Starting phenix.real_space_refine on Fri Aug 7 20:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeo_39200/08_2026/8yeo_39200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeo_39200/08_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_39200/08_2026/8yeo_39200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeo_39200/08_2026/8yeo_39200.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeo_39200/08_2026/8yeo_39200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeo_39200/08_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-2.2rc3-6140/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: 4.93, per 1000 atoms: 0.20 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: 1.88 Conformation dependent library (CDL) restraints added in 868.2 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: 2.92 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: 4.56 Time building geometry restraints manager: 2.49 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: 33641 2.19 - 4.39: 547 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' A C 25 " pdb=" C1' A C 25 " pdb=" N9 A C 25 " ideal model delta sigma weight residual 108.20 111.91 -3.71 8.00e-01 1.56e+00 2.15e+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 ... (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 - 0.036: 2567 0.036 - 0.073: 854 0.073 - 0.109: 230 0.109 - 0.146: 129 0.146 - 0.182: 16 Chirality restraints: 3796 Sorted by residual: 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 2.47 2.29 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" C1' G C 48 " pdb=" O4' G C 48 " pdb=" C2' G C 48 " pdb=" N9 G C 48 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.63e-01 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 ... (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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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= 0.213 Angle : 0.634 10.969 34247 Z= 0.432 Chirality : 0.044 0.182 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 0.00305 / 0.21 (24965) covalent geometry : angle 0.63435 / 0.43 (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 : 0.831 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: 0.8283 (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: 0.6429 (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: 0.1537 time to fit residues: 50.8601 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 : 0.918 ------------------------------------------------------------------------------- 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: 30.0000 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 F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.028478 restraints weight = 136156.492| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 4.29 r_work: 0.2350 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 24965 Z= 0.288 Angle : 0.653 12.235 34247 Z= 0.353 Chirality : 0.043 0.252 3796 Planarity : 0.005 0.052 3967 Dihedral : 18.054 174.210 4489 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.60 % Allowed : 28.71 % Favored : 67.69 % 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: -0.60 (0.16), residues: 2660 helix: 0.60 (0.18), residues: 790 sheet: 0.60 (0.27), residues: 421 loop : -1.31 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 188 TYR 0.016 0.001 TYR H 114 PHE 0.019 0.002 PHE H 329 TRP 0.012 0.002 TRP H 149 HIS 0.007 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.29 (24965) covalent geometry : angle 0.65341 / 0.35 (34247) hydrogen bonds : bond 0.04761 / 3.19 ( 879) hydrogen bonds : angle 4.71753 / 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 224 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 138 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9139 (tp) REVERT: A 51 ARG cc_start: 0.9338 (ptp-110) cc_final: 0.8638 (tmm-80) REVERT: A 71 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8251 (mpp80) REVERT: A 91 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: A 219 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: J 1 MET cc_start: 0.9598 (ppp) cc_final: 0.9380 (ppp) REVERT: J 27 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9001 (mm) REVERT: J 47 ASN cc_start: 0.9387 (m-40) cc_final: 0.8725 (m110) REVERT: J 68 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8460 (p0) REVERT: J 95 MET cc_start: 0.8666 (mtp) cc_final: 0.8151 (mtp) REVERT: J 97 MET cc_start: 0.7880 (ppp) cc_final: 0.7660 (ppp) REVERT: J 116 HIS cc_start: 0.9582 (m90) cc_final: 0.9341 (m-70) REVERT: J 142 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8932 (ptm-80) REVERT: J 143 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8771 (t) REVERT: J 322 MET cc_start: 0.9227 (mpp) cc_final: 0.8799 (ttm) REVERT: B 22 GLU cc_start: 0.9603 (OUTLIER) cc_final: 0.9211 (pt0) REVERT: B 51 LYS cc_start: 0.9538 (ttpt) cc_final: 0.9296 (tmtt) REVERT: B 104 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.5989 (pp20) REVERT: B 115 MET cc_start: 0.8160 (tmm) cc_final: 0.7914 (tmm) REVERT: D 194 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9196 (tp-100) REVERT: D 221 MET cc_start: 0.8902 (mmm) cc_final: 0.8684 (mmm) REVERT: E 18 ASN cc_start: 0.9208 (t0) cc_final: 0.8835 (t0) REVERT: E 62 MET cc_start: 0.9003 (mtm) cc_final: 0.8744 (mtm) REVERT: E 120 GLN cc_start: 0.9432 (tp40) cc_final: 0.9161 (tp-100) REVERT: F 106 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8744 (tmm) REVERT: F 120 GLN cc_start: 0.9683 (tt0) cc_final: 0.9167 (tm-30) REVERT: F 253 LYS cc_start: 0.9595 (OUTLIER) cc_final: 0.9255 (tptp) REVERT: H 221 MET cc_start: 0.8632 (mmm) cc_final: 0.8089 (mmm) REVERT: H 229 MET cc_start: 0.9304 (tpp) cc_final: 0.8226 (tpp) outliers start: 86 outliers final: 35 residues processed: 211 average time/residue: 0.1489 time to fit residues: 50.8844 Evaluate side-chains 178 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 293 ASP Chi-restraints excluded: chain I residue 304 MET 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 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 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 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 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 272 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 162 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 HIS ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS I 120 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.027875 restraints weight = 136621.462| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 4.21 r_work: 0.2328 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24965 Z= 0.293 Angle : 0.635 14.888 34247 Z= 0.341 Chirality : 0.043 0.242 3796 Planarity : 0.004 0.055 3967 Dihedral : 18.059 173.799 4478 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.23 % Allowed : 27.75 % Favored : 68.02 % 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: -0.57 (0.16), residues: 2660 helix: 0.73 (0.19), residues: 795 sheet: 0.15 (0.26), residues: 450 loop : -1.22 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.020 0.001 TYR H 114 PHE 0.013 0.001 PHE H 329 TRP 0.008 0.001 TRP H 149 HIS 0.004 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.29 (24965) covalent geometry : angle 0.63450 / 0.34 (34247) hydrogen bonds : bond 0.04601 / 3.05 ( 879) hydrogen bonds : angle 4.66393 / 3.30 ( 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 232 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 131 time to evaluate : 0.863 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: 0.9587 (OUTLIER) cc_final: 0.9154 (tp) REVERT: A 14 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8625 (mp0) REVERT: A 71 ARG cc_start: 0.8755 (mpp80) cc_final: 0.8157 (mpp80) REVERT: A 73 GLN cc_start: 0.9018 (pm20) cc_final: 0.8593 (mp10) REVERT: A 91 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8824 (tptp) REVERT: A 219 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8830 (tm-30) REVERT: J 1 MET cc_start: 0.9597 (ppp) cc_final: 0.9308 (ppp) REVERT: J 27 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (mm) REVERT: J 68 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8526 (p0) REVERT: J 95 MET cc_start: 0.8672 (mtp) cc_final: 0.8063 (mtt) REVERT: J 142 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8935 (ptm-80) REVERT: J 143 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.8754 (t) REVERT: J 249 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8093 (t) REVERT: J 322 MET cc_start: 0.9247 (mpp) cc_final: 0.8742 (ttp) REVERT: B 51 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9298 (tptp) REVERT: B 104 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6221 (pp20) REVERT: I 120 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9157 (pp30) REVERT: I 209 ILE cc_start: 0.9634 (pt) cc_final: 0.9154 (mm) REVERT: D 23 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.9066 (ptp-170) REVERT: D 103 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8816 (tptt) REVERT: D 106 MET cc_start: 0.8835 (tmm) cc_final: 0.8615 (tmm) REVERT: D 194 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9171 (tp-100) REVERT: D 221 MET cc_start: 0.8907 (mmm) cc_final: 0.8707 (mmm) REVERT: D 252 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: D 300 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9303 (mp) REVERT: E 18 ASN cc_start: 0.9244 (t0) cc_final: 0.8892 (t0) REVERT: E 120 GLN cc_start: 0.9448 (tp40) cc_final: 0.9162 (tp-100) REVERT: F 106 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8803 (tmm) REVERT: F 120 GLN cc_start: 0.9682 (tt0) cc_final: 0.9180 (tm-30) REVERT: F 253 LYS cc_start: 0.9660 (OUTLIER) cc_final: 0.9226 (tptp) REVERT: H 229 MET cc_start: 0.9379 (tpp) cc_final: 0.8344 (tpp) REVERT: H 320 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9248 (mpp) outliers start: 101 outliers final: 56 residues processed: 219 average time/residue: 0.1531 time to fit residues: 54.2843 Evaluate side-chains 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 125 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 221 ILE 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 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 B residue 104 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 23 ARG 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 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 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 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 300 LEU Chi-restraints excluded: chain D residue 329 PHE 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 232 ASP Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG 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 253 LYS 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 258 LEU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 319 VAL 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: 3.9990 chunk 188 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS B 153 GLN I 77 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.028918 restraints weight = 133403.513| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 4.15 r_work: 0.2375 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24965 Z= 0.139 Angle : 0.536 11.967 34247 Z= 0.293 Chirality : 0.041 0.218 3796 Planarity : 0.004 0.052 3967 Dihedral : 18.022 173.573 4478 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.35 % Allowed : 28.21 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.39 (0.16), residues: 2660 helix: 0.93 (0.19), residues: 795 sheet: 0.38 (0.27), residues: 438 loop : -1.18 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 176 TYR 0.021 0.001 TYR H 114 PHE 0.012 0.001 PHE B 43 TRP 0.008 0.001 TRP I 264 HIS 0.003 0.001 HIS H 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (24965) covalent geometry : angle 0.53614 / 0.29 (34247) hydrogen bonds : bond 0.03893 / 2.60 ( 879) hydrogen bonds : angle 4.36593 / 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 216 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 136 time to evaluate : 0.893 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: 0.8999 (OUTLIER) cc_final: 0.8652 (tpp) REVERT: A 6 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9125 (tp) REVERT: A 14 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: A 71 ARG cc_start: 0.8740 (mpp80) cc_final: 0.8256 (mpp80) REVERT: A 91 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8918 (tptp) REVERT: A 219 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: J 1 MET cc_start: 0.9619 (ppp) cc_final: 0.9316 (ppp) REVERT: J 27 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9025 (mm) REVERT: J 95 MET cc_start: 0.8653 (mtp) cc_final: 0.8077 (mtt) REVERT: J 116 HIS cc_start: 0.9578 (m90) cc_final: 0.9320 (m-70) REVERT: J 143 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.8921 (t) REVERT: J 249 CYS cc_start: 0.8299 (t) cc_final: 0.8067 (t) REVERT: J 322 MET cc_start: 0.9275 (mpp) cc_final: 0.8697 (ttp) REVERT: B 51 LYS cc_start: 0.9538 (ttpt) cc_final: 0.9255 (tptp) REVERT: I 120 GLN cc_start: 0.9615 (OUTLIER) cc_final: 0.9164 (tm-30) REVERT: I 209 ILE cc_start: 0.9621 (pt) cc_final: 0.9156 (mm) REVERT: I 228 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: D 84 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8850 (tt) REVERT: D 103 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8835 (tppt) REVERT: D 194 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.9227 (tp40) REVERT: D 221 MET cc_start: 0.8918 (mmm) cc_final: 0.8708 (mmm) REVERT: D 238 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8313 (pttm) REVERT: D 300 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9282 (mp) REVERT: D 328 MET cc_start: 0.8444 (tmm) cc_final: 0.7887 (ttp) REVERT: E 18 ASN cc_start: 0.9160 (t0) cc_final: 0.8765 (t0) REVERT: E 106 MET cc_start: 0.8653 (ttp) cc_final: 0.8350 (tmm) REVERT: E 120 GLN cc_start: 0.9405 (tp40) cc_final: 0.9058 (tp-100) REVERT: F 45 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8950 (mm) REVERT: F 106 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8699 (tmm) REVERT: F 120 GLN cc_start: 0.9689 (tt0) cc_final: 0.9221 (tm-30) REVERT: G 120 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8910 (tm-30) REVERT: H 229 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: H 242 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9194 (mtpp) outliers start: 80 outliers final: 42 residues processed: 205 average time/residue: 0.1535 time to fit residues: 51.2686 Evaluate side-chains 192 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 142 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 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 103 LYS Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE 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 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 45 LEU Chi-restraints excluded: chain F residue 83 THR 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 H residue 99 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 161 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** 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 = 0.2978 r_free = 0.2978 target = 0.040701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.028056 restraints weight = 135297.040| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.20 r_work: 0.2343 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24965 Z= 0.236 Angle : 0.593 14.393 34247 Z= 0.317 Chirality : 0.042 0.211 3796 Planarity : 0.004 0.052 3967 Dihedral : 17.999 173.443 4478 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.19 % Allowed : 27.50 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.17), residues: 2660 helix: 0.99 (0.19), residues: 796 sheet: 0.14 (0.26), residues: 450 loop : -1.17 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 115 TYR 0.018 0.001 TYR H 114 PHE 0.020 0.001 PHE B 43 TRP 0.007 0.001 TRP F 264 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (24965) covalent geometry : angle 0.59306 / 0.32 (34247) hydrogen bonds : bond 0.04081 / 2.71 ( 879) hydrogen bonds : angle 4.48111 / 3.16 ( 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 232 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 132 time to evaluate : 0.889 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: A 1 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8545 (tpp) REVERT: A 6 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9159 (tp) REVERT: A 14 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: A 63 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8672 (tm-30) REVERT: A 91 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8893 (tptp) REVERT: A 97 MET cc_start: 0.9386 (mmm) cc_final: 0.9134 (mmm) REVERT: A 140 ARG cc_start: 0.9162 (ttm-80) cc_final: 0.8920 (ttm110) REVERT: A 219 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8845 (tm-30) REVERT: J 1 MET cc_start: 0.9618 (ppp) cc_final: 0.9325 (ppp) REVERT: J 95 MET cc_start: 0.8688 (mtp) cc_final: 0.8098 (mtt) REVERT: J 249 CYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8082 (t) REVERT: J 322 MET cc_start: 0.9293 (mpp) cc_final: 0.8715 (ttp) REVERT: B 51 LYS cc_start: 0.9559 (ttpt) cc_final: 0.9272 (tptp) REVERT: B 104 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6556 (pp20) REVERT: B 123 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6035 (pp) REVERT: I 120 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.9197 (pp30) REVERT: I 209 ILE cc_start: 0.9625 (pt) cc_final: 0.9117 (mm) REVERT: I 228 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: I 328 MET cc_start: 0.9059 (mtt) cc_final: 0.8785 (mtt) REVERT: D 23 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.9134 (ptp-170) REVERT: D 84 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8781 (tt) REVERT: D 103 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8849 (tptt) REVERT: D 194 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9229 (tp-100) REVERT: D 238 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8188 (pttm) REVERT: D 252 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: D 300 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9282 (mp) REVERT: E 18 ASN cc_start: 0.9213 (t0) cc_final: 0.8835 (t0) REVERT: E 106 MET cc_start: 0.8680 (ttp) cc_final: 0.8331 (tmm) REVERT: E 120 GLN cc_start: 0.9412 (tp40) cc_final: 0.9099 (tp-100) REVERT: F 45 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8948 (mm) REVERT: F 106 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8764 (tmm) REVERT: F 120 GLN cc_start: 0.9695 (tt0) cc_final: 0.9232 (tm-30) REVERT: F 253 LYS cc_start: 0.9691 (OUTLIER) cc_final: 0.9391 (tptp) REVERT: H 106 MET cc_start: 0.8959 (tmm) cc_final: 0.8533 (tmm) REVERT: H 229 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8375 (tpp) REVERT: H 242 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9192 (mtpp) REVERT: H 304 MET cc_start: 0.9730 (tpp) cc_final: 0.9423 (tpp) outliers start: 100 outliers final: 57 residues processed: 221 average time/residue: 0.1642 time to fit residues: 58.1228 Evaluate side-chains 208 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 129 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 142 ARG 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 123 LEU 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 120 GLN Chi-restraints excluded: chain I residue 211 VAL 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 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 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 238 LYS 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 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 106 MET Chi-restraints excluded: chain F residue 253 LYS 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 319 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.040502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028278 restraints weight = 136108.659| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 3.96 r_work: 0.2372 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24965 Z= 0.261 Angle : 0.617 15.999 34247 Z= 0.327 Chirality : 0.042 0.408 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.044 173.147 4477 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.81 % Allowed : 27.21 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2660 helix: 0.93 (0.19), residues: 798 sheet: 0.14 (0.26), residues: 443 loop : -1.21 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 146 TYR 0.021 0.001 TYR H 114 PHE 0.015 0.001 PHE B 43 TRP 0.008 0.001 TRP F 264 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (24965) covalent geometry : angle 0.61652 / 0.33 (34247) hydrogen bonds : bond 0.04105 / 2.73 ( 879) hydrogen bonds : angle 4.53575 / 3.21 ( 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 247 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 132 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8464 (tpp) REVERT: A 6 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9139 (tp) REVERT: A 14 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: A 63 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 91 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8942 (tptp) REVERT: A 140 ARG cc_start: 0.9208 (ttm-80) cc_final: 0.8950 (ttm110) REVERT: A 219 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: J 1 MET cc_start: 0.9648 (ppp) cc_final: 0.9315 (ppp) REVERT: J 95 MET cc_start: 0.8760 (mtp) cc_final: 0.8110 (mtt) REVERT: J 249 CYS cc_start: 0.8209 (t) cc_final: 0.7968 (t) REVERT: J 322 MET cc_start: 0.9327 (mpp) cc_final: 0.8738 (ttp) REVERT: B 22 GLU cc_start: 0.9502 (OUTLIER) cc_final: 0.9223 (pt0) REVERT: B 51 LYS cc_start: 0.9489 (ttpt) cc_final: 0.9245 (tptp) REVERT: B 104 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6596 (pp20) REVERT: B 123 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6110 (pp) REVERT: I 120 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.9103 (pp30) REVERT: I 228 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: D 84 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8981 (tt) REVERT: D 103 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (tptt) REVERT: D 194 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9105 (tp-100) REVERT: D 221 MET cc_start: 0.8820 (mmm) cc_final: 0.8385 (mmm) REVERT: D 238 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8315 (pttm) REVERT: D 300 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9327 (mp) REVERT: E 18 ASN cc_start: 0.9175 (t0) cc_final: 0.8631 (t0) REVERT: E 62 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8786 (mtm) REVERT: E 120 GLN cc_start: 0.9351 (tp40) cc_final: 0.9051 (tp-100) REVERT: F 45 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9054 (mm) REVERT: F 106 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8567 (tmm) REVERT: F 120 GLN cc_start: 0.9639 (tt0) cc_final: 0.9200 (tm-30) REVERT: F 309 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: F 328 MET cc_start: 0.9179 (tmm) cc_final: 0.8969 (tmm) REVERT: G 120 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8835 (tm-30) REVERT: G 229 MET cc_start: 0.9042 (tpp) cc_final: 0.8573 (tpp) REVERT: H 106 MET cc_start: 0.9068 (tmm) cc_final: 0.8612 (tmm) REVERT: H 229 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: H 242 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9215 (mtpp) REVERT: H 284 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.9040 (mtm110) REVERT: H 304 MET cc_start: 0.9689 (tpp) cc_final: 0.9415 (tpp) REVERT: H 309 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8166 (pt0) outliers start: 115 outliers final: 68 residues processed: 232 average time/residue: 0.1596 time to fit residues: 59.6398 Evaluate side-chains 218 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 VAL 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 233 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 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 15 SER Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU 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 120 GLN 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 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 178 ASN 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 223 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 267 ASP 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 62 MET 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 258 LEU 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 27 THR 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 106 MET 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 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 36 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 108 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 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: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 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 = 0.2987 r_free = 0.2987 target = 0.040353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.028167 restraints weight = 136298.334| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 3.94 r_work: 0.2369 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 24965 Z= 0.263 Angle : 0.619 15.678 34247 Z= 0.328 Chirality : 0.042 0.229 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.094 173.009 4477 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.60 % Allowed : 26.92 % Favored : 68.48 % 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 (0.16), residues: 2660 helix: 0.98 (0.19), residues: 794 sheet: -0.01 (0.26), residues: 452 loop : -1.25 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.020 0.001 TYR H 114 PHE 0.016 0.001 PHE B 43 TRP 0.007 0.001 TRP G 264 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 (24965) covalent geometry : angle 0.61910 / 0.33 (34247) hydrogen bonds : bond 0.04145 / 2.76 ( 879) hydrogen bonds : angle 4.58536 / 3.25 ( 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 239 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 129 time to evaluate : 0.949 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: A 1 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (tpp) REVERT: A 6 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9147 (tp) REVERT: A 63 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 91 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8955 (tptp) REVERT: A 140 ARG cc_start: 0.9207 (ttm-80) cc_final: 0.8867 (ttm110) REVERT: A 219 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8815 (tm-30) REVERT: J 1 MET cc_start: 0.9639 (ppp) cc_final: 0.9319 (ppp) REVERT: J 95 MET cc_start: 0.8697 (mtp) cc_final: 0.8110 (mtt) REVERT: J 249 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7966 (t) REVERT: J 322 MET cc_start: 0.9343 (mpp) cc_final: 0.8753 (ttp) REVERT: B 22 GLU cc_start: 0.9523 (OUTLIER) cc_final: 0.9315 (tp30) REVERT: B 51 LYS cc_start: 0.9512 (ttpt) cc_final: 0.9285 (tmtt) REVERT: B 104 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: B 123 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6052 (pp) REVERT: I 120 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9108 (pp30) REVERT: I 228 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: D 23 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.9166 (ptp-170) REVERT: D 84 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8973 (tt) REVERT: D 103 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8803 (tptt) REVERT: D 194 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9101 (tp-100) REVERT: D 221 MET cc_start: 0.8761 (mmm) cc_final: 0.8449 (mmm) REVERT: D 238 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8333 (pttm) REVERT: E 18 ASN cc_start: 0.9116 (t0) cc_final: 0.8705 (t0) REVERT: E 120 GLN cc_start: 0.9354 (tp40) cc_final: 0.9057 (tp-100) REVERT: F 45 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9051 (mm) REVERT: F 106 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8693 (tmm) REVERT: F 120 GLN cc_start: 0.9627 (tt0) cc_final: 0.9181 (tm-30) REVERT: F 328 MET cc_start: 0.9151 (tmm) cc_final: 0.8936 (tmm) REVERT: G 120 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8841 (tm-30) REVERT: G 229 MET cc_start: 0.9041 (tpp) cc_final: 0.8566 (tpp) REVERT: H 106 MET cc_start: 0.9030 (tmm) cc_final: 0.8563 (tmm) REVERT: H 229 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.8470 (tpp) REVERT: H 242 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9213 (mtpp) REVERT: H 284 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9028 (ttm110) REVERT: H 304 MET cc_start: 0.9687 (tpp) cc_final: 0.9398 (tpp) outliers start: 110 outliers final: 81 residues processed: 226 average time/residue: 0.1568 time to fit residues: 57.6709 Evaluate side-chains 228 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 127 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 221 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain J residue 22 LYS 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 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 J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 123 LEU 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 120 GLN 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 20 SER 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 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 178 ASN 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 223 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 267 ASP 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 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 62 MET 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 27 THR 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 106 MET 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 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 183 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 258 LEU Chi-restraints excluded: chain H residue 284 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 13 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** E 250 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.040338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028127 restraints weight = 136680.705| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 3.95 r_work: 0.2367 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24965 Z= 0.248 Angle : 0.610 15.831 34247 Z= 0.324 Chirality : 0.042 0.223 3796 Planarity : 0.004 0.054 3967 Dihedral : 18.133 172.992 4477 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.69 % Allowed : 26.71 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2660 helix: 1.02 (0.19), residues: 794 sheet: -0.01 (0.26), residues: 456 loop : -1.25 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 146 TYR 0.020 0.001 TYR A 142 PHE 0.015 0.001 PHE B 43 TRP 0.008 0.001 TRP G 264 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (24965) covalent geometry : angle 0.61012 / 0.32 (34247) hydrogen bonds : bond 0.04060 / 2.71 ( 879) hydrogen bonds : angle 4.54646 / 3.22 ( 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 241 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 129 time to evaluate : 0.782 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: 0.9617 (OUTLIER) cc_final: 0.9168 (tp) REVERT: A 63 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 91 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8960 (tptp) REVERT: A 140 ARG cc_start: 0.9180 (ttm-80) cc_final: 0.8813 (ttm110) REVERT: A 219 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8777 (tm-30) REVERT: J 1 MET cc_start: 0.9625 (ppp) cc_final: 0.9340 (ppp) REVERT: J 95 MET cc_start: 0.8724 (mtp) cc_final: 0.8121 (mtt) REVERT: J 249 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8046 (t) REVERT: J 322 MET cc_start: 0.9341 (mpp) cc_final: 0.8759 (ttp) REVERT: B 104 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6991 (pp20) REVERT: B 123 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6212 (pp) REVERT: I 120 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.9119 (pp30) REVERT: I 228 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: D 23 ARG cc_start: 0.9473 (OUTLIER) cc_final: 0.9161 (ptp-170) REVERT: D 84 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8976 (tt) REVERT: D 103 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8813 (tptt) REVERT: D 194 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9104 (tp-100) REVERT: D 221 MET cc_start: 0.8799 (mmm) cc_final: 0.8452 (mmm) REVERT: E 18 ASN cc_start: 0.9078 (t0) cc_final: 0.8653 (t0) REVERT: E 120 GLN cc_start: 0.9342 (tp40) cc_final: 0.9019 (tp-100) REVERT: E 270 THR cc_start: 0.9718 (OUTLIER) cc_final: 0.9488 (p) REVERT: F 45 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9043 (mm) REVERT: F 106 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8604 (tmm) REVERT: F 120 GLN cc_start: 0.9634 (tt0) cc_final: 0.9180 (tm-30) REVERT: F 328 MET cc_start: 0.9193 (tmm) cc_final: 0.8982 (tmm) REVERT: G 120 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8846 (tm-30) REVERT: G 229 MET cc_start: 0.9030 (tpp) cc_final: 0.8580 (tpp) REVERT: G 304 MET cc_start: 0.9624 (ttt) cc_final: 0.9166 (tmm) REVERT: H 106 MET cc_start: 0.9057 (tmm) cc_final: 0.8580 (tmm) REVERT: H 229 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8453 (tpp) REVERT: H 242 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9224 (mtpp) REVERT: H 284 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9023 (ttm110) REVERT: H 304 MET cc_start: 0.9688 (tpp) cc_final: 0.9404 (tpp) REVERT: H 309 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8226 (pt0) outliers start: 112 outliers final: 83 residues processed: 228 average time/residue: 0.1531 time to fit residues: 56.7545 Evaluate side-chains 229 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 127 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 220 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain J residue 22 LYS 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 J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 123 LEU 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 120 GLN 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 20 SER 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 103 LYS Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 178 ASN 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 223 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 267 ASP 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 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 62 MET 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 270 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 27 THR 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 106 MET 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 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 183 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 258 LEU Chi-restraints excluded: chain H residue 284 ARG 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: 2.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 255 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 29 GLN B 106 ASN B 120 HIS ** E 250 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.041317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.029025 restraints weight = 135260.242| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 4.02 r_work: 0.2402 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24965 Z= 0.131 Angle : 0.560 15.124 34247 Z= 0.297 Chirality : 0.040 0.324 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.110 173.002 4477 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.26 % Allowed : 28.25 % Favored : 68.48 % 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: -0.31 (0.17), residues: 2660 helix: 1.14 (0.19), residues: 795 sheet: 0.28 (0.27), residues: 444 loop : -1.18 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.019 0.001 TYR A 142 PHE 0.014 0.001 PHE B 43 TRP 0.009 0.001 TRP I 264 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (24965) covalent geometry : angle 0.55980 / 0.30 (34247) hydrogen bonds : bond 0.03692 / 2.48 ( 879) hydrogen bonds : angle 4.32271 / 3.07 ( 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 214 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 136 time to evaluate : 0.891 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: 0.8836 (mmp) cc_final: 0.8577 (tpp) REVERT: A 6 ILE cc_start: 0.9588 (OUTLIER) cc_final: 0.9111 (tp) REVERT: A 63 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 71 ARG cc_start: 0.8922 (mpp80) cc_final: 0.8171 (mpp80) REVERT: A 91 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8931 (tptp) REVERT: A 140 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8745 (ttm110) REVERT: A 219 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8725 (tm-30) REVERT: J 1 MET cc_start: 0.9629 (ppp) cc_final: 0.9410 (ppp) REVERT: J 95 MET cc_start: 0.8843 (mtp) cc_final: 0.8281 (mtt) REVERT: J 322 MET cc_start: 0.9371 (mpp) cc_final: 0.8737 (ttp) REVERT: B 51 LYS cc_start: 0.9479 (ttpt) cc_final: 0.9220 (tptp) REVERT: B 104 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: B 123 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6073 (pp) REVERT: I 120 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9077 (pp30) REVERT: I 228 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: D 84 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9038 (tt) REVERT: D 194 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.9066 (tp-100) REVERT: D 221 MET cc_start: 0.8795 (mmm) cc_final: 0.8461 (mmm) REVERT: E 18 ASN cc_start: 0.8993 (t0) cc_final: 0.8562 (t0) REVERT: E 120 GLN cc_start: 0.9313 (tp40) cc_final: 0.8941 (tp-100) REVERT: E 270 THR cc_start: 0.9720 (OUTLIER) cc_final: 0.9466 (p) REVERT: F 45 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9049 (mm) REVERT: F 106 MET cc_start: 0.9214 (mmm) cc_final: 0.8643 (tmm) REVERT: F 120 GLN cc_start: 0.9619 (tt0) cc_final: 0.9161 (tm-30) REVERT: F 309 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: G 120 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8839 (tm-30) REVERT: G 229 MET cc_start: 0.8959 (tpp) cc_final: 0.8474 (tpp) REVERT: G 304 MET cc_start: 0.9602 (ttt) cc_final: 0.9158 (tmm) REVERT: H 106 MET cc_start: 0.9016 (tmm) cc_final: 0.8558 (tmm) REVERT: H 221 MET cc_start: 0.8996 (mmm) cc_final: 0.8618 (mmm) REVERT: H 229 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8461 (tpp) REVERT: H 242 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9229 (mtpp) REVERT: H 304 MET cc_start: 0.9683 (tpp) cc_final: 0.9403 (tpp) REVERT: H 328 MET cc_start: 0.8608 (tpp) cc_final: 0.8341 (tpp) outliers start: 78 outliers final: 58 residues processed: 205 average time/residue: 0.1552 time to fit residues: 51.7725 Evaluate side-chains 201 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 129 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 220 SER 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 J residue 321 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU 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 120 GLN Chi-restraints excluded: chain I residue 209 ILE 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 20 SER 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 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE 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 62 MET Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR 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 108 SER 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 142 ILE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 183 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 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 230 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** 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 = 0.3005 r_free = 0.3005 target = 0.040849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028660 restraints weight = 135864.765| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 3.94 r_work: 0.2389 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24965 Z= 0.196 Angle : 0.588 14.451 34247 Z= 0.310 Chirality : 0.041 0.262 3796 Planarity : 0.004 0.055 3967 Dihedral : 18.106 173.119 4477 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.56 % Allowed : 28.05 % Favored : 68.40 % 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: -0.31 (0.17), residues: 2660 helix: 1.14 (0.19), residues: 795 sheet: 0.23 (0.26), residues: 446 loop : -1.16 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.019 0.001 TYR A 142 PHE 0.013 0.001 PHE B 43 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 0.00426 / 0.20 (24965) covalent geometry : angle 0.58842 / 0.31 (34247) hydrogen bonds : bond 0.03797 / 2.54 ( 879) hydrogen bonds : angle 4.38045 / 3.11 ( 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 216 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 0.902 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: 0.8847 (mmp) cc_final: 0.8584 (tpp) REVERT: A 6 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9120 (tp) REVERT: A 14 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: A 63 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 71 ARG cc_start: 0.8926 (mpp80) cc_final: 0.8182 (mpp80) REVERT: A 91 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8957 (tptp) REVERT: A 140 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8838 (ttm110) REVERT: A 219 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: J 95 MET cc_start: 0.8843 (mtp) cc_final: 0.8285 (mtt) REVERT: J 322 MET cc_start: 0.9389 (mpp) cc_final: 0.8762 (ttp) REVERT: B 51 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9223 (tptp) REVERT: B 104 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: B 123 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6111 (pp) REVERT: I 120 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9094 (pp30) REVERT: I 228 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: D 84 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8992 (tt) REVERT: D 194 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9103 (tp-100) REVERT: D 221 MET cc_start: 0.8803 (mmm) cc_final: 0.8463 (mmm) REVERT: E 18 ASN cc_start: 0.9016 (t0) cc_final: 0.8590 (t0) REVERT: E 120 GLN cc_start: 0.9303 (tp40) cc_final: 0.8951 (tp-100) REVERT: E 270 THR cc_start: 0.9723 (OUTLIER) cc_final: 0.9494 (p) REVERT: F 45 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9053 (mm) REVERT: F 72 MET cc_start: 0.9406 (mtt) cc_final: 0.8982 (mpp) REVERT: F 106 MET cc_start: 0.9215 (mmm) cc_final: 0.8608 (tmm) REVERT: F 120 GLN cc_start: 0.9625 (tt0) cc_final: 0.9166 (tm-30) REVERT: F 309 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: G 229 MET cc_start: 0.9008 (tpp) cc_final: 0.8530 (tpp) REVERT: H 106 MET cc_start: 0.9025 (tmm) cc_final: 0.8570 (tmm) REVERT: H 229 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: H 242 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9224 (mtpp) REVERT: H 284 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8950 (ttm110) REVERT: H 304 MET cc_start: 0.9683 (tpp) cc_final: 0.9385 (tpp) REVERT: H 328 MET cc_start: 0.8616 (tpp) cc_final: 0.8323 (tpp) outliers start: 85 outliers final: 64 residues processed: 207 average time/residue: 0.1570 time to fit residues: 52.9416 Evaluate side-chains 209 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 129 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 220 SER Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 THR 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 J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU 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 120 GLN 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 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 20 SER 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 132 LEU 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 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 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 62 MET Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 294 THR 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 108 SER 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 142 ILE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 183 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 284 ARG 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: 6.9990 chunk 4 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS ** F 333 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029232 restraints weight = 134388.622| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.99 r_work: 0.2412 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24965 Z= 0.133 Angle : 0.571 14.827 34247 Z= 0.301 Chirality : 0.040 0.278 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.096 173.071 4477 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.22 % Allowed : 28.51 % Favored : 68.27 % 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: -0.24 (0.17), residues: 2660 helix: 1.19 (0.19), residues: 795 sheet: 0.32 (0.27), residues: 442 loop : -1.13 (0.16), residues: 1423 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 0.012 0.001 PHE B 43 TRP 0.008 0.001 TRP I 264 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24965) covalent geometry : angle 0.57124 / 0.30 (34247) hydrogen bonds : bond 0.03606 / 2.43 ( 879) hydrogen bonds : angle 4.26991 / 3.04 ( 2398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5900.21 seconds wall clock time: 102 minutes 22.60 seconds (6142.60 seconds total)