Starting phenix.real_space_refine on Sat Sep 12 05:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhg_22336/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhg_22336/09_2026/7jhg_22336.map" } 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-2.2.1-6174/lib/python3.11/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 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, 'ATP': 1} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.95, 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: 1.26 Conformation dependent library (CDL) restraints added in 530.2 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: 0.44 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: 2.33 Time building geometry restraints manager: 1.66 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: 18597 3.78 - 7.55: 108 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: 8125 27.79 - 55.57: 97 55.57 - 83.36: 16 83.36 - 111.15: 5 111.15 - 138.93: 3 Dihedral angle restraints: 8246 sinusoidal: 3284 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 8243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.938: 2086 0.938 - 1.877: 0 1.877 - 2.815: 0 2.815 - 3.753: 0 3.753 - 4.692: 1 Chirality restraints: 2087 Sorted by residual: 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 2.33 -2.36 4.69 2.00e-01 2.50e+01 5.50e+02 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 ... (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: 1.010 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 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= 0.208 Angle : 0.787 18.887 18732 Z= 0.441 Chirality : 0.114 4.692 2087 Planarity : 0.007 0.059 2363 Dihedral : 10.047 138.933 5044 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/Z covalent geometry : bond 0.00355 / 0.21 (13781) covalent geometry : angle 0.77880 / 0.44 (18716) SS BOND : bond 0.00430 / 0.23 ( 5) SS BOND : angle 4.91287 / 2.84 ( 10) hydrogen bonds : bond 0.20111 / 13.47 ( 448) hydrogen bonds : angle 8.81068 / 6.22 ( 1326) link_ALPHA1-4 : bond 0.00905 / 0.48 ( 1) link_ALPHA1-4 : angle 0.93869 / 0.52 ( 3) link_TRANS : bond 0.00144 / 0.08 ( 1) link_TRANS : angle 0.21407 / 0.12 ( 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 : 0.536 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: 0.1388 time to fit residues: 91.5065 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 : 0.537 ------------------------------------------------------------------------------- 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: 8.9990 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... A 37 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.123356 restraints weight = 26502.619| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 4.59 r_work: 0.3409 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 13788 Z= 0.245 Angle : 0.720 8.816 18732 Z= 0.363 Chirality : 0.047 0.185 2087 Planarity : 0.006 0.053 2363 Dihedral : 9.009 149.694 1889 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.69 % Allowed : 10.51 % Favored : 85.80 % 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: -2.02 (0.19), residues: 1683 helix: -1.18 (0.22), residues: 437 sheet: -1.24 (0.26), residues: 372 loop : -1.40 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 101 TYR 0.038 0.002 TYR L 50 PHE 0.021 0.002 PHE G 91 TRP 0.027 0.002 TRP H 119 HIS 0.008 0.002 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (13781) covalent geometry : angle 0.71850 / 0.36 (18716) SS BOND : bond 0.00318 / 0.15 ( 5) SS BOND : angle 1.42073 / 0.85 ( 10) hydrogen bonds : bond 0.04129 / 2.83 ( 448) hydrogen bonds : angle 5.94054 / 4.16 ( 1326) link_ALPHA1-4 : bond 0.00476 / 0.25 ( 1) link_ALPHA1-4 : angle 2.52925 / 1.27 ( 3) link_TRANS : bond 0.00135 / 0.07 ( 1) link_TRANS : angle 0.37854 / 0.18 ( 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 322 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 SER cc_start: 0.8090 (m) cc_final: 0.7675 (t) REVERT: A 225 PHE cc_start: 0.7600 (m-10) cc_final: 0.7350 (m-10) REVERT: A 268 GLU cc_start: 0.8646 (tp30) cc_final: 0.8093 (pm20) REVERT: G 30 THR cc_start: 0.7990 (m) cc_final: 0.7771 (p) REVERT: G 147 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7724 (ptt90) REVERT: G 201 TYR cc_start: 0.7313 (m-80) cc_final: 0.6366 (m-80) REVERT: M 22 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5833 (tm-30) REVERT: M 55 ASP cc_start: 0.6236 (p0) cc_final: 0.5232 (t0) REVERT: M 171 TYR cc_start: 0.7839 (t80) cc_final: 0.7544 (t80) REVERT: M 195 LEU cc_start: 0.8649 (tp) cc_final: 0.8378 (tp) REVERT: L 5 MET cc_start: 0.6738 (ptp) cc_final: 0.5603 (ppp) REVERT: L 43 LYS cc_start: 0.8866 (tppt) cc_final: 0.8567 (mmmm) REVERT: L 150 LYS cc_start: 0.8622 (mttt) cc_final: 0.8355 (mtmm) REVERT: H 109 TYR cc_start: 0.7753 (p90) cc_final: 0.7381 (p90) REVERT: H 154 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8826 (tp) REVERT: N 43 MET cc_start: 0.6803 (ttm) cc_final: 0.6566 (ttm) REVERT: N 48 GLN cc_start: 0.6622 (tt0) cc_final: 0.5672 (tp40) outliers start: 54 outliers final: 31 residues processed: 307 average time/residue: 0.1193 time to fit residues: 53.9414 Evaluate side-chains 230 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP 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 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 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 H residue 72 THR 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: 0.7980 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN G 148 ASN M 124 ASN M 218 ASN M 355 GLN L 101 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119559 restraints weight = 27402.507| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.95 r_work: 0.3484 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13788 Z= 0.135 Angle : 0.604 10.446 18732 Z= 0.297 Chirality : 0.043 0.156 2087 Planarity : 0.004 0.047 2363 Dihedral : 8.618 133.492 1889 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.94 % Allowed : 13.99 % Favored : 83.07 % 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: -1.41 (0.20), residues: 1683 helix: -0.38 (0.24), residues: 432 sheet: -1.03 (0.26), residues: 369 loop : -1.11 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 98 TYR 0.017 0.001 TYR H 161 PHE 0.015 0.001 PHE M 250 TRP 0.026 0.002 TRP M 10 HIS 0.007 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13781) covalent geometry : angle 0.60380 / 0.30 (18716) SS BOND : bond 0.00291 / 0.15 ( 5) SS BOND : angle 1.04738 / 0.62 ( 10) hydrogen bonds : bond 0.03260 / 2.17 ( 448) hydrogen bonds : angle 5.40245 / 3.81 ( 1326) link_ALPHA1-4 : bond 0.00345 / 0.18 ( 1) link_ALPHA1-4 : angle 1.80047 / 0.91 ( 3) link_TRANS : bond 0.00017 / 0.01 ( 1) link_TRANS : angle 0.18371 / 0.09 ( 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 269 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8643 (mtt) cc_final: 0.8442 (mtm) REVERT: A 99 SER cc_start: 0.8036 (m) cc_final: 0.7638 (t) REVERT: A 268 GLU cc_start: 0.8496 (tp30) cc_final: 0.8074 (pm20) REVERT: A 417 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7349 (ptm160) REVERT: G 105 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7908 (tm-30) REVERT: G 107 TYR cc_start: 0.6655 (m-80) cc_final: 0.6426 (m-80) REVERT: G 121 TYR cc_start: 0.7874 (t80) cc_final: 0.7467 (t80) REVERT: G 147 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (ptt90) REVERT: G 189 MET cc_start: 0.7666 (mmt) cc_final: 0.7289 (mmt) REVERT: G 320 GLN cc_start: 0.8741 (tp40) cc_final: 0.8400 (tp-100) REVERT: M 22 GLU cc_start: 0.6404 (mt-10) cc_final: 0.5986 (tm-30) REVERT: M 42 LYS cc_start: 0.7678 (mmmt) cc_final: 0.6913 (mttp) REVERT: M 55 ASP cc_start: 0.6155 (p0) cc_final: 0.5107 (t0) REVERT: M 171 TYR cc_start: 0.7752 (t80) cc_final: 0.7511 (t80) REVERT: M 195 LEU cc_start: 0.8599 (tp) cc_final: 0.8353 (tp) REVERT: L 5 MET cc_start: 0.6612 (ptp) cc_final: 0.5897 (ppp) REVERT: L 43 LYS cc_start: 0.8739 (tppt) cc_final: 0.8446 (mmmm) REVERT: L 117 PHE cc_start: 0.8388 (m-80) cc_final: 0.8102 (m-80) REVERT: L 150 LYS cc_start: 0.8617 (mttt) cc_final: 0.8365 (mtmm) REVERT: H 154 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8899 (tp) REVERT: H 164 GLU cc_start: 0.7751 (tp30) cc_final: 0.7512 (mm-30) REVERT: N 45 TRP cc_start: 0.7312 (m100) cc_final: 0.7078 (m-10) outliers start: 43 outliers final: 31 residues processed: 259 average time/residue: 0.1063 time to fit residues: 41.6261 Evaluate side-chains 221 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 40 ASP 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 147 ARG Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain M residue 124 ASN Chi-restraints excluded: chain M residue 279 PHE 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 171 ASP 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 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: 1.9990 chunk 108 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN L 91 GLN H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.147508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.114211 restraints weight = 26117.949| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.06 r_work: 0.3414 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13788 Z= 0.143 Angle : 0.583 8.056 18732 Z= 0.291 Chirality : 0.043 0.148 2087 Planarity : 0.004 0.062 2363 Dihedral : 8.166 116.052 1889 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.34 % Allowed : 14.74 % Favored : 81.91 % 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: -0.97 (0.20), residues: 1683 helix: 0.07 (0.25), residues: 427 sheet: -0.86 (0.26), residues: 379 loop : -0.82 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.018 0.001 TYR L 50 PHE 0.017 0.001 PHE H 71 TRP 0.031 0.001 TRP M 10 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13781) covalent geometry : angle 0.58249 / 0.29 (18716) SS BOND : bond 0.00561 / 0.28 ( 5) SS BOND : angle 1.19486 / 0.70 ( 10) hydrogen bonds : bond 0.03017 / 2.02 ( 448) hydrogen bonds : angle 5.14985 / 3.64 ( 1326) link_ALPHA1-4 : bond 0.00377 / 0.20 ( 1) link_ALPHA1-4 : angle 1.68791 / 0.87 ( 3) link_TRANS : bond 0.00015 / 0.01 ( 1) link_TRANS : angle 0.02897 / 0.02 ( 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 252 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8130 (m-70) REVERT: A 65 ARG cc_start: 0.8668 (tpp-160) cc_final: 0.8422 (tpp80) REVERT: A 99 SER cc_start: 0.8296 (m) cc_final: 0.7911 (t) REVERT: A 268 GLU cc_start: 0.8529 (tp30) cc_final: 0.8104 (pm20) REVERT: A 417 ARG cc_start: 0.7691 (ttt90) cc_final: 0.7314 (ptm160) REVERT: G 105 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7672 (tm-30) REVERT: G 107 TYR cc_start: 0.6832 (m-80) cc_final: 0.6477 (m-80) REVERT: G 189 MET cc_start: 0.7558 (mmt) cc_final: 0.7176 (mmt) REVERT: G 320 GLN cc_start: 0.8765 (tp40) cc_final: 0.8418 (tp-100) REVERT: M 22 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6093 (tm-30) REVERT: M 55 ASP cc_start: 0.6206 (p0) cc_final: 0.5021 (t0) REVERT: M 171 TYR cc_start: 0.7842 (t80) cc_final: 0.7594 (t80) REVERT: M 195 LEU cc_start: 0.8638 (tp) cc_final: 0.8434 (tp) REVERT: M 365 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8378 (tm-30) REVERT: L 5 MET cc_start: 0.6815 (ptp) cc_final: 0.6001 (ppp) REVERT: L 43 LYS cc_start: 0.8806 (tppt) cc_final: 0.8514 (mmmm) REVERT: L 150 LYS cc_start: 0.8569 (mttt) cc_final: 0.8332 (mtmm) outliers start: 49 outliers final: 35 residues processed: 241 average time/residue: 0.1019 time to fit residues: 38.0299 Evaluate side-chains 223 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS 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 434 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 222 GLN Chi-restraints excluded: chain G residue 308 VAL 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 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 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 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 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: 0.9980 chunk 153 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS G 36 HIS M 203 HIS H 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.112714 restraints weight = 26318.691| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.12 r_work: 0.3387 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13788 Z= 0.139 Angle : 0.580 8.905 18732 Z= 0.286 Chirality : 0.043 0.147 2087 Planarity : 0.004 0.046 2363 Dihedral : 7.963 115.395 1889 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.89 % Allowed : 14.20 % Favored : 81.91 % 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: -0.72 (0.21), residues: 1683 helix: 0.32 (0.25), residues: 422 sheet: -0.65 (0.26), residues: 380 loop : -0.71 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 101 TYR 0.018 0.001 TYR G 98 PHE 0.017 0.001 PHE G 273 TRP 0.035 0.002 TRP N 45 HIS 0.008 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13781) covalent geometry : angle 0.57932 / 0.29 (18716) SS BOND : bond 0.00294 / 0.14 ( 5) SS BOND : angle 1.08182 / 0.63 ( 10) hydrogen bonds : bond 0.02914 / 1.95 ( 448) hydrogen bonds : angle 4.95322 / 3.50 ( 1326) link_ALPHA1-4 : bond 0.00103 / 0.05 ( 1) link_ALPHA1-4 : angle 1.60367 / 0.83 ( 3) link_TRANS : bond 0.00069 / 0.04 ( 1) link_TRANS : angle 0.12238 / 0.06 ( 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 266 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8268 (m-70) REVERT: A 65 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8068 (mtm180) REVERT: A 73 PHE cc_start: 0.7216 (m-80) cc_final: 0.6889 (m-80) REVERT: A 268 GLU cc_start: 0.8547 (tp30) cc_final: 0.8130 (pm20) REVERT: A 417 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7375 (ptm160) REVERT: G 105 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7665 (tm-30) REVERT: G 107 TYR cc_start: 0.6901 (m-80) cc_final: 0.6519 (m-80) REVERT: G 320 GLN cc_start: 0.8781 (tp40) cc_final: 0.8370 (tp40) REVERT: M 22 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6043 (tm-30) REVERT: M 171 TYR cc_start: 0.7848 (t80) cc_final: 0.7626 (t80) REVERT: M 291 GLU cc_start: 0.7159 (tp30) cc_final: 0.6937 (tp30) REVERT: M 365 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8394 (tm-30) REVERT: L 5 MET cc_start: 0.6830 (ptp) cc_final: 0.6156 (ppp) REVERT: L 43 LYS cc_start: 0.8840 (tppt) cc_final: 0.8463 (mmmm) REVERT: N 29 LEU cc_start: 0.7957 (mt) cc_final: 0.7675 (mt) outliers start: 57 outliers final: 41 residues processed: 254 average time/residue: 0.1070 time to fit residues: 41.2936 Evaluate side-chains 219 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 261 ILE 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 B residue 264 VAL Chi-restraints excluded: chain G residue 40 ASP 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 120 ASP Chi-restraints excluded: chain M residue 279 PHE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 62 ARG 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 118 optimal weight: 0.0010 chunk 167 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 257 HIS ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.148241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115425 restraints weight = 26534.915| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.09 r_work: 0.3427 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13788 Z= 0.106 Angle : 0.560 7.490 18732 Z= 0.278 Chirality : 0.042 0.191 2087 Planarity : 0.004 0.049 2363 Dihedral : 7.860 115.450 1889 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 16.25 % 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: -0.51 (0.21), residues: 1683 helix: 0.57 (0.26), residues: 423 sheet: -0.61 (0.26), residues: 387 loop : -0.58 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.015 0.001 TYR G 272 PHE 0.019 0.001 PHE L 210 TRP 0.040 0.002 TRP N 45 HIS 0.010 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13781) covalent geometry : angle 0.55970 / 0.28 (18716) SS BOND : bond 0.00313 / 0.17 ( 5) SS BOND : angle 1.12158 / 0.65 ( 10) hydrogen bonds : bond 0.02761 / 1.85 ( 448) hydrogen bonds : angle 4.82969 / 3.42 ( 1326) link_ALPHA1-4 : bond 0.00246 / 0.13 ( 1) link_ALPHA1-4 : angle 1.64757 / 0.84 ( 3) link_TRANS : bond 0.00067 / 0.04 ( 1) link_TRANS : angle 0.07510 / 0.04 ( 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 237 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.8192 (m-70) REVERT: A 65 ARG cc_start: 0.8671 (tpp-160) cc_final: 0.8099 (mtm180) REVERT: A 93 MET cc_start: 0.8833 (mtp) cc_final: 0.8617 (mtp) REVERT: A 268 GLU cc_start: 0.8515 (tp30) cc_final: 0.8126 (pm20) REVERT: A 417 ARG cc_start: 0.7716 (ttt90) cc_final: 0.7358 (ptm160) REVERT: G 105 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7653 (tm-30) REVERT: G 107 TYR cc_start: 0.6820 (m-80) cc_final: 0.6374 (m-80) REVERT: G 189 MET cc_start: 0.7615 (mmt) cc_final: 0.7248 (mmp) REVERT: G 320 GLN cc_start: 0.8702 (tp40) cc_final: 0.8296 (tp40) REVERT: M 22 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6100 (tm-30) REVERT: M 62 TRP cc_start: 0.8231 (t-100) cc_final: 0.7697 (t-100) REVERT: M 171 TYR cc_start: 0.7787 (t80) cc_final: 0.7576 (t80) REVERT: M 365 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8404 (tm-30) REVERT: L 5 MET cc_start: 0.6719 (ptp) cc_final: 0.6215 (ppp) REVERT: H 220 ASN cc_start: 0.8487 (m-40) cc_final: 0.8158 (p0) outliers start: 43 outliers final: 31 residues processed: 228 average time/residue: 0.0984 time to fit residues: 34.6538 Evaluate side-chains 212 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS 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 261 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 548 LEU 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 B residue 264 VAL 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 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 62 ARG 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 H residue 51 VAL Chi-restraints excluded: chain H residue 158 VAL 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 52 LYS Chi-restraints excluded: chain N residue 102 VAL 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: 0.9990 chunk 78 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 142 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 223 HIS M 39 HIS L 38 GLN H 87 ASN N 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109795 restraints weight = 26350.382| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.34 r_work: 0.3348 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5730 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= 0.167 Angle : 0.596 7.117 18732 Z= 0.297 Chirality : 0.044 0.186 2087 Planarity : 0.004 0.048 2363 Dihedral : 7.994 116.961 1889 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.34 % Allowed : 16.25 % Favored : 80.41 % 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: 0.57 (0.26), residues: 422 sheet: -0.66 (0.26), residues: 387 loop : -0.59 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 258 TYR 0.019 0.002 TYR L 50 PHE 0.017 0.001 PHE A 29 TRP 0.038 0.002 TRP M 10 HIS 0.015 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (13781) covalent geometry : angle 0.59526 / 0.30 (18716) SS BOND : bond 0.00389 / 0.21 ( 5) SS BOND : angle 1.25730 / 0.71 ( 10) hydrogen bonds : bond 0.02952 / 1.99 ( 448) hydrogen bonds : angle 4.91162 / 3.47 ( 1326) link_ALPHA1-4 : bond 0.00240 / 0.13 ( 1) link_ALPHA1-4 : angle 1.54253 / 0.79 ( 3) link_TRANS : bond 0.00006 / 0.00 ( 1) link_TRANS : angle 0.10327 / 0.06 ( 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 233 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8086 (mtm180) REVERT: A 266 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7266 (mt-10) REVERT: A 268 GLU cc_start: 0.8672 (tp30) cc_final: 0.8184 (pm20) REVERT: A 417 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7521 (ptm160) REVERT: A 453 LEU cc_start: 0.8393 (mp) cc_final: 0.7483 (tp) REVERT: G 105 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 189 MET cc_start: 0.7641 (mmt) cc_final: 0.7164 (mmp) REVERT: G 320 GLN cc_start: 0.8751 (tp40) cc_final: 0.8344 (tp40) REVERT: M 10 TRP cc_start: 0.7662 (m-10) cc_final: 0.7372 (m-90) REVERT: M 22 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6101 (tm-30) REVERT: M 62 TRP cc_start: 0.8311 (t-100) cc_final: 0.7373 (t-100) REVERT: M 171 TYR cc_start: 0.7881 (t80) cc_final: 0.7605 (t80) REVERT: M 365 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8426 (tm-30) REVERT: L 5 MET cc_start: 0.6900 (ptp) cc_final: 0.6354 (ppp) outliers start: 49 outliers final: 35 residues processed: 223 average time/residue: 0.0903 time to fit residues: 31.7445 Evaluate side-chains 213 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 261 ILE 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 B residue 264 VAL 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 299 ARG 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 62 ARG 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 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 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: 0.0870 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.146282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110255 restraints weight = 26359.247| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.25 r_work: 0.3373 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13788 Z= 0.166 Angle : 0.610 8.619 18732 Z= 0.306 Chirality : 0.044 0.285 2087 Planarity : 0.004 0.050 2363 Dihedral : 8.066 116.841 1889 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.48 % Allowed : 16.45 % Favored : 80.07 % 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: -0.55 (0.21), residues: 1683 helix: 0.60 (0.26), residues: 422 sheet: -0.72 (0.26), residues: 378 loop : -0.59 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 101 TYR 0.019 0.002 TYR L 50 PHE 0.023 0.001 PHE L 210 TRP 0.045 0.002 TRP M 10 HIS 0.010 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (13781) covalent geometry : angle 0.60926 / 0.31 (18716) SS BOND : bond 0.00383 / 0.22 ( 5) SS BOND : angle 1.24052 / 0.70 ( 10) hydrogen bonds : bond 0.02953 / 1.99 ( 448) hydrogen bonds : angle 4.94124 / 3.49 ( 1326) link_ALPHA1-4 : bond 0.00049 / 0.03 ( 1) link_ALPHA1-4 : angle 1.48132 / 0.76 ( 3) link_TRANS : bond 0.00027 / 0.01 ( 1) link_TRANS : angle 0.12480 / 0.07 ( 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 234 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8716 (tpp-160) cc_final: 0.8099 (mtm180) REVERT: A 266 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7195 (mt-10) REVERT: A 268 GLU cc_start: 0.8685 (tp30) cc_final: 0.8206 (pm20) REVERT: A 417 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7476 (ptm160) REVERT: B 235 HIS cc_start: 0.6882 (m-70) cc_final: 0.6635 (t70) REVERT: G 105 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7615 (tm-30) REVERT: G 107 TYR cc_start: 0.7051 (m-80) cc_final: 0.6478 (m-80) REVERT: G 189 MET cc_start: 0.7622 (mmt) cc_final: 0.7159 (mmp) REVERT: M 10 TRP cc_start: 0.7749 (m-10) cc_final: 0.7429 (m-90) REVERT: M 22 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6052 (tm-30) REVERT: M 171 TYR cc_start: 0.7907 (t80) cc_final: 0.7659 (t80) REVERT: M 365 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8437 (tm-30) REVERT: L 5 MET cc_start: 0.6863 (ptp) cc_final: 0.6479 (ppp) REVERT: L 117 PHE cc_start: 0.8875 (m-80) cc_final: 0.8640 (m-80) REVERT: L 196 GLU cc_start: 0.8617 (tt0) cc_final: 0.8156 (tp30) outliers start: 51 outliers final: 44 residues processed: 223 average time/residue: 0.0976 time to fit residues: 33.9158 Evaluate side-chains 222 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 261 ILE 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 B residue 264 VAL 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 173 LEU 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 M residue 178 ILE 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 187 TYR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110395 restraints weight = 26561.329| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.32 r_work: 0.3367 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13788 Z= 0.146 Angle : 0.598 8.227 18732 Z= 0.297 Chirality : 0.044 0.229 2087 Planarity : 0.004 0.051 2363 Dihedral : 7.987 116.314 1889 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.48 % Allowed : 16.66 % 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: -0.51 (0.21), residues: 1683 helix: 0.66 (0.26), residues: 422 sheet: -0.75 (0.26), residues: 384 loop : -0.55 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.017 0.001 TYR L 50 PHE 0.019 0.001 PHE H 71 TRP 0.038 0.002 TRP M 10 HIS 0.010 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (13781) covalent geometry : angle 0.59776 / 0.30 (18716) SS BOND : bond 0.00373 / 0.22 ( 5) SS BOND : angle 1.17823 / 0.67 ( 10) hydrogen bonds : bond 0.02918 / 2.00 ( 448) hydrogen bonds : angle 4.94726 / 3.50 ( 1326) link_ALPHA1-4 : bond 0.00040 / 0.02 ( 1) link_ALPHA1-4 : angle 1.47636 / 0.75 ( 3) link_TRANS : bond 0.00063 / 0.03 ( 1) link_TRANS : angle 0.14367 / 0.07 ( 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 234 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8732 (tpp-160) cc_final: 0.8110 (mtm180) REVERT: A 266 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7219 (mt-10) REVERT: A 268 GLU cc_start: 0.8671 (tp30) cc_final: 0.8352 (pm20) REVERT: A 417 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7487 (ptm160) REVERT: B 235 HIS cc_start: 0.6882 (m-70) cc_final: 0.6616 (t70) REVERT: G 85 MET cc_start: 0.8779 (tpp) cc_final: 0.8513 (mmt) REVERT: G 105 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 107 TYR cc_start: 0.7072 (m-80) cc_final: 0.6504 (m-80) REVERT: G 189 MET cc_start: 0.7597 (mmt) cc_final: 0.7149 (mmp) REVERT: M 10 TRP cc_start: 0.7757 (m-10) cc_final: 0.7459 (m-90) REVERT: M 22 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6031 (tm-30) REVERT: M 62 TRP cc_start: 0.8346 (t-100) cc_final: 0.7462 (t-100) REVERT: M 171 TYR cc_start: 0.7901 (t80) cc_final: 0.7666 (t80) REVERT: M 204 MET cc_start: 0.7719 (tpt) cc_final: 0.7461 (tpt) REVERT: M 365 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8437 (tm-30) REVERT: L 5 MET cc_start: 0.6836 (ptp) cc_final: 0.6484 (ppp) REVERT: L 117 PHE cc_start: 0.8881 (m-80) cc_final: 0.8666 (m-80) REVERT: L 196 GLU cc_start: 0.8650 (tt0) cc_final: 0.8172 (tp30) REVERT: N 125 GLN cc_start: 0.7428 (tm-30) cc_final: 0.7169 (tm-30) outliers start: 51 outliers final: 39 residues processed: 222 average time/residue: 0.0921 time to fit residues: 31.9299 Evaluate side-chains 211 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 261 ILE 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 B residue 264 VAL 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 138 LEU 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 120 ASP Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 258 PHE Chi-restraints excluded: chain M residue 317 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 257 HIS L 38 GLN 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 = 0.4096 r_free = 0.4096 target = 0.148648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119363 restraints weight = 26541.015| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.69 r_work: 0.3319 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13788 Z= 0.115 Angle : 0.613 15.881 18732 Z= 0.302 Chirality : 0.044 0.251 2087 Planarity : 0.004 0.054 2363 Dihedral : 7.890 116.336 1889 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.53 % Allowed : 17.75 % Favored : 79.73 % 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: -0.39 (0.21), residues: 1683 helix: 0.78 (0.26), residues: 421 sheet: -0.74 (0.26), residues: 388 loop : -0.46 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.027 0.001 TYR L 141 PHE 0.025 0.001 PHE L 210 TRP 0.037 0.002 TRP M 10 HIS 0.017 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (13781) covalent geometry : angle 0.61208 / 0.30 (18716) SS BOND : bond 0.00361 / 0.22 ( 5) SS BOND : angle 1.09513 / 0.62 ( 10) hydrogen bonds : bond 0.02853 / 1.97 ( 448) hydrogen bonds : angle 4.90709 / 3.48 ( 1326) link_ALPHA1-4 : bond 0.00256 / 0.13 ( 1) link_ALPHA1-4 : angle 1.40294 / 0.72 ( 3) link_TRANS : bond 0.00118 / 0.06 ( 1) link_TRANS : angle 0.23217 / 0.11 ( 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 223 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8140 (mtm180) REVERT: A 266 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7264 (mt-10) REVERT: A 268 GLU cc_start: 0.8689 (tp30) cc_final: 0.8383 (pm20) REVERT: A 417 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7464 (ptm160) REVERT: A 453 LEU cc_start: 0.8412 (mp) cc_final: 0.7652 (tp) REVERT: B 235 HIS cc_start: 0.6984 (m-70) cc_final: 0.6662 (t70) REVERT: G 85 MET cc_start: 0.8827 (tpp) cc_final: 0.8543 (mmt) REVERT: G 105 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7580 (tm-30) REVERT: G 107 TYR cc_start: 0.7033 (m-80) cc_final: 0.6497 (m-80) REVERT: G 189 MET cc_start: 0.7601 (mmt) cc_final: 0.7147 (mmp) REVERT: M 10 TRP cc_start: 0.7820 (m-10) cc_final: 0.7521 (m-10) REVERT: M 22 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6011 (tm-30) REVERT: M 62 TRP cc_start: 0.8313 (t-100) cc_final: 0.7658 (t-100) REVERT: M 171 TYR cc_start: 0.7933 (t80) cc_final: 0.7685 (t80) REVERT: M 244 VAL cc_start: 0.8278 (t) cc_final: 0.8015 (m) REVERT: M 365 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8506 (tm-30) REVERT: L 5 MET cc_start: 0.6811 (ptp) cc_final: 0.6419 (ppp) REVERT: L 7 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7867 (mt0) REVERT: L 196 GLU cc_start: 0.8696 (tt0) cc_final: 0.8236 (tp30) REVERT: N 99 ASP cc_start: 0.5837 (t0) cc_final: 0.5355 (m-30) REVERT: N 125 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7187 (tm-30) outliers start: 37 outliers final: 33 residues processed: 215 average time/residue: 0.0989 time to fit residues: 32.9466 Evaluate side-chains 210 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 261 ILE 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 B residue 264 VAL 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 120 ASP Chi-restraints excluded: chain M residue 317 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 103 THR 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 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 158 VAL 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 52 LYS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 0.0010 chunk 148 optimal weight: 0.0050 chunk 107 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.147114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118537 restraints weight = 26497.453| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.44 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13788 Z= 0.109 Angle : 0.612 16.826 18732 Z= 0.300 Chirality : 0.043 0.266 2087 Planarity : 0.004 0.053 2363 Dihedral : 7.820 116.564 1889 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.91 % Allowed : 18.77 % Favored : 79.32 % 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: -0.28 (0.21), residues: 1683 helix: 0.88 (0.26), residues: 425 sheet: -0.63 (0.26), residues: 381 loop : -0.42 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 258 TYR 0.033 0.001 TYR H 192 PHE 0.026 0.001 PHE M 258 TRP 0.046 0.002 TRP H 170 HIS 0.009 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13781) covalent geometry : angle 0.61113 / 0.30 (18716) SS BOND : bond 0.00379 / 0.24 ( 5) SS BOND : angle 1.07619 / 0.63 ( 10) hydrogen bonds : bond 0.02916 / 2.04 ( 448) hydrogen bonds : angle 4.82193 / 3.42 ( 1326) link_ALPHA1-4 : bond 0.00190 / 0.10 ( 1) link_ALPHA1-4 : angle 1.35293 / 0.68 ( 3) link_TRANS : bond 0.00150 / 0.08 ( 1) link_TRANS : angle 0.34296 / 0.16 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3315.16 seconds wall clock time: 57 minutes 45.50 seconds (3465.50 seconds total)