: 0.8241 (p90) cc_final: 0.8002 (p90) REVERT: H 229 MET cc_start: 0.7770 (tmm) cc_final: 0.7348 (tmm) REVERT: H 307 LYS cc_start: 0.7645 (mptt) cc_final: 0.7414 (mptt) outliers start: 77 outliers final: 54 residues processed: 589 average time/residue: 0.6283 time to fit residues: 427.3857 Evaluate side-chains 595 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 534 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 305 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 139 PHE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 120 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 202 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 208 GLN D 18 ASN D 77 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 77 GLN F 140 ASN C 77 GLN C 252 GLN G 77 GLN H 18 ASN H 178 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.170864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.141404 restraints weight = 32605.921| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.44 r_work: 0.4078 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24832 Z= 0.175 Angle : 0.582 9.834 34043 Z= 0.309 Chirality : 0.042 0.206 3770 Planarity : 0.005 0.060 3967 Dihedral : 17.912 173.490 4406 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.14 % Allowed : 30.43 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2664 helix: 1.00 (0.18), residues: 812 sheet: 0.37 (0.25), residues: 492 loop : -1.10 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 204 TYR 0.034 0.001 TYR H 125 PHE 0.028 0.001 PHE G 273 TRP 0.008 0.001 TRP H 33 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00412 (24832) covalent geometry : angle 0.58178 (34043) hydrogen bonds : bond 0.04078 ( 736) hydrogen bonds : angle 5.12989 ( 2003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21754.91 seconds wall clock time: 367 minutes 17.65 seconds (22037.65 seconds total)