Starting phenix.real_space_refine on Sat Jul 4 22:42:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeo_39200/07_2026/8yeo_39200.cif" } resolution = 3.44 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= 0.000 sd= 0.001 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 118 5.49 5 S 120 5.16 5 C 15024 2.51 5 N 4065 2.21 5 O 4870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24197 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2010 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "J" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "I" 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: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 12, 'rna3p_pur': 21, 'rna3p_pyr': 10} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2412 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "E" 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: "F" 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: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "H" 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: "N" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 5.01, per 1000 atoms: 0.21 Number of scatterers: 24197 At special positions: 0 Unit cell: (136.85, 145.35, 164.05, 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 120 16.00 P 118 15.00 O 4870 8.00 N 4065 7.00 C 15024 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: 1.70 Conformation dependent library (CDL) restraints added in 975.5 milliseconds 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5106 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 38 sheets defined 33.8% alpha, 19.4% beta 40 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.824A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.563A pdb=" N CYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'J' and resid 2 through 9 Processing helix chain 'J' and resid 15 through 31 removed outlier: 3.882A pdb=" N TYR J 23 " --> pdb=" O LYS J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'J' and resid 87 through 93 Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.861A pdb=" N GLU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 removed outlier: 3.651A pdb=" N ASN J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 179 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 201 through 206 Processing helix chain 'J' and resid 217 through 221 removed outlier: 3.709A pdb=" N GLU J 221 " --> pdb=" O LYS J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.533A pdb=" N ALA J 227 " --> pdb=" O ASN J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 242 removed outlier: 3.530A pdb=" N GLU J 241 " --> pdb=" O ASN J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 267 removed outlier: 4.311A pdb=" N LEU J 258 " --> pdb=" O ALA J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 293 removed outlier: 3.644A pdb=" N PHE J 288 " --> pdb=" O THR J 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 289 " --> pdb=" O VAL J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 316 through 318 No H-bonds generated for 'chain 'J' and resid 316 through 318' Processing helix chain 'J' and resid 326 through 340 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.534A pdb=" N ASP B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.553A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 4.358A pdb=" N ARG B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.196A pdb=" N LYS B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 Processing helix chain 'I' and resid 145 through 152 removed outlier: 6.178A pdb=" N ARG I 150 " --> pdb=" O PHE I 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG I 152 " --> pdb=" O TRP I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.625A pdb=" N GLN I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 259 removed outlier: 3.594A pdb=" N ALA I 257 " --> pdb=" O LYS I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.649A pdb=" N TYR I 271 " --> pdb=" O ASP I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 306 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.536A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.644A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.877A pdb=" N GLU E 68 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.412A pdb=" N MET E 106 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.675A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.512A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 153 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 186 through 201 removed outlier: 3.721A pdb=" N GLN E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.562A pdb=" N ILE E 254 " --> pdb=" O HIS E 250 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.812A 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 removed outlier: 3.766A pdb=" N LEU E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.688A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.644A pdb=" N TRP F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.677A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.651A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 112 through 129 removed outlier: 3.596A pdb=" N TYR G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.506A pdb=" N LEU G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS G 153 " --> pdb=" O ARG G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.654A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.735A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.526A pdb=" N ILE G 305 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 4.033A pdb=" N LEU G 323 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 324 " --> pdb=" O MET G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.914A pdb=" N ARG H 40 " --> pdb=" O PHE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 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 removed outlier: 3.555A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.526A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.618A pdb=" N LEU H 148 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.577A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.644A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.894A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 305 removed outlier: 3.503A pdb=" N ARG H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.520A pdb=" N ILE A 138 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 12 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 144 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.520A pdb=" N ILE A 138 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 12 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 5 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 112 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU A 7 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 110 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU A 9 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 108 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE A 102 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 101 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU A 63 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 103 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 61 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN A 105 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE A 59 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A 107 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 57 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 109 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 55 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU A 111 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 13.960A pdb=" N VAL A 55 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LEU A 162 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 160 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 228 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 221 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 5.967A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 218 removed outlier: 6.120A pdb=" N ASP A 214 " --> pdb=" O LEU J 160 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER J 162 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS A 216 " --> pdb=" O SER J 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA7, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'J' and resid 301 through 305 removed outlier: 3.665A pdb=" N HIS J 304 " --> pdb=" O ILE J 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 42 removed outlier: 3.561A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.006A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 142 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'I' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.815A pdb=" N ILE I 157 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 50 through 57 Processing sheet with id=AB7, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AB8, first strand: chain 'I' and resid 260 through 262 Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.583A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 31 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.999A pdb=" N ILE D 157 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 160 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 35 current: chain 'E' and resid 158 through 164 Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 99 current: chain 'E' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'E' and resid 50 through 57 Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.614A pdb=" N SER F 20 " --> pdb=" O SER F 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AD1, first strand: chain 'F' and resid 50 through 56 Processing sheet with id=AD2, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AD3, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.733A pdb=" N GLY G 327 " --> pdb=" O PHE G 21 " (cutoff:3.500A) 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 30 through 35 current: chain 'G' and resid 158 through 164 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 99 current: chain 'G' and resid 242 through 243 Processing sheet with id=AD6, first strand: chain 'G' and resid 50 through 56 Processing sheet with id=AD7, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.673A 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 Processing sheet with id=AD9, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE1, first strand: chain 'H' and resid 50 through 57 Processing sheet with id=AE2, first strand: chain 'H' and resid 242 through 243 815 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6902 1.34 - 1.46: 5472 1.46 - 1.58: 12164 1.58 - 1.70: 234 1.70 - 1.82: 193 Bond restraints: 24965 Sorted by residual: bond pdb=" C3' C T 39 " pdb=" C2' C T 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" C1' DC T 7 " pdb=" N1 DC T 7 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.54e+00 bond pdb=" C1' C T 44 " pdb=" N1 C T 44 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.46e+00 bond pdb=" C1' C T 39 " pdb=" N1 C T 39 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.76e+00 bond pdb=" C1' DT T 23 " pdb=" N1 DT T 23 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.56e+00 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 33727 2.19 - 4.39: 461 4.39 - 6.58: 44 6.58 - 8.77: 8 8.77 - 10.97: 7 Bond angle restraints: 34247 Sorted by residual: angle pdb=" O4' C T 20 " pdb=" C4' C T 20 " pdb=" C3' C T 20 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" O4' C T 44 " pdb=" C4' C T 44 " pdb=" C3' C T 44 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O4 U C 34 " pdb=" C4 U C 34 " pdb=" C5 U C 34 " ideal model delta sigma weight residual 125.90 123.13 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT T 48 " pdb=" C4 DT T 48 " pdb=" O4 DT T 48 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" O4' DT T 32 " pdb=" C4' DT T 32 " pdb=" C3' DT T 32 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 34242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 14095 34.58 - 69.16: 913 69.16 - 103.74: 61 103.74 - 138.32: 0 138.32 - 172.90: 3 Dihedral angle restraints: 15072 sinusoidal: 7168 harmonic: 7904 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual -128.00 44.90 -172.90 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U C 44 " pdb=" C1' U C 44 " pdb=" N1 U C 44 " pdb=" C2 U C 44 " ideal model delta sinusoidal sigma weight residual 232.00 60.18 171.82 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' G C 43 " pdb=" C1' G C 43 " pdb=" N9 G C 43 " pdb=" C4 G C 43 " ideal model delta sinusoidal sigma weight residual 254.00 172.64 81.36 1 1.70e+01 3.46e-03 2.82e+01 ... (remaining 15069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2550 0.035 - 0.069: 887 0.069 - 0.104: 216 0.104 - 0.139: 123 0.139 - 0.173: 20 Chirality restraints: 3796 Sorted by residual: chirality pdb=" CB ILE B 102 " pdb=" CA ILE B 102 " pdb=" CG1 ILE B 102 " pdb=" CG2 ILE B 102 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C1' A C 22 " pdb=" O4' A C 22 " pdb=" C2' A C 22 " pdb=" N9 A C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 3793 not shown) Planarity restraints: 3967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG J 188 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C ARG J 188 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG J 188 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU J 189 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 182 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO J 183 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 183 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 183 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 328 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C MET E 328 " 0.037 2.00e-02 2.50e+03 pdb=" O MET E 328 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 329 " -0.012 2.00e-02 2.50e+03 ... (remaining 3964 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5400 2.78 - 3.31: 21486 3.31 - 3.84: 41441 3.84 - 4.37: 47699 4.37 - 4.90: 81238 Nonbonded interactions: 197264 Sorted by model distance: nonbonded pdb=" O2' G C 11 " pdb=" O PHE H 21 " model vdw 2.252 3.040 nonbonded pdb=" O2' A C 22 " pdb=" O4' U C 23 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP D 94 " pdb=" OG1 THR D 212 " model vdw 2.263 3.040 nonbonded pdb=" O PHE I 21 " pdb=" O2' G C 5 " model vdw 2.270 3.040 nonbonded pdb=" O ALA F 143 " pdb=" OG SER F 174 " model vdw 2.274 3.040 ... (remaining 197259 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 'D' and resid 12 through 333) selection = (chain 'E' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'F' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'G' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'H' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'I' and (resid 12 through 50 or resid 79 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.140 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.003 0.043 24965 Z= 0.210 Angle : 0.616 10.969 34247 Z= 0.407 Chirality : 0.042 0.173 3796 Planarity : 0.004 0.059 3967 Dihedral : 20.198 172.898 9966 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.42 % Allowed : 30.31 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.16), residues: 2660 helix: -0.07 (0.18), residues: 762 sheet: 0.63 (0.26), residues: 466 loop : -1.42 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 188 TYR 0.009 0.001 TYR B 96 PHE 0.013 0.001 PHE I 273 TRP 0.006 0.001 TRP H 33 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.21 (24965) covalent geometry : angle 0.61584 / 0.41 (34247) hydrogen bonds : bond 0.16885 / 11.53 ( 879) hydrogen bonds : angle 5.79092 / 4.05 ( 2398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.9655 (ppp) cc_final: 0.9418 (ppp) REVERT: J 47 ASN cc_start: 0.8740 (m-40) cc_final: 0.8284 (m110) REVERT: J 95 MET cc_start: 0.8344 (mtp) cc_final: 0.7972 (mtp) REVERT: J 97 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6428 (ppp) REVERT: D 221 MET cc_start: 0.8649 (mmm) cc_final: 0.8335 (mmm) REVERT: D 328 MET cc_start: 0.7297 (tmm) cc_final: 0.7019 (ttp) REVERT: E 18 ASN cc_start: 0.8098 (t0) cc_final: 0.7670 (t0) REVERT: E 120 GLN cc_start: 0.8492 (tp40) cc_final: 0.8249 (tp-100) REVERT: H 229 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8202 (tpp) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 0.1542 time to fit residues: 50.6113 Evaluate side-chains 141 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN J 21 ASN J 29 GLN J 213 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS B 130 HIS I 120 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.028678 restraints weight = 136055.490| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 4.25 r_work: 0.2357 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24965 Z= 0.286 Angle : 0.637 12.148 34247 Z= 0.347 Chirality : 0.042 0.255 3796 Planarity : 0.005 0.053 3967 Dihedral : 18.101 174.264 4489 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.31 % Allowed : 28.63 % Favored : 68.06 % 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: -0.60 (0.16), residues: 2660 helix: 0.62 (0.18), residues: 790 sheet: 0.46 (0.27), residues: 438 loop : -1.29 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.015 0.001 TYR H 169 PHE 0.019 0.002 PHE J 92 TRP 0.012 0.002 TRP H 149 HIS 0.009 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 (24965) covalent geometry : angle 0.63665 / 0.35 (34247) hydrogen bonds : bond 0.04851 / 3.25 ( 879) hydrogen bonds : angle 4.71956 / 3.33 ( 2398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 137 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9119 (tp) REVERT: A 71 ARG cc_start: 0.8800 (mpp80) cc_final: 0.8253 (mpp80) REVERT: A 91 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: A 219 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8779 (tm-30) REVERT: J 1 MET cc_start: 0.9614 (ppp) cc_final: 0.9365 (ppp) REVERT: J 27 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8995 (mm) REVERT: J 47 ASN cc_start: 0.9374 (m-40) cc_final: 0.8701 (m110) REVERT: J 68 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8446 (p0) REVERT: J 95 MET cc_start: 0.8670 (mtp) cc_final: 0.8155 (mtp) REVERT: J 97 MET cc_start: 0.7861 (ppp) cc_final: 0.7629 (ppp) REVERT: J 142 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (ptm-80) REVERT: J 143 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8774 (t) REVERT: J 322 MET cc_start: 0.9192 (mpp) cc_final: 0.8768 (ttm) REVERT: B 22 GLU cc_start: 0.9591 (OUTLIER) cc_final: 0.9208 (pt0) REVERT: B 51 LYS cc_start: 0.9521 (ttpt) cc_final: 0.9275 (tmtt) REVERT: B 104 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.5916 (pp20) REVERT: B 115 MET cc_start: 0.8151 (tmm) cc_final: 0.7852 (tmm) REVERT: D 194 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.9198 (tp-100) REVERT: D 221 MET cc_start: 0.8894 (mmm) cc_final: 0.8627 (mmm) REVERT: E 18 ASN cc_start: 0.9185 (t0) cc_final: 0.8804 (t0) REVERT: E 62 MET cc_start: 0.8985 (mtm) cc_final: 0.8719 (mtm) REVERT: E 120 GLN cc_start: 0.9428 (tp40) cc_final: 0.9129 (tp-100) REVERT: F 106 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8699 (tmm) REVERT: F 120 GLN cc_start: 0.9679 (tt0) cc_final: 0.9162 (tm-30) REVERT: F 253 LYS cc_start: 0.9589 (OUTLIER) cc_final: 0.9229 (tptp) REVERT: H 221 MET cc_start: 0.8579 (mmm) cc_final: 0.8052 (mmm) REVERT: H 229 MET cc_start: 0.9273 (tpp) cc_final: 0.8177 (tpp) outliers start: 79 outliers final: 33 residues processed: 205 average time/residue: 0.1496 time to fit residues: 49.6922 Evaluate side-chains 176 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 162 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 overall best weight: 4.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.028753 restraints weight = 135243.072| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 4.18 r_work: 0.2359 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24965 Z= 0.210 Angle : 0.563 14.231 34247 Z= 0.308 Chirality : 0.041 0.265 3796 Planarity : 0.004 0.052 3967 Dihedral : 18.081 173.591 4478 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.39 % Allowed : 28.05 % Favored : 68.56 % 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: -0.46 (0.16), residues: 2660 helix: 0.81 (0.19), residues: 795 sheet: 0.42 (0.27), residues: 438 loop : -1.21 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 176 TYR 0.019 0.001 TYR H 114 PHE 0.020 0.001 PHE J 92 TRP 0.008 0.001 TRP H 149 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (24965) covalent geometry : angle 0.56341 / 0.31 (34247) hydrogen bonds : bond 0.04284 / 2.86 ( 879) hydrogen bonds : angle 4.49318 / 3.18 ( 2398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 134 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9571 (OUTLIER) cc_final: 0.9127 (tp) REVERT: A 71 ARG cc_start: 0.8770 (mpp80) cc_final: 0.8201 (mpp80) REVERT: A 73 GLN cc_start: 0.9008 (pm20) cc_final: 0.8609 (mp10) REVERT: A 91 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8880 (tptp) REVERT: A 219 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: J 1 MET cc_start: 0.9601 (ppp) cc_final: 0.9312 (ppp) REVERT: J 27 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8996 (mm) REVERT: J 95 MET cc_start: 0.8664 (mtp) cc_final: 0.8045 (mtt) REVERT: J 116 HIS cc_start: 0.9589 (m90) cc_final: 0.9338 (m-70) REVERT: J 142 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8937 (ptm-80) REVERT: J 143 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.8751 (t) REVERT: J 249 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (t) REVERT: J 322 MET cc_start: 0.9217 (mpp) cc_final: 0.8703 (ttp) REVERT: B 51 LYS cc_start: 0.9541 (ttpt) cc_final: 0.9269 (tptp) REVERT: D 103 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8783 (tptt) REVERT: D 106 MET cc_start: 0.8807 (tmm) cc_final: 0.8571 (tmm) REVERT: D 194 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.9187 (tp-100) REVERT: E 18 ASN cc_start: 0.9191 (t0) cc_final: 0.8812 (t0) REVERT: E 120 GLN cc_start: 0.9447 (tp40) cc_final: 0.9138 (tp-100) REVERT: F 106 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8708 (tmm) REVERT: F 120 GLN cc_start: 0.9679 (tt0) cc_final: 0.9174 (tm-30) REVERT: H 229 MET cc_start: 0.9299 (tpp) cc_final: 0.8225 (tpp) REVERT: H 320 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9221 (mpp) outliers start: 81 outliers final: 44 residues processed: 202 average time/residue: 0.1444 time to fit residues: 47.2443 Evaluate side-chains 185 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 142 ARG Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 4 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028856 restraints weight = 133910.425| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 4.16 r_work: 0.2368 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24965 Z= 0.176 Angle : 0.547 11.677 34247 Z= 0.297 Chirality : 0.041 0.271 3796 Planarity : 0.004 0.051 3967 Dihedral : 18.097 173.149 4478 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.77 % Allowed : 27.54 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.17), residues: 2660 helix: 0.96 (0.19), residues: 796 sheet: 0.25 (0.27), residues: 448 loop : -1.14 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 176 TYR 0.021 0.001 TYR H 114 PHE 0.021 0.001 PHE J 92 TRP 0.007 0.001 TRP F 264 HIS 0.002 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (24965) covalent geometry : angle 0.54695 / 0.30 (34247) hydrogen bonds : bond 0.03918 / 2.61 ( 879) hydrogen bonds : angle 4.37786 / 3.09 ( 2398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 133 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9036 (mmp) cc_final: 0.8636 (tpp) REVERT: A 6 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9113 (tp) REVERT: A 14 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: A 71 ARG cc_start: 0.8773 (mpp80) cc_final: 0.8284 (mtm-85) REVERT: A 73 GLN cc_start: 0.9023 (pm20) cc_final: 0.7659 (pm20) REVERT: A 91 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8909 (tptp) REVERT: A 219 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: J 1 MET cc_start: 0.9615 (ppp) cc_final: 0.9318 (ppp) REVERT: J 27 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9015 (mm) REVERT: J 95 MET cc_start: 0.8671 (mtp) cc_final: 0.8065 (mtt) REVERT: J 143 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.8889 (t) REVERT: J 249 CYS cc_start: 0.8281 (t) cc_final: 0.8050 (t) REVERT: J 322 MET cc_start: 0.9281 (mpp) cc_final: 0.8731 (ttp) REVERT: B 51 LYS cc_start: 0.9538 (ttpt) cc_final: 0.9263 (tptp) REVERT: B 104 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6226 (pp20) REVERT: I 209 ILE cc_start: 0.9625 (pt) cc_final: 0.9164 (mm) REVERT: D 84 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8796 (tt) REVERT: D 103 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8751 (tptt) REVERT: D 106 MET cc_start: 0.8789 (tmm) cc_final: 0.8579 (tmm) REVERT: D 194 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9173 (tp-100) REVERT: D 221 MET cc_start: 0.8712 (mmm) cc_final: 0.8305 (mmm) REVERT: D 252 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: D 328 MET cc_start: 0.8470 (tmm) cc_final: 0.7952 (ttp) REVERT: E 18 ASN cc_start: 0.9171 (t0) cc_final: 0.8779 (t0) REVERT: E 106 MET cc_start: 0.8629 (ttp) cc_final: 0.8300 (tmm) REVERT: E 120 GLN cc_start: 0.9421 (tp40) cc_final: 0.9080 (tp-100) REVERT: F 23 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8765 (ptp90) REVERT: F 45 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8933 (mm) REVERT: F 106 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8733 (tmm) REVERT: F 120 GLN cc_start: 0.9683 (tt0) cc_final: 0.9189 (tm-30) REVERT: F 221 MET cc_start: 0.8732 (mmm) cc_final: 0.8325 (mmm) REVERT: F 253 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9289 (tptp) REVERT: H 221 MET cc_start: 0.8769 (mmm) cc_final: 0.8284 (mmm) REVERT: H 229 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8298 (tpp) REVERT: H 320 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9226 (mpp) outliers start: 90 outliers final: 48 residues processed: 211 average time/residue: 0.1462 time to fit residues: 50.2134 Evaluate side-chains 198 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 161 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS I 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.029239 restraints weight = 132952.080| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 4.05 r_work: 0.2406 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24965 Z= 0.166 Angle : 0.536 13.171 34247 Z= 0.291 Chirality : 0.040 0.274 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.062 172.977 4478 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.52 % Allowed : 27.84 % Favored : 68.65 % 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: -0.30 (0.17), residues: 2660 helix: 1.05 (0.19), residues: 796 sheet: 0.41 (0.27), residues: 438 loop : -1.15 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 115 TYR 0.018 0.001 TYR H 114 PHE 0.022 0.001 PHE J 92 TRP 0.007 0.001 TRP F 264 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (24965) covalent geometry : angle 0.53567 / 0.29 (34247) hydrogen bonds : bond 0.03784 / 2.52 ( 879) hydrogen bonds : angle 4.31831 / 3.05 ( 2398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 134 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8893 (mmp) cc_final: 0.8515 (tpp) REVERT: A 6 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9100 (tp) REVERT: A 14 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8600 (mp0) REVERT: A 71 ARG cc_start: 0.8738 (mpp80) cc_final: 0.8284 (mpp80) REVERT: A 91 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8963 (tptp) REVERT: A 140 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8962 (ttm110) REVERT: A 219 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: J 1 MET cc_start: 0.9649 (ppp) cc_final: 0.9320 (ppp) REVERT: J 95 MET cc_start: 0.8775 (mtp) cc_final: 0.8124 (mtt) REVERT: J 116 HIS cc_start: 0.9575 (m90) cc_final: 0.9278 (m-70) REVERT: J 143 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9383 (m) REVERT: J 249 CYS cc_start: 0.8197 (t) cc_final: 0.7962 (t) REVERT: J 322 MET cc_start: 0.9314 (mpp) cc_final: 0.8755 (ttp) REVERT: B 51 LYS cc_start: 0.9466 (ttpt) cc_final: 0.9214 (tptp) REVERT: B 104 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6201 (pp20) REVERT: B 123 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5516 (pp) REVERT: I 209 ILE cc_start: 0.9581 (pt) cc_final: 0.9131 (mm) REVERT: I 228 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: I 328 MET cc_start: 0.8839 (mtt) cc_final: 0.8593 (mtt) REVERT: D 23 ARG cc_start: 0.9438 (OUTLIER) cc_final: 0.9049 (ptp-170) REVERT: D 84 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8947 (tt) REVERT: D 106 MET cc_start: 0.8937 (tmm) cc_final: 0.8699 (tmm) REVERT: D 194 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9070 (tp-100) REVERT: D 221 MET cc_start: 0.8775 (mmm) cc_final: 0.8490 (mmm) REVERT: D 238 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8278 (pttm) REVERT: D 300 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9188 (mp) REVERT: E 18 ASN cc_start: 0.9130 (t0) cc_final: 0.8715 (t0) REVERT: E 120 GLN cc_start: 0.9357 (tp40) cc_final: 0.9015 (tp-100) REVERT: F 23 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8828 (ptp90) REVERT: F 45 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9043 (mm) REVERT: F 106 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8732 (tmm) REVERT: F 120 GLN cc_start: 0.9599 (tt0) cc_final: 0.9171 (tm-30) REVERT: H 221 MET cc_start: 0.8952 (mmm) cc_final: 0.8474 (mmm) REVERT: H 229 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8487 (tpp) REVERT: H 242 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9192 (mtpp) REVERT: H 320 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.9229 (mpp) outliers start: 84 outliers final: 49 residues processed: 209 average time/residue: 0.1586 time to fit residues: 52.9346 Evaluate side-chains 198 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 GLU Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 320 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 246 optimal weight: 0.0370 chunk 250 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN B 120 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.042407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.029875 restraints weight = 131928.375| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 4.06 r_work: 0.2437 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24965 Z= 0.108 Angle : 0.520 13.871 34247 Z= 0.280 Chirality : 0.040 0.429 3796 Planarity : 0.003 0.049 3967 Dihedral : 18.021 172.806 4477 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.64 % Allowed : 28.30 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.17), residues: 2660 helix: 1.08 (0.19), residues: 799 sheet: 0.60 (0.28), residues: 402 loop : -1.14 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.017 0.001 TYR H 114 PHE 0.022 0.001 PHE J 92 TRP 0.007 0.001 TRP I 264 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (24965) covalent geometry : angle 0.52024 / 0.28 (34247) hydrogen bonds : bond 0.03517 / 2.36 ( 879) hydrogen bonds : angle 4.17399 / 2.96 ( 2398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8870 (mmp) cc_final: 0.8489 (tpp) REVERT: A 6 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9095 (tp) REVERT: A 14 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: A 63 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8646 (tm-30) REVERT: A 91 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8929 (tptp) REVERT: A 140 ARG cc_start: 0.9160 (ttm-80) cc_final: 0.8921 (ttm110) REVERT: A 219 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8756 (tm-30) REVERT: A 247 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9163 (pm20) REVERT: J 1 MET cc_start: 0.9657 (ppp) cc_final: 0.9335 (ppp) REVERT: J 95 MET cc_start: 0.8790 (mtp) cc_final: 0.8136 (mtt) REVERT: J 143 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.8944 (t) REVERT: J 249 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8063 (t) REVERT: J 322 MET cc_start: 0.9340 (mpp) cc_final: 0.8771 (ttp) REVERT: B 51 LYS cc_start: 0.9422 (ttpt) cc_final: 0.9094 (tmmt) REVERT: B 104 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6169 (pp20) REVERT: B 123 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5466 (pp) REVERT: I 21 PHE cc_start: 0.9181 (m-80) cc_final: 0.8741 (m-80) REVERT: I 209 ILE cc_start: 0.9575 (pt) cc_final: 0.9137 (mm) REVERT: D 84 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9009 (tt) REVERT: D 106 MET cc_start: 0.8918 (tmm) cc_final: 0.8716 (tmm) REVERT: D 194 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.9029 (tp-100) REVERT: D 221 MET cc_start: 0.8799 (mmm) cc_final: 0.8358 (mmm) REVERT: D 238 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8300 (pttm) REVERT: D 300 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9168 (mp) REVERT: E 18 ASN cc_start: 0.9004 (t0) cc_final: 0.8557 (t0) REVERT: E 120 GLN cc_start: 0.9360 (tp40) cc_final: 0.8969 (tp-100) REVERT: F 23 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8803 (ptp90) REVERT: F 45 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9054 (mm) REVERT: F 106 MET cc_start: 0.9195 (mmm) cc_final: 0.8645 (tmm) REVERT: F 120 GLN cc_start: 0.9604 (tt0) cc_final: 0.9164 (tm-30) REVERT: H 106 MET cc_start: 0.8878 (tmm) cc_final: 0.8408 (tmm) REVERT: H 221 MET cc_start: 0.8940 (mmm) cc_final: 0.8413 (mmm) REVERT: H 229 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8471 (tpp) REVERT: H 242 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9212 (mtpp) REVERT: H 320 MET cc_start: 0.9445 (mpp) cc_final: 0.9186 (mpp) outliers start: 63 outliers final: 38 residues processed: 194 average time/residue: 0.1674 time to fit residues: 52.4829 Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 36 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027586 restraints weight = 137527.942| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 3.99 r_work: 0.2347 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 24965 Z= 0.380 Angle : 0.715 15.380 34247 Z= 0.376 Chirality : 0.044 0.297 3796 Planarity : 0.005 0.053 3967 Dihedral : 18.116 172.559 4477 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.14 % Allowed : 27.12 % 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: -0.52 (0.17), residues: 2660 helix: 0.86 (0.19), residues: 797 sheet: 0.08 (0.26), residues: 458 loop : -1.22 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 146 TYR 0.021 0.002 TYR H 169 PHE 0.018 0.002 PHE J 92 TRP 0.008 0.002 TRP F 264 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.38 (24965) covalent geometry : angle 0.71517 / 0.38 (34247) hydrogen bonds : bond 0.04703 / 3.09 ( 879) hydrogen bonds : angle 4.74793 / 3.35 ( 2398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 126 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9168 (tp) REVERT: A 14 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: A 63 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 91 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8852 (tptp) REVERT: A 140 ARG cc_start: 0.9218 (ttm-80) cc_final: 0.8951 (ttm110) REVERT: A 219 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8879 (tm-30) REVERT: A 247 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9223 (pm20) REVERT: J 1 MET cc_start: 0.9636 (ppp) cc_final: 0.9304 (ppp) REVERT: J 95 MET cc_start: 0.8726 (mtp) cc_final: 0.8109 (mtt) REVERT: J 322 MET cc_start: 0.9347 (mpp) cc_final: 0.8739 (ttp) REVERT: B 51 LYS cc_start: 0.9533 (ttpt) cc_final: 0.9253 (tptp) REVERT: B 104 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: I 69 LYS cc_start: 0.9465 (tppt) cc_final: 0.9260 (mtmm) REVERT: I 228 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: D 194 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9191 (tp-100) REVERT: D 238 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8304 (pttm) REVERT: D 300 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9178 (mp) REVERT: D 328 MET cc_start: 0.8670 (tmm) cc_final: 0.8223 (ttp) REVERT: E 18 ASN cc_start: 0.9148 (t0) cc_final: 0.8738 (t0) REVERT: E 120 GLN cc_start: 0.9373 (tp40) cc_final: 0.9091 (tp-100) REVERT: F 45 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9027 (mm) REVERT: F 106 MET cc_start: 0.9210 (mmm) cc_final: 0.8523 (tmm) REVERT: F 120 GLN cc_start: 0.9650 (tt0) cc_final: 0.9199 (tm-30) REVERT: G 229 MET cc_start: 0.9114 (tpp) cc_final: 0.8679 (tpp) REVERT: H 106 MET cc_start: 0.9049 (tmm) cc_final: 0.8649 (tmm) REVERT: H 229 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.8527 (tpp) REVERT: H 242 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9189 (mtpp) REVERT: H 284 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.9084 (ttm110) REVERT: H 304 MET cc_start: 0.9697 (tpp) cc_final: 0.9392 (tpp) outliers start: 99 outliers final: 62 residues processed: 215 average time/residue: 0.1661 time to fit residues: 57.2876 Evaluate side-chains 194 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 118 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 GLU Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 319 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028467 restraints weight = 135438.324| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 3.95 r_work: 0.2380 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 24965 Z= 0.214 Angle : 0.601 15.681 34247 Z= 0.318 Chirality : 0.041 0.300 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.149 172.276 4477 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.35 % Allowed : 27.71 % Favored : 68.94 % 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 (0.17), residues: 2660 helix: 1.01 (0.19), residues: 798 sheet: 0.07 (0.26), residues: 450 loop : -1.17 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 146 TYR 0.024 0.001 TYR A 142 PHE 0.020 0.001 PHE J 92 TRP 0.008 0.001 TRP G 264 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (24965) covalent geometry : angle 0.60093 / 0.32 (34247) hydrogen bonds : bond 0.04022 / 2.69 ( 879) hydrogen bonds : angle 4.48342 / 3.17 ( 2398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 132 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9125 (tp) REVERT: A 63 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8699 (tm-30) REVERT: A 91 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8942 (tptp) REVERT: A 140 ARG cc_start: 0.9187 (ttm-80) cc_final: 0.8804 (ttm110) REVERT: A 219 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: A 247 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9209 (pm20) REVERT: J 1 MET cc_start: 0.9616 (ppp) cc_final: 0.9310 (ppp) REVERT: J 95 MET cc_start: 0.8753 (mtp) cc_final: 0.8128 (mtt) REVERT: J 322 MET cc_start: 0.9358 (mpp) cc_final: 0.8759 (ttp) REVERT: B 22 GLU cc_start: 0.9531 (OUTLIER) cc_final: 0.9313 (tp30) REVERT: B 51 LYS cc_start: 0.9512 (ttpt) cc_final: 0.9254 (tptp) REVERT: B 104 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6692 (pp20) REVERT: I 228 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: D 84 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8956 (tt) REVERT: D 194 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9100 (tp-100) REVERT: D 221 MET cc_start: 0.8725 (mmm) cc_final: 0.8254 (mmm) REVERT: D 238 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8327 (pttm) REVERT: D 300 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9202 (mp) REVERT: E 18 ASN cc_start: 0.9063 (t0) cc_final: 0.8620 (t0) REVERT: E 120 GLN cc_start: 0.9366 (tp40) cc_final: 0.9046 (tp-100) REVERT: F 45 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9046 (mm) REVERT: F 106 MET cc_start: 0.9224 (mmm) cc_final: 0.8643 (tmm) REVERT: F 120 GLN cc_start: 0.9622 (tt0) cc_final: 0.9138 (tm-30) REVERT: F 309 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: F 333 GLN cc_start: 0.8340 (pt0) cc_final: 0.8044 (pt0) REVERT: G 229 MET cc_start: 0.9015 (tpp) cc_final: 0.8552 (tpp) REVERT: H 106 MET cc_start: 0.9076 (tmm) cc_final: 0.8605 (tmm) REVERT: H 229 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8424 (tpp) REVERT: H 304 MET cc_start: 0.9683 (tpp) cc_final: 0.9412 (tpp) REVERT: H 309 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8190 (pt0) outliers start: 80 outliers final: 59 residues processed: 202 average time/residue: 0.1525 time to fit residues: 50.0437 Evaluate side-chains 201 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 127 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 228 GLU Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 246 optimal weight: 0.0770 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.029158 restraints weight = 135057.500| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 4.00 r_work: 0.2406 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24965 Z= 0.143 Angle : 0.565 14.739 34247 Z= 0.300 Chirality : 0.040 0.296 3796 Planarity : 0.004 0.054 3967 Dihedral : 18.130 172.423 4477 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.85 % Allowed : 28.42 % 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: -0.29 (0.17), residues: 2660 helix: 1.11 (0.19), residues: 799 sheet: 0.33 (0.27), residues: 438 loop : -1.14 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 146 TYR 0.018 0.001 TYR A 142 PHE 0.018 0.001 PHE J 92 TRP 0.008 0.001 TRP I 264 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24965) covalent geometry : angle 0.56486 / 0.30 (34247) hydrogen bonds : bond 0.03640 / 2.45 ( 879) hydrogen bonds : angle 4.28976 / 3.05 ( 2398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 132 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9089 (tp) REVERT: A 63 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 71 ARG cc_start: 0.8929 (mpp80) cc_final: 0.8226 (mpp80) REVERT: A 91 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8929 (tptp) REVERT: A 140 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8704 (ttm110) REVERT: A 219 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8779 (tm-30) REVERT: A 247 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9139 (tm-30) REVERT: J 1 MET cc_start: 0.9621 (ppp) cc_final: 0.9349 (ppp) REVERT: J 95 MET cc_start: 0.8771 (mtp) cc_final: 0.8131 (mtt) REVERT: J 322 MET cc_start: 0.9348 (mpp) cc_final: 0.8729 (ttp) REVERT: B 22 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.9215 (pt0) REVERT: B 51 LYS cc_start: 0.9491 (ttpt) cc_final: 0.9218 (tptp) REVERT: B 104 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6739 (pp20) REVERT: B 123 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6024 (pp) REVERT: D 84 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9003 (tt) REVERT: D 194 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.9074 (tp-100) REVERT: D 221 MET cc_start: 0.8740 (mmm) cc_final: 0.8242 (mmm) REVERT: D 238 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8353 (pttm) REVERT: D 300 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9193 (mp) REVERT: E 18 ASN cc_start: 0.9010 (t0) cc_final: 0.8594 (t0) REVERT: E 120 GLN cc_start: 0.9343 (tp40) cc_final: 0.8960 (tp-100) REVERT: F 45 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9050 (mm) REVERT: F 106 MET cc_start: 0.9208 (mmm) cc_final: 0.8698 (tmm) REVERT: F 120 GLN cc_start: 0.9605 (tt0) cc_final: 0.9153 (tm-30) REVERT: F 333 GLN cc_start: 0.8267 (pt0) cc_final: 0.7992 (pt0) REVERT: G 229 MET cc_start: 0.8970 (tpp) cc_final: 0.8486 (tpp) REVERT: H 106 MET cc_start: 0.9097 (tmm) cc_final: 0.8627 (tmm) REVERT: H 221 MET cc_start: 0.8973 (mmm) cc_final: 0.8568 (mmm) REVERT: H 229 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8466 (tpp) REVERT: H 304 MET cc_start: 0.9695 (tpp) cc_final: 0.9418 (tpp) outliers start: 68 outliers final: 50 residues processed: 192 average time/residue: 0.1556 time to fit residues: 48.7317 Evaluate side-chains 192 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 129 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 230 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.041123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.028838 restraints weight = 135350.552| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.98 r_work: 0.2399 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24965 Z= 0.187 Angle : 0.593 14.444 34247 Z= 0.310 Chirality : 0.041 0.355 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.132 172.555 4477 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.06 % Allowed : 28.42 % Favored : 68.52 % 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 (0.17), residues: 2660 helix: 1.12 (0.19), residues: 798 sheet: 0.26 (0.26), residues: 448 loop : -1.11 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.016 0.001 TYR A 142 PHE 0.018 0.001 PHE J 92 TRP 0.007 0.001 TRP I 264 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (24965) covalent geometry : angle 0.59279 / 0.31 (34247) hydrogen bonds : bond 0.03803 / 2.54 ( 879) hydrogen bonds : angle 4.34127 / 3.09 ( 2398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 130 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 63 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 71 ARG cc_start: 0.8918 (mpp80) cc_final: 0.8217 (mpp80) REVERT: A 91 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8938 (tptp) REVERT: A 140 ARG cc_start: 0.9109 (ttm-80) cc_final: 0.8346 (ttm170) REVERT: A 219 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: A 247 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9113 (tm-30) REVERT: J 1 MET cc_start: 0.9627 (ppp) cc_final: 0.9406 (ppp) REVERT: J 95 MET cc_start: 0.8883 (mtp) cc_final: 0.8270 (mtt) REVERT: J 322 MET cc_start: 0.9352 (mpp) cc_final: 0.8735 (ttp) REVERT: B 51 LYS cc_start: 0.9472 (ttpt) cc_final: 0.9242 (tmtt) REVERT: B 104 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: B 123 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6114 (pp) REVERT: I 228 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: D 84 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8965 (tt) REVERT: D 194 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9105 (tp-100) REVERT: D 221 MET cc_start: 0.8745 (mmm) cc_final: 0.8223 (mmm) REVERT: D 238 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8347 (pttm) REVERT: D 300 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9196 (mp) REVERT: E 18 ASN cc_start: 0.9044 (t0) cc_final: 0.8609 (t0) REVERT: E 120 GLN cc_start: 0.9325 (tp40) cc_final: 0.8982 (tp-100) REVERT: F 45 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9039 (mm) REVERT: F 106 MET cc_start: 0.9216 (mmm) cc_final: 0.8689 (tmm) REVERT: F 120 GLN cc_start: 0.9622 (tt0) cc_final: 0.9167 (tm-30) REVERT: F 309 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: F 333 GLN cc_start: 0.8276 (pt0) cc_final: 0.8009 (pt0) REVERT: G 229 MET cc_start: 0.8995 (tpp) cc_final: 0.8532 (tpp) REVERT: H 106 MET cc_start: 0.9129 (tmm) cc_final: 0.8817 (tmm) REVERT: H 229 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8508 (tpp) REVERT: H 304 MET cc_start: 0.9680 (tpp) cc_final: 0.9389 (tpp) REVERT: H 309 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8259 (pt0) outliers start: 73 outliers final: 54 residues processed: 195 average time/residue: 0.1568 time to fit residues: 50.3322 Evaluate side-chains 198 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 129 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 GLU Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 122 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS I 256 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029446 restraints weight = 134053.114| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 4.00 r_work: 0.2421 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24965 Z= 0.127 Angle : 0.568 14.380 34247 Z= 0.298 Chirality : 0.040 0.294 3796 Planarity : 0.003 0.054 3967 Dihedral : 18.112 172.489 4477 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.72 % Allowed : 28.76 % Favored : 68.52 % 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: -0.21 (0.17), residues: 2660 helix: 1.18 (0.19), residues: 798 sheet: 0.37 (0.26), residues: 443 loop : -1.11 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.018 0.001 TYR A 142 PHE 0.020 0.001 PHE J 92 TRP 0.008 0.001 TRP I 264 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24965) covalent geometry : angle 0.56752 / 0.30 (34247) hydrogen bonds : bond 0.03564 / 2.41 ( 879) hydrogen bonds : angle 4.22362 / 3.00 ( 2398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5410.17 seconds wall clock time: 94 minutes 4.64 seconds (5644.64 seconds total)