Starting phenix.real_space_refine on Fri Jun 20 17:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yeo_39200/06_2025/8yeo_39200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yeo_39200/06_2025/8yeo_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_39200/06_2025/8yeo_39200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yeo_39200/06_2025/8yeo_39200.map" model { file = "/net/cci-nas-00/data/ceres_data/8yeo_39200/06_2025/8yeo_39200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yeo_39200/06_2025/8yeo_39200.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.21, per 1000 atoms: 0.59 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: 7.40 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 8.56 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: 9.70 Time building geometry restraints manager: 7.73 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=" N ASP B 36 " pdb=" CA ASP B 36 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.24e+00 bond pdb=" CA PRO H 63 " pdb=" C PRO H 63 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.01e+00 bond pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.77e-02 3.19e+03 1.99e+00 bond pdb=" CA ASP G 51 " pdb=" C ASP G 51 " ideal model delta sigma weight residual 1.528 1.511 0.017 1.33e-02 5.65e+03 1.54e+00 bond pdb=" O5' G C 57 " pdb=" C5' G C 57 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.54e+00 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 33779 2.19 - 4.39: 409 4.39 - 6.58: 44 6.58 - 8.77: 8 8.77 - 10.97: 7 Bond angle restraints: 34247 Sorted by residual: angle pdb=" CA GLU G 278 " pdb=" CB GLU G 278 " pdb=" CG GLU G 278 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CB MET D 229 " pdb=" CG MET D 229 " pdb=" SD MET D 229 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET E 328 " pdb=" CG MET E 328 " pdb=" SD MET E 328 " ideal model delta sigma weight residual 112.70 123.57 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 123.17 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C PRO A 115 " pdb=" N HIS A 116 " pdb=" CA HIS A 116 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+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 - 0.038: 2761 0.038 - 0.077: 774 0.077 - 0.115: 173 0.115 - 0.154: 78 0.154 - 0.192: 10 Chirality restraints: 3796 Sorted by residual: chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.60 -0.19 2.00e-01 2.50e+01 9.24e-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 chirality pdb=" C1' A C 22 " pdb=" O4' A C 22 " pdb=" C2' A C 22 " pdb=" N9 A C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.12e-01 ... (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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 61.720 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 0.041 24965 Z= 0.127 Angle : 0.597 10.969 34247 Z= 0.318 Chirality : 0.041 0.192 3796 Planarity : 0.004 0.059 3967 Dihedral : 20.198 172.898 9966 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP H 33 HIS 0.003 0.001 HIS J 35 PHE 0.013 0.001 PHE I 273 TYR 0.009 0.001 TYR B 96 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.16885 ( 879) hydrogen bonds : angle 5.79092 ( 2398) covalent geometry : bond 0.00264 (24965) covalent geometry : angle 0.59692 (34247) *********************** 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 : 2.547 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: 0.8739 (m-40) cc_final: 0.8284 (m110) REVERT: J 95 MET cc_start: 0.8344 (mtp) cc_final: 0.7972 (mtp) REVERT: J 97 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6428 (ppp) REVERT: D 221 MET cc_start: 0.8649 (mmm) cc_final: 0.8335 (mmm) REVERT: D 328 MET cc_start: 0.7297 (tmm) cc_final: 0.7019 (ttp) REVERT: E 18 ASN cc_start: 0.8098 (t0) cc_final: 0.7670 (t0) REVERT: E 120 GLN cc_start: 0.8492 (tp40) cc_final: 0.8249 (tp-100) REVERT: H 229 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8202 (tpp) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 0.3797 time to fit residues: 124.4560 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 : 2.712 ------------------------------------------------------------------------------- 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 233 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 185 GLN J 21 ASN J 29 GLN J 213 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 ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.028525 restraints weight = 135880.075| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 4.24 r_work: 0.2351 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 24965 Z= 0.287 Angle : 0.625 9.652 34247 Z= 0.334 Chirality : 0.041 0.247 3796 Planarity : 0.004 0.055 3967 Dihedral : 18.031 172.297 4489 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.22 % Allowed : 28.84 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2660 helix: 0.64 (0.18), residues: 790 sheet: 0.42 (0.27), residues: 440 loop : -1.28 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 149 HIS 0.005 0.001 HIS A 60 PHE 0.018 0.001 PHE J 92 TYR 0.017 0.001 TYR H 114 ARG 0.004 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 879) hydrogen bonds : angle 4.66714 ( 2398) covalent geometry : bond 0.00618 (24965) covalent geometry : angle 0.62528 (34247) *********************** 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 212 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 135 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 51 ARG cc_start: 0.9341 (ptp-110) cc_final: 0.8666 (tmm-80) REVERT: A 63 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 71 ARG cc_start: 0.8742 (mpp80) cc_final: 0.8150 (mpp80) REVERT: A 91 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8903 (tptp) REVERT: A 219 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8812 (tm-30) REVERT: J 1 MET cc_start: 0.9603 (ppp) cc_final: 0.9357 (ppp) REVERT: J 27 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8985 (mm) REVERT: J 68 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8473 (p0) REVERT: J 95 MET cc_start: 0.8652 (mtp) cc_final: 0.8029 (mtt) REVERT: J 97 MET cc_start: 0.7908 (ppp) cc_final: 0.7692 (ppp) REVERT: J 116 HIS cc_start: 0.9575 (m90) cc_final: 0.9336 (m-70) REVERT: J 142 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8934 (ptm-80) REVERT: J 143 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.8747 (t) REVERT: J 322 MET cc_start: 0.9191 (mpp) cc_final: 0.8634 (ttm) REVERT: B 51 LYS cc_start: 0.9542 (ttpt) cc_final: 0.9288 (tmtt) REVERT: B 115 MET cc_start: 0.8150 (tmm) cc_final: 0.7915 (tmm) REVERT: D 103 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8779 (tptt) REVERT: D 194 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9190 (tp-100) REVERT: E 18 ASN cc_start: 0.9211 (t0) cc_final: 0.8833 (t0) REVERT: E 62 MET cc_start: 0.8981 (mtm) cc_final: 0.8712 (mtm) REVERT: E 120 GLN cc_start: 0.9442 (tp40) cc_final: 0.9137 (tp-100) REVERT: F 106 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8691 (tmm) REVERT: F 120 GLN cc_start: 0.9676 (tt0) cc_final: 0.9180 (tm-30) REVERT: H 221 MET cc_start: 0.8669 (mmm) cc_final: 0.8090 (mmm) REVERT: H 229 MET cc_start: 0.9302 (tpp) cc_final: 0.8206 (tpp) outliers start: 77 outliers final: 32 residues processed: 202 average time/residue: 0.4667 time to fit residues: 154.1527 Evaluate side-chains 169 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 4.725 ------------------------------------------------------------------------------- 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 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 42 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 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 272 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 97 optimal weight: 0.1980 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** 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 = 0.2981 r_free = 0.2981 target = 0.040901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.028213 restraints weight = 136793.432| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.20 r_work: 0.2342 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24965 Z= 0.250 Angle : 0.587 10.629 34247 Z= 0.314 Chirality : 0.041 0.263 3796 Planarity : 0.004 0.054 3967 Dihedral : 18.047 171.731 4478 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.19 % Allowed : 27.25 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2660 helix: 0.82 (0.19), residues: 796 sheet: 0.20 (0.26), residues: 450 loop : -1.19 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 149 HIS 0.004 0.001 HIS A 95 PHE 0.018 0.001 PHE J 92 TYR 0.020 0.001 TYR H 114 ARG 0.003 0.000 ARG J 176 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 879) hydrogen bonds : angle 4.50789 ( 2398) covalent geometry : bond 0.00540 (24965) covalent geometry : angle 0.58726 (34247) *********************** 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 234 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 134 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9154 (tp) REVERT: A 14 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8627 (mp0) REVERT: A 51 ARG cc_start: 0.9342 (ptp-110) cc_final: 0.8672 (tmm-80) REVERT: A 63 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 71 ARG cc_start: 0.8699 (mpp80) cc_final: 0.8215 (mpp80) REVERT: A 91 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: A 219 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8820 (tm-30) REVERT: J 1 MET cc_start: 0.9588 (ppp) cc_final: 0.9307 (ppp) REVERT: J 27 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9026 (mm) REVERT: J 68 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8517 (p0) REVERT: J 95 MET cc_start: 0.8630 (mtp) cc_final: 0.8044 (mtt) REVERT: J 116 HIS cc_start: 0.9633 (m90) cc_final: 0.9360 (m-70) REVERT: J 142 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8931 (ptm-80) REVERT: J 143 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8791 (t) REVERT: J 249 CYS cc_start: 0.8307 (t) cc_final: 0.8052 (t) REVERT: J 322 MET cc_start: 0.9285 (mpp) cc_final: 0.8858 (ttm) REVERT: B 51 LYS cc_start: 0.9561 (ttpt) cc_final: 0.9276 (tptp) REVERT: B 104 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6286 (pp20) REVERT: D 103 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8846 (tppt) REVERT: D 106 MET cc_start: 0.8824 (tmm) cc_final: 0.8607 (tmm) REVERT: D 194 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9212 (tp-100) REVERT: D 221 MET cc_start: 0.8724 (mmm) cc_final: 0.8450 (mmm) REVERT: D 238 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8310 (pttm) REVERT: D 300 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9302 (mp) REVERT: E 18 ASN cc_start: 0.9226 (t0) cc_final: 0.8855 (t0) REVERT: E 120 GLN cc_start: 0.9452 (tp40) cc_final: 0.9149 (tp-100) REVERT: F 23 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8762 (ptp90) REVERT: F 106 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: F 120 GLN cc_start: 0.9682 (tt0) cc_final: 0.9192 (tm-30) REVERT: F 253 LYS cc_start: 0.9663 (OUTLIER) cc_final: 0.9250 (tptp) REVERT: F 333 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: H 229 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8287 (tpp) REVERT: H 320 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.9278 (mpp) outliers start: 100 outliers final: 47 residues processed: 221 average time/residue: 0.3833 time to fit residues: 135.1104 Evaluate side-chains 193 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain 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 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 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain D residue 14 SER 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 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 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 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 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 253 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 333 GLN 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 H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 320 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 243 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 239 optimal weight: 0.4980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3009 r_free = 0.3009 target = 0.041724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.029004 restraints weight = 134675.772| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 4.21 r_work: 0.2376 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24965 Z= 0.137 Angle : 0.535 12.052 34247 Z= 0.284 Chirality : 0.040 0.267 3796 Planarity : 0.004 0.052 3967 Dihedral : 17.994 171.015 4478 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.01 % Allowed : 27.96 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2660 helix: 1.03 (0.19), residues: 796 sheet: 0.42 (0.27), residues: 438 loop : -1.17 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.007 0.001 HIS A 215 PHE 0.019 0.001 PHE J 92 TYR 0.019 0.001 TYR H 114 ARG 0.002 0.000 ARG G 150 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 879) hydrogen bonds : angle 4.26504 ( 2398) covalent geometry : bond 0.00307 (24965) covalent geometry : angle 0.53478 (34247) *********************** 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 209 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 137 time to evaluate : 2.660 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: 0.9012 (mmp) cc_final: 0.8610 (tpp) REVERT: A 6 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9111 (tp) REVERT: A 14 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: A 63 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 91 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: A 219 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8823 (tm-30) REVERT: A 247 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9237 (pm20) REVERT: J 1 MET cc_start: 0.9613 (ppp) cc_final: 0.9328 (ppp) REVERT: J 27 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9049 (mm) REVERT: J 95 MET cc_start: 0.8689 (mtp) cc_final: 0.8105 (mtt) REVERT: J 116 HIS cc_start: 0.9672 (m90) cc_final: 0.9457 (m90) REVERT: J 143 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9297 (m) REVERT: J 249 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8048 (t) REVERT: J 322 MET cc_start: 0.9296 (mpp) cc_final: 0.8742 (ttp) REVERT: B 22 GLU cc_start: 0.9561 (OUTLIER) cc_final: 0.9213 (pt0) REVERT: B 51 LYS cc_start: 0.9539 (ttpt) cc_final: 0.9246 (tptp) REVERT: B 104 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6325 (pp20) REVERT: B 123 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.5907 (pp) REVERT: I 21 PHE cc_start: 0.9306 (m-80) cc_final: 0.8853 (m-80) REVERT: I 209 ILE cc_start: 0.9600 (pt) cc_final: 0.9205 (mm) REVERT: I 228 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: I 328 MET cc_start: 0.8975 (mtt) cc_final: 0.8290 (mtt) REVERT: D 23 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8909 (ptp-170) REVERT: D 84 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8830 (tt) REVERT: D 194 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9174 (tp-100) REVERT: D 221 MET cc_start: 0.8689 (mmm) cc_final: 0.8394 (mmm) REVERT: D 252 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: D 300 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9284 (mp) REVERT: E 18 ASN cc_start: 0.9181 (t0) cc_final: 0.8792 (t0) REVERT: E 120 GLN cc_start: 0.9445 (tp40) cc_final: 0.9080 (tp-100) REVERT: F 45 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8933 (mm) REVERT: F 106 MET cc_start: 0.9319 (mmm) cc_final: 0.8625 (tmm) REVERT: F 120 GLN cc_start: 0.9694 (tt0) cc_final: 0.9223 (tm-30) REVERT: F 333 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6786 (mt0) REVERT: H 106 MET cc_start: 0.8981 (tmm) cc_final: 0.8527 (tmm) REVERT: H 229 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: H 320 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9252 (mpp) outliers start: 72 outliers final: 40 residues processed: 198 average time/residue: 0.3509 time to fit residues: 112.1595 Evaluate side-chains 191 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 130 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 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 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 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 252 GLN 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 211 VAL 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 99 VAL Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 320 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 90 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.040555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.028281 restraints weight = 136292.406| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 3.99 r_work: 0.2371 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24965 Z= 0.260 Angle : 0.609 13.475 34247 Z= 0.318 Chirality : 0.041 0.280 3796 Planarity : 0.004 0.054 3967 Dihedral : 18.021 170.806 4478 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.40 % Allowed : 27.08 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2660 helix: 0.97 (0.19), residues: 798 sheet: 0.18 (0.26), residues: 448 loop : -1.16 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 264 HIS 0.006 0.001 HIS A 215 PHE 0.018 0.001 PHE B 43 TYR 0.019 0.001 TYR H 114 ARG 0.006 0.001 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 879) hydrogen bonds : angle 4.49005 ( 2398) covalent geometry : bond 0.00566 (24965) covalent geometry : angle 0.60925 (34247) *********************** 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 234 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 129 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9111 (tp) REVERT: A 14 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: A 63 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 71 ARG cc_start: 0.8831 (mpp80) cc_final: 0.8077 (mpp80) REVERT: A 91 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8925 (tptp) REVERT: A 140 ARG cc_start: 0.9246 (ttm-80) cc_final: 0.8921 (ttm110) REVERT: A 219 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8851 (tm-30) REVERT: J 1 MET cc_start: 0.9615 (ppp) cc_final: 0.9298 (ppp) REVERT: J 36 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9168 (pt) REVERT: J 95 MET cc_start: 0.8761 (mtp) cc_final: 0.8391 (mtp) REVERT: J 116 HIS cc_start: 0.9714 (m90) cc_final: 0.9442 (m90) REVERT: J 322 MET cc_start: 0.9341 (mpp) cc_final: 0.8728 (ttp) REVERT: B 22 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9291 (tp30) REVERT: B 51 LYS cc_start: 0.9500 (ttpt) cc_final: 0.9235 (tptp) REVERT: B 104 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: I 228 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: I 328 MET cc_start: 0.9057 (mtt) cc_final: 0.8755 (mtt) REVERT: D 84 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8967 (tt) REVERT: D 194 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9152 (tp-100) REVERT: D 221 MET cc_start: 0.8810 (mmm) cc_final: 0.8591 (mmm) REVERT: D 238 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8301 (pttm) REVERT: E 18 ASN cc_start: 0.9198 (t0) cc_final: 0.8802 (t0) REVERT: E 120 GLN cc_start: 0.9379 (tp40) cc_final: 0.9068 (tp-100) REVERT: F 45 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (mm) REVERT: F 106 MET cc_start: 0.9228 (mmm) cc_final: 0.8652 (tmm) REVERT: F 120 GLN cc_start: 0.9634 (tt0) cc_final: 0.9194 (tm-30) REVERT: F 253 LYS cc_start: 0.9712 (OUTLIER) cc_final: 0.9434 (tptp) REVERT: F 328 MET cc_start: 0.9157 (tmm) cc_final: 0.8940 (tmm) REVERT: F 333 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: G 229 MET cc_start: 0.9060 (tpp) cc_final: 0.8596 (tpp) REVERT: H 106 MET cc_start: 0.9061 (tmm) cc_final: 0.8658 (tmm) REVERT: H 229 MET cc_start: 0.9452 (tpp) cc_final: 0.8466 (tpp) REVERT: H 242 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9181 (mtpp) REVERT: H 284 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.9069 (ttm110) outliers start: 105 outliers final: 62 residues processed: 223 average time/residue: 0.3603 time to fit residues: 127.7045 Evaluate side-chains 203 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 125 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain J residue 36 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 B residue 7 ILE Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 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 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 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 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 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 164 ILE 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 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 253 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 GLN 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 223 VAL 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 Chi-restraints excluded: chain H residue 319 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 217 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN B 56 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.040312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028128 restraints weight = 136346.486| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.95 r_work: 0.2365 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 24965 Z= 0.271 Angle : 0.623 14.159 34247 Z= 0.325 Chirality : 0.042 0.289 3796 Planarity : 0.004 0.057 3967 Dihedral : 18.070 170.521 4477 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.48 % Allowed : 26.45 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2660 helix: 0.94 (0.19), residues: 797 sheet: 0.09 (0.26), residues: 450 loop : -1.20 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 264 HIS 0.006 0.001 HIS A 215 PHE 0.018 0.001 PHE B 43 TYR 0.020 0.001 TYR H 114 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 879) hydrogen bonds : angle 4.53726 ( 2398) covalent geometry : bond 0.00589 (24965) covalent geometry : angle 0.62256 (34247) *********************** 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 236 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 129 time to evaluate : 2.515 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: 0.9606 (OUTLIER) cc_final: 0.9144 (tp) REVERT: A 14 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: A 63 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 91 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8941 (tptp) REVERT: A 103 ASP cc_start: 0.9145 (m-30) cc_final: 0.8873 (t0) REVERT: A 219 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8787 (tm-30) REVERT: A 247 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9216 (pm20) REVERT: J 1 MET cc_start: 0.9621 (ppp) cc_final: 0.9323 (ppp) REVERT: J 95 MET cc_start: 0.8760 (mtp) cc_final: 0.8390 (mtp) REVERT: J 116 HIS cc_start: 0.9727 (m90) cc_final: 0.9447 (m90) REVERT: J 135 MET cc_start: 0.8346 (tpp) cc_final: 0.8130 (tpp) REVERT: J 322 MET cc_start: 0.9324 (mpp) cc_final: 0.8736 (ttp) REVERT: B 51 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9304 (tmtt) REVERT: B 104 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: B 123 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6125 (pp) REVERT: I 228 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: I 328 MET cc_start: 0.9039 (mtt) cc_final: 0.8742 (mtt) REVERT: D 84 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8945 (tt) REVERT: D 194 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.9138 (tp-100) REVERT: D 221 MET cc_start: 0.8831 (mmm) cc_final: 0.8620 (mmm) REVERT: D 238 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8544 (pttm) REVERT: E 18 ASN cc_start: 0.9194 (t0) cc_final: 0.8644 (t0) REVERT: E 67 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9026 (mm) REVERT: E 106 MET cc_start: 0.8652 (ttp) cc_final: 0.8073 (tmm) REVERT: E 120 GLN cc_start: 0.9375 (tp40) cc_final: 0.9068 (tp-100) REVERT: F 45 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9045 (mm) REVERT: F 106 MET cc_start: 0.9229 (mmm) cc_final: 0.8712 (tmm) REVERT: F 120 GLN cc_start: 0.9627 (tt0) cc_final: 0.9182 (tm-30) REVERT: F 221 MET cc_start: 0.8793 (mmm) cc_final: 0.8404 (mmm) REVERT: F 328 MET cc_start: 0.9199 (tmm) cc_final: 0.8977 (tmm) REVERT: G 229 MET cc_start: 0.9024 (tpp) cc_final: 0.8585 (tpp) REVERT: H 106 MET cc_start: 0.9111 (tmm) cc_final: 0.8666 (tmm) REVERT: H 229 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8444 (tpp) REVERT: H 242 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9198 (mtpp) outliers start: 107 outliers final: 73 residues processed: 222 average time/residue: 0.3519 time to fit residues: 126.3054 Evaluate side-chains 212 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 124 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain 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 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 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 14 SER 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 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 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 67 LEU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 229 MET 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 238 LYS Chi-restraints excluded: chain H residue 27 THR 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 229 MET Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 167 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.041334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028991 restraints weight = 134692.189| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 4.03 r_work: 0.2401 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24965 Z= 0.145 Angle : 0.555 14.578 34247 Z= 0.289 Chirality : 0.040 0.280 3796 Planarity : 0.003 0.054 3967 Dihedral : 18.049 170.133 4477 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.35 % Allowed : 27.54 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2660 helix: 1.08 (0.19), residues: 797 sheet: 0.36 (0.27), residues: 443 loop : -1.15 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 264 HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE J 92 TYR 0.026 0.001 TYR A 142 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 879) hydrogen bonds : angle 4.26293 ( 2398) covalent geometry : bond 0.00323 (24965) covalent geometry : angle 0.55518 (34247) *********************** 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 214 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 134 time to evaluate : 3.041 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: 0.9580 (OUTLIER) cc_final: 0.9058 (tp) REVERT: A 14 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: A 63 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 71 ARG cc_start: 0.8880 (mpp80) cc_final: 0.8167 (mpp80) REVERT: A 91 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8919 (tptp) REVERT: A 103 ASP cc_start: 0.9125 (m-30) cc_final: 0.8872 (t0) REVERT: A 140 ARG cc_start: 0.9215 (ttm-80) cc_final: 0.8885 (ttm110) REVERT: A 219 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: A 247 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9151 (tm-30) REVERT: J 1 MET cc_start: 0.9620 (ppp) cc_final: 0.9403 (ppp) REVERT: J 95 MET cc_start: 0.8850 (mtp) cc_final: 0.8393 (mtp) REVERT: J 116 HIS cc_start: 0.9743 (m90) cc_final: 0.9428 (m90) REVERT: J 322 MET cc_start: 0.9370 (mpp) cc_final: 0.8756 (ttp) REVERT: B 51 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9270 (tmtt) REVERT: B 104 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: B 123 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.5994 (pp) REVERT: I 228 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: I 328 MET cc_start: 0.8915 (mtt) cc_final: 0.8688 (mtt) REVERT: D 84 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8970 (tt) REVERT: D 194 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.9093 (tp-100) REVERT: D 221 MET cc_start: 0.8865 (mmm) cc_final: 0.8620 (mmm) REVERT: D 238 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8363 (pttm) REVERT: E 18 ASN cc_start: 0.9127 (t0) cc_final: 0.8718 (t0) REVERT: E 106 MET cc_start: 0.8602 (ttp) cc_final: 0.8130 (tmm) REVERT: E 120 GLN cc_start: 0.9344 (tp40) cc_final: 0.8977 (tp-100) REVERT: F 45 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9070 (mm) REVERT: F 106 MET cc_start: 0.9208 (mmm) cc_final: 0.8756 (tmm) REVERT: F 120 GLN cc_start: 0.9617 (tt0) cc_final: 0.9160 (tm-30) REVERT: F 309 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: F 333 GLN cc_start: 0.8403 (pt0) cc_final: 0.8079 (pm20) REVERT: G 229 MET cc_start: 0.8960 (tpp) cc_final: 0.8494 (tpp) REVERT: G 304 MET cc_start: 0.9575 (ttt) cc_final: 0.9188 (tmm) REVERT: H 106 MET cc_start: 0.9131 (tmm) cc_final: 0.8728 (tmm) REVERT: H 221 MET cc_start: 0.8995 (mmm) cc_final: 0.8580 (mmm) REVERT: H 229 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8527 (tpp) outliers start: 80 outliers final: 56 residues processed: 204 average time/residue: 0.3670 time to fit residues: 120.9524 Evaluate side-chains 199 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 129 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE 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 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 27 THR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 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 99 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 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 267 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN ** B 120 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 = 0.3018 r_free = 0.3018 target = 0.041203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028937 restraints weight = 134860.725| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 3.98 r_work: 0.2401 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24965 Z= 0.162 Angle : 0.560 13.513 34247 Z= 0.291 Chirality : 0.040 0.279 3796 Planarity : 0.003 0.056 3967 Dihedral : 18.044 170.232 4477 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.56 % Allowed : 27.29 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2660 helix: 1.13 (0.19), residues: 798 sheet: 0.41 (0.27), residues: 443 loop : -1.12 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.004 0.001 HIS A 215 PHE 0.013 0.001 PHE J 92 TYR 0.013 0.001 TYR H 114 ARG 0.005 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 879) hydrogen bonds : angle 4.23202 ( 2398) covalent geometry : bond 0.00360 (24965) covalent geometry : angle 0.55960 (34247) *********************** 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 216 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 2.832 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: 0.9077 (mmp) cc_final: 0.8754 (tpp) REVERT: A 6 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9060 (tp) REVERT: A 14 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 63 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 71 ARG cc_start: 0.8904 (mpp80) cc_final: 0.8177 (mpp80) REVERT: A 91 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8903 (tptp) REVERT: A 103 ASP cc_start: 0.9126 (m-30) cc_final: 0.8860 (t0) REVERT: A 140 ARG cc_start: 0.9180 (ttm-80) cc_final: 0.8838 (ttm110) REVERT: A 219 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: A 247 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9142 (tm-30) REVERT: J 95 MET cc_start: 0.8861 (mtp) cc_final: 0.8425 (mtp) REVERT: J 116 HIS cc_start: 0.9747 (m90) cc_final: 0.9440 (m90) REVERT: J 322 MET cc_start: 0.9371 (mpp) cc_final: 0.8775 (ttm) REVERT: B 51 LYS cc_start: 0.9474 (ttpt) cc_final: 0.9167 (tmmt) REVERT: B 104 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: B 123 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6147 (pp) REVERT: I 228 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: D 84 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8953 (tt) REVERT: D 194 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9108 (tp-100) REVERT: D 221 MET cc_start: 0.8844 (mmm) cc_final: 0.8605 (mmm) REVERT: D 238 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8371 (pttm) REVERT: E 18 ASN cc_start: 0.9137 (t0) cc_final: 0.8589 (t0) REVERT: E 106 MET cc_start: 0.8598 (ttp) cc_final: 0.8142 (tmm) REVERT: E 120 GLN cc_start: 0.9340 (tp40) cc_final: 0.8978 (tp-100) REVERT: E 270 THR cc_start: 0.9725 (OUTLIER) cc_final: 0.9483 (p) REVERT: F 45 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9035 (mm) REVERT: F 106 MET cc_start: 0.9203 (mmm) cc_final: 0.8555 (tmm) REVERT: F 120 GLN cc_start: 0.9627 (tt0) cc_final: 0.9164 (tm-30) REVERT: F 309 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: G 229 MET cc_start: 0.8979 (tpp) cc_final: 0.8517 (tpp) REVERT: G 304 MET cc_start: 0.9621 (ttt) cc_final: 0.9158 (tmm) REVERT: H 106 MET cc_start: 0.9153 (tmm) cc_final: 0.8857 (tmm) REVERT: H 229 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8609 (tpp) REVERT: H 242 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9182 (mtpp) REVERT: H 284 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9020 (mtm110) REVERT: H 309 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (pt0) outliers start: 85 outliers final: 61 residues processed: 205 average time/residue: 0.4070 time to fit residues: 134.3944 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 : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 ILE 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 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 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 44 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU 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 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 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 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 108 SER Chi-restraints excluded: chain F residue 269 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 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 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 93 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 167 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS B 135 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.029118 restraints weight = 135108.099| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 4.03 r_work: 0.2408 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 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 : 0.003 0.056 24965 Z= 0.153 Angle : 0.568 14.462 34247 Z= 0.293 Chirality : 0.040 0.279 3796 Planarity : 0.004 0.053 3967 Dihedral : 18.067 170.106 4477 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.73 % Allowed : 27.08 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2660 helix: 1.16 (0.19), residues: 801 sheet: 0.42 (0.27), residues: 443 loop : -1.09 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.003 0.001 HIS A 215 PHE 0.013 0.001 PHE J 92 TYR 0.018 0.001 TYR A 142 ARG 0.011 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 879) hydrogen bonds : angle 4.18593 ( 2398) covalent geometry : bond 0.00341 (24965) covalent geometry : angle 0.56819 (34247) *********************** 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 220 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 131 time to evaluate : 2.931 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: 0.9076 (mmp) cc_final: 0.8750 (tpp) REVERT: A 6 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9047 (tp) REVERT: A 14 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: A 63 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 71 ARG cc_start: 0.8898 (mpp80) cc_final: 0.8166 (mpp80) REVERT: A 91 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8920 (tptp) REVERT: A 103 ASP cc_start: 0.9112 (m-30) cc_final: 0.8863 (t0) REVERT: A 140 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8815 (ttm110) REVERT: A 219 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: A 247 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9149 (tm-30) REVERT: J 95 MET cc_start: 0.8854 (mtp) cc_final: 0.8445 (mtp) REVERT: J 116 HIS cc_start: 0.9750 (m90) cc_final: 0.9458 (m90) REVERT: J 322 MET cc_start: 0.9383 (mpp) cc_final: 0.8717 (mpp) REVERT: B 51 LYS cc_start: 0.9432 (ttpt) cc_final: 0.9135 (tmmt) REVERT: B 104 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6975 (pp20) REVERT: B 123 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6030 (pp) REVERT: I 228 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: D 84 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8965 (tt) REVERT: D 194 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9086 (tp-100) REVERT: D 221 MET cc_start: 0.8858 (mmm) cc_final: 0.8620 (mmm) REVERT: D 238 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8394 (pttm) REVERT: E 18 ASN cc_start: 0.9117 (t0) cc_final: 0.8568 (t0) REVERT: E 67 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9010 (mm) REVERT: E 106 MET cc_start: 0.8604 (ttp) cc_final: 0.8192 (tmm) REVERT: E 120 GLN cc_start: 0.9334 (tp40) cc_final: 0.8970 (tp-100) REVERT: E 270 THR cc_start: 0.9727 (OUTLIER) cc_final: 0.9493 (p) REVERT: F 45 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9043 (mm) REVERT: F 106 MET cc_start: 0.9200 (mmm) cc_final: 0.8538 (tmm) REVERT: F 120 GLN cc_start: 0.9619 (tt0) cc_final: 0.9158 (tm-30) REVERT: F 309 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: G 229 MET cc_start: 0.8969 (tpp) cc_final: 0.8514 (tpp) REVERT: G 304 MET cc_start: 0.9598 (ttt) cc_final: 0.9148 (tmm) REVERT: H 106 MET cc_start: 0.9140 (tmm) cc_final: 0.8781 (tmm) REVERT: H 221 MET cc_start: 0.8967 (mmm) cc_final: 0.8582 (mmm) REVERT: H 229 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8598 (tpp) REVERT: H 242 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9177 (mtpp) REVERT: H 309 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8274 (pt0) outliers start: 89 outliers final: 66 residues processed: 207 average time/residue: 0.3854 time to fit residues: 130.2592 Evaluate side-chains 213 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 129 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 92 PHE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 54 LEU 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 137 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 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 44 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 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 67 LEU 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 219 CYS 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 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 108 SER Chi-restraints excluded: chain F residue 269 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 264 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 213 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.028961 restraints weight = 135751.797| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 3.98 r_work: 0.2402 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24965 Z= 0.176 Angle : 0.583 14.456 34247 Z= 0.299 Chirality : 0.040 0.277 3796 Planarity : 0.004 0.052 3967 Dihedral : 18.093 170.146 4477 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.73 % Allowed : 26.92 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2660 helix: 1.22 (0.19), residues: 798 sheet: 0.39 (0.27), residues: 443 loop : -1.09 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.003 0.001 HIS A 215 PHE 0.013 0.001 PHE J 92 TYR 0.013 0.001 TYR A 142 ARG 0.009 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 879) hydrogen bonds : angle 4.22251 ( 2398) covalent geometry : bond 0.00391 (24965) covalent geometry : angle 0.58288 (34247) ********************** 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 218 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 129 time to evaluate : 3.401 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: 0.9081 (mmp) cc_final: 0.8751 (tpp) REVERT: A 6 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9119 (tp) REVERT: A 14 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: A 63 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 71 ARG cc_start: 0.8911 (mpp80) cc_final: 0.8169 (mpp80) REVERT: A 91 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8921 (tptp) REVERT: A 103 ASP cc_start: 0.9108 (m-30) cc_final: 0.8855 (t0) REVERT: A 219 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8775 (tm-30) REVERT: A 247 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9141 (tm-30) REVERT: J 95 MET cc_start: 0.8830 (mtp) cc_final: 0.8420 (mtp) REVERT: J 116 HIS cc_start: 0.9746 (m90) cc_final: 0.9453 (m90) REVERT: J 322 MET cc_start: 0.9309 (mpp) cc_final: 0.8637 (mpp) REVERT: B 51 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9131 (tmmt) REVERT: B 104 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: B 123 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6111 (pp) REVERT: I 210 TYR cc_start: 0.9357 (m-10) cc_final: 0.9076 (m-10) REVERT: I 228 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: D 84 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8958 (tt) REVERT: D 194 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.9110 (tp-100) REVERT: D 221 MET cc_start: 0.8850 (mmm) cc_final: 0.8615 (mmm) REVERT: D 238 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8385 (pttm) REVERT: E 18 ASN cc_start: 0.9130 (t0) cc_final: 0.8582 (t0) REVERT: E 67 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9011 (mm) REVERT: E 106 MET cc_start: 0.8624 (ttp) cc_final: 0.8210 (tmm) REVERT: E 120 GLN cc_start: 0.9332 (tp40) cc_final: 0.8968 (tp-100) REVERT: E 270 THR cc_start: 0.9728 (OUTLIER) cc_final: 0.9494 (p) REVERT: F 45 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9040 (mm) REVERT: F 106 MET cc_start: 0.9208 (mmm) cc_final: 0.8574 (tmm) REVERT: F 120 GLN cc_start: 0.9629 (tt0) cc_final: 0.9168 (tm-30) REVERT: F 309 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: G 229 MET cc_start: 0.8987 (tpp) cc_final: 0.8535 (tpp) REVERT: G 304 MET cc_start: 0.9600 (ttt) cc_final: 0.9140 (tmm) REVERT: H 106 MET cc_start: 0.9153 (tmm) cc_final: 0.8502 (tmm) REVERT: H 221 MET cc_start: 0.8986 (mmm) cc_final: 0.8601 (mmm) REVERT: H 229 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.8548 (tpp) REVERT: H 242 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9181 (mtpp) REVERT: H 284 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8993 (mtm110) outliers start: 89 outliers final: 70 residues processed: 207 average time/residue: 0.3714 time to fit residues: 126.0144 Evaluate side-chains 217 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 129 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain 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 54 LEU 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 137 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 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 44 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU 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 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 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 67 LEU 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 270 THR Chi-restraints excluded: chain E residue 329 PHE 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 108 SER Chi-restraints excluded: chain F residue 269 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 258 LEU Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 9 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.040816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.028620 restraints weight = 135778.756| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 3.97 r_work: 0.2390 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24965 Z= 0.207 Angle : 0.604 14.436 34247 Z= 0.309 Chirality : 0.041 0.323 3796 Planarity : 0.004 0.054 3967 Dihedral : 18.149 170.142 4477 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.93 % Allowed : 26.75 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2660 helix: 1.20 (0.19), residues: 795 sheet: 0.33 (0.26), residues: 443 loop : -1.11 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 264 HIS 0.003 0.001 HIS A 215 PHE 0.012 0.001 PHE J 92 TYR 0.014 0.001 TYR A 142 ARG 0.009 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 879) hydrogen bonds : angle 4.29671 ( 2398) covalent geometry : bond 0.00458 (24965) covalent geometry : angle 0.60359 (34247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12372.05 seconds wall clock time: 218 minutes 42.55 seconds (13122.55 seconds total)