Starting phenix.real_space_refine on Wed Mar 4 13:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhg_22336/03_2026/7jhg_22336.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.49 5 S 51 5.16 5 C 8589 2.51 5 N 2260 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3083 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'TAK': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.98, per 1000 atoms: 0.22 Number of scatterers: 13457 At special positions: 0 Unit cell: (100.842, 129.654, 164.64, 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 51 16.00 P 6 15.00 O 2551 8.00 N 2260 7.00 C 8589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " distance=2.04 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 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " TRANS " VAL A 13 " - " PHE M 371 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 662.9 milliseconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 27 sheets defined 29.3% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.742A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 114 through 135 removed outlier: 3.545A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 3.654A pdb=" N GLY A 169 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.973A pdb=" N THR A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.984A pdb=" N ASP A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.896A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.786A pdb=" N MET A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 549 removed outlier: 3.606A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 4.100A pdb=" N VAL B 215 " --> pdb=" O HIS B 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.698A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.570A pdb=" N ASP G 40 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE G 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.632A pdb=" N ALA G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.908A pdb=" N GLU G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.595A pdb=" N GLU G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.595A pdb=" N ARG G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.665A pdb=" N LEU G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.516A pdb=" N LEU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 223 removed outlier: 3.778A pdb=" N ALA G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 removed outlier: 3.756A pdb=" N ALA G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 284 through 295 removed outlier: 3.624A pdb=" N GLU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 324 removed outlier: 3.683A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 324 " --> pdb=" O GLN G 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 32 removed outlier: 3.540A pdb=" N LEU M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 66 through 73 removed outlier: 3.798A pdb=" N SER M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.753A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 163 removed outlier: 4.014A pdb=" N THR M 157 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.690A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 219 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'M' and resid 272 through 284 Processing helix chain 'M' and resid 286 through 297 removed outlier: 3.881A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 3.894A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 326 Processing helix chain 'M' and resid 334 through 352 removed outlier: 4.047A pdb=" N ALA M 338 " --> pdb=" O PRO M 334 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR M 341 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA M 342 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.747A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 128' Processing helix chain 'L' and resid 185 through 190 removed outlier: 4.018A pdb=" N GLU L 188 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 189 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.592A pdb=" N LEU H 205 " --> pdb=" O SER H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.583A pdb=" N VAL A 34 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR A 23 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 32 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 83 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU A 96 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 81 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404 removed outlier: 3.530A pdb=" N LYS A 427 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 242 through 243 removed outlier: 3.574A pdb=" N LYS B 270 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 255 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 14.468A pdb=" N ALA G 71 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N LYS G 47 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL G 49 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TRP G 75 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE G 51 " --> pdb=" O TRP G 75 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 154 through 156 removed outlier: 6.904A pdb=" N VAL G 155 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 207 through 208 removed outlier: 6.628A pdb=" N VAL G 207 " --> pdb=" O VAL G 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'G' and resid 278 through 280 removed outlier: 4.231A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.552A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.552A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'M' and resid 145 through 147 removed outlier: 8.149A pdb=" N SER M 145 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR M 225 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU M 147 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N ASN M 227 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA M 223 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 170 through 171 removed outlier: 3.951A pdb=" N LYS M 170 " --> pdb=" O ASP M 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.169A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.169A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.510A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.510A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER L 68 " --> pdb=" O ASP L 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.143A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.662A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA L 194 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.518A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER H 10 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AC4, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.826A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 136 through 140 removed outlier: 4.561A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 136 through 140 removed outlier: 4.561A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 185 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.735A pdb=" N TYR H 210 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.572A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 67 through 69 removed outlier: 3.552A pdb=" N PHE N 68 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP N 45 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL N 59 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET N 43 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL N 126 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS N 105 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN N 122 " --> pdb=" O CYS N 105 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE N 107 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP N 120 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4259 1.34 - 1.46: 3233 1.46 - 1.58: 6199 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13781 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.74e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.53e+01 ... (remaining 13776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 18592 3.78 - 7.55: 113 7.55 - 11.33: 9 11.33 - 15.11: 0 15.11 - 18.89: 2 Bond angle restraints: 18716 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 121.49 15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.99 -7.95 1.15e+00 7.59e-01 4.80e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.67 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 8174 27.79 - 55.57: 111 55.57 - 83.36: 16 83.36 - 111.15: 5 111.15 - 138.93: 3 Dihedral angle restraints: 8309 sinusoidal: 3347 harmonic: 4962 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 21.16 71.84 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" C5' ADP G 402 " pdb=" O5' ADP G 402 " pdb=" PA ADP G 402 " pdb=" O2A ADP G 402 " ideal model delta sinusoidal sigma weight residual 300.00 161.07 138.93 1 2.00e+01 2.50e-03 4.21e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 54.97 -114.97 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 8306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1863 0.081 - 0.162: 211 0.162 - 0.243: 11 0.243 - 0.325: 1 0.325 - 0.406: 1 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 GLC D 2 " pdb=" O4 GLC D 1 " pdb=" C2 GLC D 2 " pdb=" O5 GLC D 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.21e+00 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.36 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 2084 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO L 9 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 430 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 431 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 144 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.031 5.00e-02 4.00e+02 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4072 2.83 - 3.35: 11344 3.35 - 3.87: 21751 3.87 - 4.38: 24405 4.38 - 4.90: 42434 Nonbonded interactions: 104006 Sorted by model distance: nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.318 3.040 nonbonded pdb=" O HIS A 220 " pdb=" OG1 THR A 223 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR G 89 " pdb=" O1B ADP G 402 " model vdw 2.329 3.040 nonbonded pdb=" O TYR M 90 " pdb=" OG1 THR M 93 " model vdw 2.346 3.040 nonbonded pdb=" OD2 ASP G 52 " pdb=" OG SER G 54 " model vdw 2.347 3.040 ... (remaining 104001 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.004 0.082 13788 Z= 0.209 Angle : 0.793 18.887 18732 Z= 0.442 Chirality : 0.051 0.406 2087 Planarity : 0.007 0.059 2363 Dihedral : 10.253 138.933 5107 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.17), residues: 1683 helix: -2.89 (0.15), residues: 430 sheet: -1.67 (0.26), residues: 334 loop : -2.12 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 435 TYR 0.018 0.002 TYR H 102 PHE 0.029 0.002 PHE A 225 TRP 0.019 0.002 TRP A 200 HIS 0.009 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00358 (13781) covalent geometry : angle 0.78460 (18716) SS BOND : bond 0.00430 ( 5) SS BOND : angle 4.91287 ( 10) hydrogen bonds : bond 0.20111 ( 448) hydrogen bonds : angle 8.81068 ( 1326) link_ALPHA1-4 : bond 0.00905 ( 1) link_ALPHA1-4 : angle 0.93869 ( 3) link_TRANS : bond 0.00144 ( 1) link_TRANS : angle 0.21407 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.488 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 65 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7347 (mtm180) REVERT: A 117 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 141 ASP cc_start: 0.7325 (t0) cc_final: 0.6963 (m-30) REVERT: A 226 LYS cc_start: 0.8228 (tttt) cc_final: 0.7960 (tptp) REVERT: A 268 GLU cc_start: 0.8602 (tp30) cc_final: 0.7788 (pm20) REVERT: A 536 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 204 SER cc_start: 0.6588 (m) cc_final: 0.6289 (p) REVERT: B 249 SER cc_start: 0.7198 (t) cc_final: 0.6839 (p) REVERT: B 251 MET cc_start: 0.7669 (ttm) cc_final: 0.7425 (ttt) REVERT: B 261 LYS cc_start: 0.8681 (tptt) cc_final: 0.8359 (mmtm) REVERT: G 30 THR cc_start: 0.8416 (m) cc_final: 0.8022 (p) REVERT: G 39 TYR cc_start: 0.7490 (t80) cc_final: 0.6744 (t80) REVERT: G 58 LYS cc_start: 0.8106 (tttt) cc_final: 0.7902 (tptm) REVERT: G 105 GLN cc_start: 0.7779 (mt0) cc_final: 0.7543 (tm-30) REVERT: G 119 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7624 (pt0) REVERT: G 189 MET cc_start: 0.7968 (mmt) cc_final: 0.7458 (mmp) REVERT: G 198 ILE cc_start: 0.8086 (mt) cc_final: 0.7752 (mm) REVERT: G 201 TYR cc_start: 0.6626 (m-80) cc_final: 0.5778 (m-80) REVERT: G 206 MET cc_start: 0.6808 (mtm) cc_final: 0.6432 (ttm) REVERT: G 240 ILE cc_start: 0.6535 (tt) cc_final: 0.5593 (tt) REVERT: G 264 LYS cc_start: 0.8493 (mttt) cc_final: 0.8255 (mtmt) REVERT: G 280 TYR cc_start: 0.7134 (m-80) cc_final: 0.6694 (m-10) REVERT: M 10 TRP cc_start: 0.6793 (m-10) cc_final: 0.6530 (m-10) REVERT: M 22 GLU cc_start: 0.6652 (mt-10) cc_final: 0.5860 (tm-30) REVERT: M 55 ASP cc_start: 0.5917 (p0) cc_final: 0.5533 (t70) REVERT: M 90 TYR cc_start: 0.6264 (m-80) cc_final: 0.5268 (m-80) REVERT: M 171 TYR cc_start: 0.7592 (t80) cc_final: 0.7039 (t80) REVERT: M 189 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8379 (mmtm) REVERT: M 203 HIS cc_start: 0.4667 (m90) cc_final: 0.4441 (m-70) REVERT: M 270 SER cc_start: 0.4901 (t) cc_final: 0.4429 (p) REVERT: M 313 LYS cc_start: 0.6910 (mttt) cc_final: 0.6683 (tppt) REVERT: M 332 ASN cc_start: 0.7701 (p0) cc_final: 0.7048 (t0) REVERT: M 355 GLN cc_start: 0.8654 (mt0) cc_final: 0.8228 (tt0) REVERT: M 356 THR cc_start: 0.8225 (p) cc_final: 0.7775 (t) REVERT: L 5 MET cc_start: 0.5736 (ptp) cc_final: 0.5454 (ptp) REVERT: L 25 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7482 (mmm160) REVERT: L 71 ASP cc_start: 0.7756 (t70) cc_final: 0.7521 (t70) REVERT: L 80 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7683 (tp40) REVERT: L 101 GLN cc_start: 0.8452 (mm110) cc_final: 0.8098 (mm110) REVERT: L 143 ARG cc_start: 0.7960 (ttt-90) cc_final: 0.7309 (tpt90) REVERT: L 150 LYS cc_start: 0.8603 (mttt) cc_final: 0.8110 (mtmm) REVERT: L 191 LYS cc_start: 0.9083 (tttm) cc_final: 0.8532 (tptp) REVERT: L 196 GLU cc_start: 0.8387 (tt0) cc_final: 0.7489 (tp30) REVERT: H 163 PRO cc_start: 0.7586 (Cg_exo) cc_final: 0.7128 (Cg_endo) REVERT: H 164 GLU cc_start: 0.7655 (tp30) cc_final: 0.7368 (mm-30) REVERT: H 196 SER cc_start: 0.8345 (p) cc_final: 0.8003 (t) REVERT: H 217 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8233 (tppt) REVERT: N 16 SER cc_start: 0.7336 (p) cc_final: 0.6899 (p) REVERT: N 48 GLN cc_start: 0.5981 (tt0) cc_final: 0.4516 (tp40) REVERT: N 89 TYR cc_start: 0.6404 (m-80) cc_final: 0.5561 (m-80) REVERT: N 90 LEU cc_start: 0.6749 (tp) cc_final: 0.6326 (tp) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.1340 time to fit residues: 87.5087 Evaluate side-chains 256 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 77 HIS A 135 HIS A 146 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 252 GLN M 39 HIS M 64 HIS M 124 ASN M 335 GLN L 91 GLN L 125 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.150905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122434 restraints weight = 26418.472| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.58 r_work: 0.3380 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13788 Z= 0.252 Angle : 0.724 8.756 18732 Z= 0.367 Chirality : 0.047 0.185 2087 Planarity : 0.006 0.052 2363 Dihedral : 9.473 150.346 1952 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.75 % Allowed : 10.65 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.19), residues: 1683 helix: -1.06 (0.23), residues: 430 sheet: -1.18 (0.26), residues: 379 loop : -1.39 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 101 TYR 0.041 0.002 TYR L 50 PHE 0.022 0.002 PHE G 91 TRP 0.029 0.002 TRP H 119 HIS 0.008 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00582 (13781) covalent geometry : angle 0.72360 (18716) SS BOND : bond 0.00924 ( 5) SS BOND : angle 1.29223 ( 10) hydrogen bonds : bond 0.03866 ( 448) hydrogen bonds : angle 5.85071 ( 1326) link_ALPHA1-4 : bond 0.01160 ( 1) link_ALPHA1-4 : angle 1.88665 ( 3) link_TRANS : bond 0.00117 ( 1) link_TRANS : angle 0.41616 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8145 (m) cc_final: 0.7728 (t) REVERT: A 225 PHE cc_start: 0.7715 (m-10) cc_final: 0.7455 (m-10) REVERT: A 268 GLU cc_start: 0.8663 (tp30) cc_final: 0.8101 (pm20) REVERT: A 417 ARG cc_start: 0.7731 (ttt90) cc_final: 0.7353 (ptm160) REVERT: G 30 THR cc_start: 0.8011 (m) cc_final: 0.7794 (p) REVERT: G 121 TYR cc_start: 0.8012 (t80) cc_final: 0.7573 (t80) REVERT: G 147 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7758 (ptt90) REVERT: G 157 ASP cc_start: 0.8449 (t0) cc_final: 0.8236 (t0) REVERT: M 22 GLU cc_start: 0.6172 (mt-10) cc_final: 0.5879 (tm-30) REVERT: M 55 ASP cc_start: 0.6174 (p0) cc_final: 0.5165 (t0) REVERT: M 171 TYR cc_start: 0.7841 (t80) cc_final: 0.7544 (t80) REVERT: M 195 LEU cc_start: 0.8676 (tp) cc_final: 0.8421 (tp) REVERT: M 355 GLN cc_start: 0.8486 (mt0) cc_final: 0.8285 (mt0) REVERT: L 5 MET cc_start: 0.6801 (ptp) cc_final: 0.5657 (ppp) REVERT: L 43 LYS cc_start: 0.8903 (tppt) cc_final: 0.8637 (mmmm) REVERT: L 150 LYS cc_start: 0.8635 (mttt) cc_final: 0.8335 (mtmm) REVERT: H 154 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8835 (tp) REVERT: N 43 MET cc_start: 0.6837 (ttm) cc_final: 0.6579 (ttm) outliers start: 55 outliers final: 31 residues processed: 312 average time/residue: 0.1086 time to fit residues: 49.3678 Evaluate side-chains 226 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 17 TYR Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 0.0980 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 0.0000 chunk 59 optimal weight: 0.0570 chunk 73 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 42 HIS A 543 ASN G 148 ASN M 124 ASN M 218 ASN L 101 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.155074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.119436 restraints weight = 27516.877| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.12 r_work: 0.3508 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13788 Z= 0.106 Angle : 0.594 10.747 18732 Z= 0.293 Chirality : 0.043 0.156 2087 Planarity : 0.004 0.047 2363 Dihedral : 8.891 136.799 1952 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.94 % Allowed : 14.27 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1683 helix: -0.32 (0.24), residues: 432 sheet: -0.95 (0.27), residues: 359 loop : -1.06 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 98 TYR 0.018 0.001 TYR H 161 PHE 0.015 0.001 PHE M 250 TRP 0.027 0.001 TRP M 10 HIS 0.005 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00238 (13781) covalent geometry : angle 0.59342 (18716) SS BOND : bond 0.00266 ( 5) SS BOND : angle 1.02537 ( 10) hydrogen bonds : bond 0.03194 ( 448) hydrogen bonds : angle 5.35674 ( 1326) link_ALPHA1-4 : bond 0.00426 ( 1) link_ALPHA1-4 : angle 2.13563 ( 3) link_TRANS : bond 0.00117 ( 1) link_TRANS : angle 0.22012 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8033 (m) cc_final: 0.7651 (t) REVERT: A 268 GLU cc_start: 0.8495 (tp30) cc_final: 0.8067 (pm20) REVERT: A 417 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7385 (ptm160) REVERT: G 30 THR cc_start: 0.7999 (m) cc_final: 0.7793 (p) REVERT: G 105 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7852 (tm-30) REVERT: G 121 TYR cc_start: 0.7818 (t80) cc_final: 0.7381 (t80) REVERT: G 201 TYR cc_start: 0.7399 (m-10) cc_final: 0.7071 (m-10) REVERT: G 320 GLN cc_start: 0.8738 (tp40) cc_final: 0.8399 (tp-100) REVERT: M 22 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5906 (tm-30) REVERT: M 39 HIS cc_start: 0.6190 (p90) cc_final: 0.5966 (p-80) REVERT: M 42 LYS cc_start: 0.7654 (mmmt) cc_final: 0.6925 (mttp) REVERT: M 55 ASP cc_start: 0.6171 (p0) cc_final: 0.5047 (t0) REVERT: M 171 TYR cc_start: 0.7731 (t80) cc_final: 0.7486 (t80) REVERT: M 195 LEU cc_start: 0.8563 (tp) cc_final: 0.8286 (tp) REVERT: M 355 GLN cc_start: 0.8492 (mt0) cc_final: 0.8288 (mt0) REVERT: L 5 MET cc_start: 0.6539 (ptp) cc_final: 0.5819 (ppp) REVERT: L 91 GLN cc_start: 0.8902 (tm130) cc_final: 0.8682 (tm-30) REVERT: H 16 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: H 154 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8887 (tp) REVERT: H 164 GLU cc_start: 0.7785 (tp30) cc_final: 0.7543 (mm-30) REVERT: N 45 TRP cc_start: 0.7297 (m100) cc_final: 0.7068 (m-10) REVERT: N 89 TYR cc_start: 0.7635 (m-80) cc_final: 0.7325 (m-10) outliers start: 43 outliers final: 30 residues processed: 255 average time/residue: 0.1010 time to fit residues: 39.3576 Evaluate side-chains 229 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 124 ASN Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 86 optimal weight: 6.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 39 HIS M 49 GLN M 124 ASN M 203 HIS L 7 GLN H 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112584 restraints weight = 25930.351| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.32 r_work: 0.3381 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13788 Z= 0.175 Angle : 0.609 8.153 18732 Z= 0.305 Chirality : 0.043 0.151 2087 Planarity : 0.004 0.050 2363 Dihedral : 8.561 116.516 1952 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.28 % Allowed : 14.33 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1683 helix: -0.01 (0.25), residues: 426 sheet: -0.89 (0.26), residues: 375 loop : -0.88 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.022 0.002 TYR L 50 PHE 0.015 0.001 PHE G 91 TRP 0.028 0.002 TRP M 10 HIS 0.024 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00407 (13781) covalent geometry : angle 0.60796 (18716) SS BOND : bond 0.00343 ( 5) SS BOND : angle 1.26165 ( 10) hydrogen bonds : bond 0.03050 ( 448) hydrogen bonds : angle 5.19951 ( 1326) link_ALPHA1-4 : bond 0.00239 ( 1) link_ALPHA1-4 : angle 1.78502 ( 3) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.09005 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8421 (tpp80) REVERT: A 99 SER cc_start: 0.8407 (m) cc_final: 0.8029 (t) REVERT: A 268 GLU cc_start: 0.8607 (tp30) cc_final: 0.8101 (pm20) REVERT: A 417 ARG cc_start: 0.7705 (ttt90) cc_final: 0.7321 (ptm160) REVERT: G 105 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7816 (tm-30) REVERT: G 121 TYR cc_start: 0.8083 (t80) cc_final: 0.7765 (t80) REVERT: G 189 MET cc_start: 0.7581 (mmt) cc_final: 0.7137 (mmt) REVERT: G 320 GLN cc_start: 0.8789 (tp40) cc_final: 0.8451 (tp-100) REVERT: M 22 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6099 (tm-30) REVERT: M 55 ASP cc_start: 0.6222 (p0) cc_final: 0.5055 (t0) REVERT: M 171 TYR cc_start: 0.7872 (t80) cc_final: 0.7608 (t80) REVERT: M 195 LEU cc_start: 0.8659 (tp) cc_final: 0.8454 (tp) REVERT: M 365 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8427 (tm-30) REVERT: L 5 MET cc_start: 0.6742 (ptp) cc_final: 0.6048 (ppp) REVERT: L 91 GLN cc_start: 0.9068 (tm130) cc_final: 0.8816 (tm-30) REVERT: N 89 TYR cc_start: 0.7590 (m-80) cc_final: 0.7250 (m-10) outliers start: 48 outliers final: 36 residues processed: 239 average time/residue: 0.0922 time to fit residues: 34.1073 Evaluate side-chains 211 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 HIS M 355 GLN ** L 7 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 = 0.4101 r_free = 0.4101 target = 0.149074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114778 restraints weight = 26492.894| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.06 r_work: 0.3420 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13788 Z= 0.146 Angle : 0.579 8.327 18732 Z= 0.288 Chirality : 0.043 0.150 2087 Planarity : 0.004 0.049 2363 Dihedral : 8.242 116.047 1952 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.41 % Allowed : 15.02 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1683 helix: 0.20 (0.25), residues: 427 sheet: -0.74 (0.26), residues: 380 loop : -0.79 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 76 TYR 0.018 0.001 TYR G 98 PHE 0.022 0.001 PHE H 71 TRP 0.031 0.002 TRP N 45 HIS 0.017 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00343 (13781) covalent geometry : angle 0.57851 (18716) SS BOND : bond 0.00226 ( 5) SS BOND : angle 1.10115 ( 10) hydrogen bonds : bond 0.02924 ( 448) hydrogen bonds : angle 5.10490 ( 1326) link_ALPHA1-4 : bond 0.00209 ( 1) link_ALPHA1-4 : angle 1.71372 ( 3) link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.07271 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8674 (tpp-160) cc_final: 0.8405 (tpp80) REVERT: A 99 SER cc_start: 0.8366 (m) cc_final: 0.8038 (t) REVERT: A 268 GLU cc_start: 0.8523 (tp30) cc_final: 0.8074 (pm20) REVERT: A 417 ARG cc_start: 0.7711 (ttt90) cc_final: 0.7333 (ptm160) REVERT: G 105 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7750 (tm-30) REVERT: G 189 MET cc_start: 0.7549 (mmt) cc_final: 0.7155 (mmt) REVERT: G 320 GLN cc_start: 0.8772 (tp40) cc_final: 0.8413 (tp-100) REVERT: M 22 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6072 (tm-30) REVERT: M 90 TYR cc_start: 0.7017 (m-80) cc_final: 0.6763 (m-80) REVERT: M 171 TYR cc_start: 0.7847 (t80) cc_final: 0.7618 (t80) REVERT: M 365 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8392 (tm-30) REVERT: L 5 MET cc_start: 0.6746 (ptp) cc_final: 0.6213 (ppp) REVERT: L 196 GLU cc_start: 0.8540 (tt0) cc_final: 0.8186 (tp30) REVERT: N 29 LEU cc_start: 0.8133 (mt) cc_final: 0.7834 (mt) outliers start: 50 outliers final: 37 residues processed: 235 average time/residue: 0.0987 time to fit residues: 35.5518 Evaluate side-chains 213 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 41 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 HIS L 7 GLN L 91 GLN ** L 199 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.147674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113624 restraints weight = 26286.536| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.17 r_work: 0.3451 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13788 Z= 0.116 Angle : 0.564 7.690 18732 Z= 0.281 Chirality : 0.043 0.185 2087 Planarity : 0.004 0.047 2363 Dihedral : 8.033 116.364 1952 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.62 % Allowed : 15.56 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1683 helix: 0.44 (0.26), residues: 428 sheet: -0.68 (0.26), residues: 382 loop : -0.66 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.015 0.001 TYR G 272 PHE 0.019 0.001 PHE H 71 TRP 0.040 0.002 TRP N 45 HIS 0.010 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00271 (13781) covalent geometry : angle 0.56365 (18716) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.98652 ( 10) hydrogen bonds : bond 0.02811 ( 448) hydrogen bonds : angle 4.95797 ( 1326) link_ALPHA1-4 : bond 0.00352 ( 1) link_ALPHA1-4 : angle 1.49594 ( 3) link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 0.01728 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8676 (tpp-160) cc_final: 0.8080 (mtm180) REVERT: A 99 SER cc_start: 0.8405 (m) cc_final: 0.8056 (t) REVERT: A 268 GLU cc_start: 0.8479 (tp30) cc_final: 0.8062 (pm20) REVERT: A 417 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7366 (ptm160) REVERT: A 453 LEU cc_start: 0.8046 (mp) cc_final: 0.6988 (tp) REVERT: G 105 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7844 (tm-30) REVERT: G 189 MET cc_start: 0.7578 (mmt) cc_final: 0.7147 (mmt) REVERT: G 320 GLN cc_start: 0.8702 (tp40) cc_final: 0.8288 (tp40) REVERT: M 22 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6044 (tm-30) REVERT: M 90 TYR cc_start: 0.6968 (m-80) cc_final: 0.6762 (m-80) REVERT: M 171 TYR cc_start: 0.7824 (t80) cc_final: 0.7580 (t80) REVERT: M 291 GLU cc_start: 0.7057 (tp30) cc_final: 0.6805 (tp30) REVERT: M 365 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8422 (tm-30) REVERT: L 5 MET cc_start: 0.6909 (ptp) cc_final: 0.6161 (ppp) REVERT: L 196 GLU cc_start: 0.8508 (tt0) cc_final: 0.8131 (tp30) REVERT: N 29 LEU cc_start: 0.8102 (mt) cc_final: 0.7863 (mt) REVERT: N 99 ASP cc_start: 0.5700 (t0) cc_final: 0.5500 (m-30) outliers start: 53 outliers final: 37 residues processed: 234 average time/residue: 0.0929 time to fit residues: 34.1770 Evaluate side-chains 214 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN H 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112011 restraints weight = 26106.403| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.10 r_work: 0.3426 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13788 Z= 0.138 Angle : 0.585 8.359 18732 Z= 0.291 Chirality : 0.043 0.155 2087 Planarity : 0.004 0.051 2363 Dihedral : 8.037 116.131 1952 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.34 % Allowed : 16.79 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1683 helix: 0.56 (0.26), residues: 428 sheet: -0.65 (0.26), residues: 381 loop : -0.62 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 258 TYR 0.016 0.001 TYR L 50 PHE 0.014 0.001 PHE H 71 TRP 0.029 0.002 TRP N 45 HIS 0.015 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00325 (13781) covalent geometry : angle 0.58393 (18716) SS BOND : bond 0.00354 ( 5) SS BOND : angle 1.20561 ( 10) hydrogen bonds : bond 0.02859 ( 448) hydrogen bonds : angle 4.93535 ( 1326) link_ALPHA1-4 : bond 0.00171 ( 1) link_ALPHA1-4 : angle 1.41720 ( 3) link_TRANS : bond 0.00047 ( 1) link_TRANS : angle 0.11843 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8671 (tpp-160) cc_final: 0.8075 (mtm180) REVERT: A 268 GLU cc_start: 0.8581 (tp30) cc_final: 0.8142 (pm20) REVERT: A 417 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7427 (ptm160) REVERT: A 432 TYR cc_start: 0.6263 (m-10) cc_final: 0.5947 (m-10) REVERT: G 105 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7912 (tm-30) REVERT: G 189 MET cc_start: 0.7542 (mmt) cc_final: 0.7120 (mmt) REVERT: M 22 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6084 (tm-30) REVERT: M 62 TRP cc_start: 0.8305 (t-100) cc_final: 0.7435 (t-100) REVERT: M 171 TYR cc_start: 0.7816 (t80) cc_final: 0.7587 (t80) REVERT: M 291 GLU cc_start: 0.7152 (tp30) cc_final: 0.6909 (tp30) REVERT: M 365 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8438 (tm-30) REVERT: L 5 MET cc_start: 0.6917 (ptp) cc_final: 0.6186 (ppp) REVERT: L 196 GLU cc_start: 0.8487 (tt0) cc_final: 0.8274 (tp30) REVERT: N 99 ASP cc_start: 0.5785 (t0) cc_final: 0.5465 (m-30) outliers start: 49 outliers final: 39 residues processed: 229 average time/residue: 0.0986 time to fit residues: 34.9340 Evaluate side-chains 213 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 HIS B 257 HIS G 223 HIS M 39 HIS L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113744 restraints weight = 25888.700| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.68 r_work: 0.3240 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13788 Z= 0.251 Angle : 0.677 8.756 18732 Z= 0.342 Chirality : 0.046 0.221 2087 Planarity : 0.005 0.059 2363 Dihedral : 8.458 116.212 1952 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.55 % Allowed : 17.34 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1683 helix: 0.29 (0.25), residues: 425 sheet: -0.80 (0.26), residues: 376 loop : -0.70 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 101 TYR 0.028 0.002 TYR H 97 PHE 0.026 0.002 PHE H 71 TRP 0.046 0.003 TRP M 10 HIS 0.011 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00586 (13781) covalent geometry : angle 0.67679 (18716) SS BOND : bond 0.00496 ( 5) SS BOND : angle 1.41040 ( 10) hydrogen bonds : bond 0.03327 ( 448) hydrogen bonds : angle 5.23824 ( 1326) link_ALPHA1-4 : bond 0.00267 ( 1) link_ALPHA1-4 : angle 1.20412 ( 3) link_TRANS : bond 0.00045 ( 1) link_TRANS : angle 0.31573 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7674 (tpp) cc_final: 0.7441 (tpt) REVERT: A 417 ARG cc_start: 0.7842 (ttt90) cc_final: 0.7499 (ptm160) REVERT: A 425 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7181 (mp0) REVERT: B 235 HIS cc_start: 0.6960 (m-70) cc_final: 0.6592 (t70) REVERT: G 85 MET cc_start: 0.8912 (tpp) cc_final: 0.8666 (mmt) REVERT: G 105 GLN cc_start: 0.8594 (tm-30) cc_final: 0.7983 (tm-30) REVERT: G 189 MET cc_start: 0.7566 (mmt) cc_final: 0.7086 (mmt) REVERT: M 22 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6062 (tm-30) REVERT: M 171 TYR cc_start: 0.8044 (t80) cc_final: 0.7790 (t80) REVERT: M 365 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8534 (tm-30) REVERT: L 5 MET cc_start: 0.7071 (ptp) cc_final: 0.6797 (ptp) outliers start: 52 outliers final: 41 residues processed: 223 average time/residue: 0.0946 time to fit residues: 32.7037 Evaluate side-chains 206 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 39 HIS Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 258 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 145 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 240 HIS L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116921 restraints weight = 25970.968| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 4.30 r_work: 0.3331 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13788 Z= 0.117 Angle : 0.608 9.851 18732 Z= 0.305 Chirality : 0.043 0.164 2087 Planarity : 0.004 0.055 2363 Dihedral : 8.205 115.753 1952 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.39 % Allowed : 18.43 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1683 helix: 0.60 (0.26), residues: 423 sheet: -0.84 (0.26), residues: 354 loop : -0.60 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 258 TYR 0.016 0.001 TYR G 272 PHE 0.017 0.001 PHE A 29 TRP 0.046 0.002 TRP M 10 HIS 0.025 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00273 (13781) covalent geometry : angle 0.60769 (18716) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.02295 ( 10) hydrogen bonds : bond 0.02810 ( 448) hydrogen bonds : angle 5.03448 ( 1326) link_ALPHA1-4 : bond 0.00026 ( 1) link_ALPHA1-4 : angle 1.23504 ( 3) link_TRANS : bond 0.00149 ( 1) link_TRANS : angle 0.22914 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8055 (mtm180) REVERT: A 268 GLU cc_start: 0.8680 (tp30) cc_final: 0.8322 (pm20) REVERT: A 417 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7468 (ptm160) REVERT: B 235 HIS cc_start: 0.6749 (m-70) cc_final: 0.6536 (t70) REVERT: G 85 MET cc_start: 0.8787 (tpp) cc_final: 0.8526 (mmt) REVERT: G 105 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7947 (tm-30) REVERT: G 189 MET cc_start: 0.7530 (mmt) cc_final: 0.7096 (mmt) REVERT: M 22 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6039 (tm-30) REVERT: M 62 TRP cc_start: 0.8367 (t-100) cc_final: 0.7539 (t-100) REVERT: M 171 TYR cc_start: 0.7865 (t80) cc_final: 0.7644 (t80) REVERT: M 204 MET cc_start: 0.7792 (tpt) cc_final: 0.7575 (tpt) REVERT: M 251 LYS cc_start: 0.8188 (mttt) cc_final: 0.7326 (mmtp) REVERT: M 291 GLU cc_start: 0.7408 (tp30) cc_final: 0.7097 (tp30) REVERT: M 365 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8483 (tm-30) REVERT: L 5 MET cc_start: 0.6806 (ptp) cc_final: 0.6592 (ptp) REVERT: N 99 ASP cc_start: 0.5928 (t0) cc_final: 0.5150 (m-30) outliers start: 35 outliers final: 29 residues processed: 209 average time/residue: 0.0903 time to fit residues: 29.6655 Evaluate side-chains 205 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS L 80 GLN L 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110606 restraints weight = 26044.981| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.05 r_work: 0.3365 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13788 Z= 0.154 Angle : 0.618 10.395 18732 Z= 0.309 Chirality : 0.044 0.178 2087 Planarity : 0.004 0.056 2363 Dihedral : 8.212 115.909 1952 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.25 % Allowed : 19.04 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1683 helix: 0.61 (0.26), residues: 421 sheet: -0.83 (0.26), residues: 352 loop : -0.61 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.021 0.001 TYR L 50 PHE 0.025 0.002 PHE L 210 TRP 0.068 0.003 TRP H 170 HIS 0.009 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00366 (13781) covalent geometry : angle 0.61718 (18716) SS BOND : bond 0.00439 ( 5) SS BOND : angle 1.20433 ( 10) hydrogen bonds : bond 0.02902 ( 448) hydrogen bonds : angle 5.06337 ( 1326) link_ALPHA1-4 : bond 0.00125 ( 1) link_ALPHA1-4 : angle 1.17848 ( 3) link_TRANS : bond 0.00077 ( 1) link_TRANS : angle 0.17368 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8098 (mtm180) REVERT: A 417 ARG cc_start: 0.7813 (ttt90) cc_final: 0.7486 (ptm160) REVERT: A 425 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7101 (mp0) REVERT: B 235 HIS cc_start: 0.6780 (m-70) cc_final: 0.6444 (t70) REVERT: G 85 MET cc_start: 0.8816 (tpp) cc_final: 0.8570 (mmt) REVERT: G 105 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 189 MET cc_start: 0.7476 (mmt) cc_final: 0.7059 (mmt) REVERT: M 22 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6049 (tm-30) REVERT: M 171 TYR cc_start: 0.7747 (t80) cc_final: 0.7487 (t80) REVERT: M 204 MET cc_start: 0.7793 (tpt) cc_final: 0.7570 (tpt) REVERT: M 251 LYS cc_start: 0.8195 (mttt) cc_final: 0.7306 (mmtp) REVERT: M 291 GLU cc_start: 0.7392 (tp30) cc_final: 0.7140 (tp30) REVERT: M 365 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8489 (tm-30) REVERT: H 199 THR cc_start: 0.7765 (m) cc_final: 0.7491 (t) outliers start: 33 outliers final: 27 residues processed: 212 average time/residue: 0.0962 time to fit residues: 31.2022 Evaluate side-chains 202 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 187 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 0.0000 chunk 148 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110034 restraints weight = 26204.738| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.13 r_work: 0.3385 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13788 Z= 0.127 Angle : 0.622 10.725 18732 Z= 0.308 Chirality : 0.043 0.167 2087 Planarity : 0.004 0.055 2363 Dihedral : 8.132 115.678 1952 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 19.39 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1683 helix: 0.69 (0.26), residues: 426 sheet: -0.80 (0.26), residues: 354 loop : -0.61 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 258 TYR 0.019 0.001 TYR L 50 PHE 0.021 0.001 PHE L 117 TRP 0.055 0.002 TRP H 170 HIS 0.010 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00301 (13781) covalent geometry : angle 0.62158 (18716) SS BOND : bond 0.00457 ( 5) SS BOND : angle 1.30452 ( 10) hydrogen bonds : bond 0.02794 ( 448) hydrogen bonds : angle 4.99689 ( 1326) link_ALPHA1-4 : bond 0.00087 ( 1) link_ALPHA1-4 : angle 1.15328 ( 3) link_TRANS : bond 0.00124 ( 1) link_TRANS : angle 0.22968 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3328.38 seconds wall clock time: 57 minutes 46.55 seconds (3466.55 seconds total)