Starting phenix.real_space_refine on Sun Jul 5 02:53:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p97_71401/07_2026/9p97_71401.map" } resolution = 2.92 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= 0.013 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 57 5.16 5 C 7687 2.51 5 N 2102 2.21 5 O 2391 1.98 5 H 11798 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24041 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 11507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 11507 Classifications: {'peptide': 760} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 724} Chain breaks: 1 Chain: "B" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 5750 Classifications: {'peptide': 375} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3296 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "L" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3284 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.10, per 1000 atoms: 0.17 Number of scatterers: 24041 At special positions: 0 Unit cell: (98.736, 142.494, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 57 16.00 O 2391 8.00 N 2102 7.00 C 7687 6.00 H 11798 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 96 " distance=2.03 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 253 " " NAG A1202 " - " ASN A 303 " " NAG B2003 " - " ASN B 415 " " NAG C 1 " - " ASN A 426 " " NAG D 1 " - " ASN A 31 " " NAG E 1 " - " ASN A 708 " " NAG F 1 " - " ASN B 260 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 609.6 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 18.8% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.541A pdb=" N ASN A 128 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 218 removed outlier: 3.705A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.627A pdb=" N GLN A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.992A pdb=" N GLY A 280 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.612A pdb=" N GLN A 314 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 360 through 369 Processing helix chain 'A' and resid 379 through 384 removed outlier: 4.164A pdb=" N LEU A 383 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 removed outlier: 3.685A pdb=" N ALA A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.615A pdb=" N CYS A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.565A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.677A pdb=" N PHE B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 4.015A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.691A pdb=" N ILE B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 300 through 306 removed outlier: 4.626A pdb=" N THR B 304 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.597A pdb=" N LEU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.767A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 removed outlier: 3.569A pdb=" N GLN H 139 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 140 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 141 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'H' and resid 208 through 211 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.750A pdb=" N LEU L 134 " --> pdb=" O SER L 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 136' Processing helix chain 'L' and resid 191 through 196 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 4.312A pdb=" N ARG A 657 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ALA A 6 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N VAL A 655 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N ALA A 653 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 26 removed outlier: 10.688A pdb=" N THR A 33 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 54 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.550A pdb=" N LEU A 225 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 183 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA A 224 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 185 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 226 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 187 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A 228 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 189 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A 349 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 320 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 351 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 322 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 392 removed outlier: 4.564A pdb=" N SER A 389 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 421 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 451 removed outlier: 11.880A pdb=" N LEU A 456 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N LYS A 476 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR A 458 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 471 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.515A pdb=" N ARG A 546 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG A 534 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU A 544 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AA9, first strand: chain 'A' and resid 563 through 565 removed outlier: 3.564A pdb=" N GLN A 613 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 662 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 671 Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 735 Processing sheet with id=AB4, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.515A pdb=" N ARG B 108 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 109 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS B 452 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 111 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB6, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'B' and resid 211 through 217 removed outlier: 7.180A pdb=" N VAL B 213 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N SER B 176 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER B 215 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE B 174 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 134 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B 266 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 136 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR B 268 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 138 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 263 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE B 326 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 265 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 328 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE B 267 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ALA B 348 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY B 350 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 327 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.584A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.645A pdb=" N THR H 115 " --> pdb=" O TRP H 95 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE H 34 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP H 36 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.645A pdb=" N THR H 115 " --> pdb=" O TRP H 95 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR H 110 " --> pdb=" O TRP H 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.553A pdb=" N TYR H 183 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.553A pdb=" N TYR H 183 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.668A pdb=" N TRP L 42 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'L' and resid 123 through 127 removed outlier: 3.803A pdb=" N VAL L 142 " --> pdb=" O PHE L 127 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR L 181 " --> pdb=" O ASP L 147 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER L 184 " --> pdb=" O THR L 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 162 through 164 removed outlier: 4.687A pdb=" N TRP L 157 " --> pdb=" O VAL L 164 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 154 " --> pdb=" O THR L 205 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1209 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: 6.17 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11778 1.03 - 1.23: 72 1.23 - 1.42: 5247 1.42 - 1.62: 7125 1.62 - 1.81: 82 Bond restraints: 24304 Sorted by residual: bond pdb=" N ALA A 181 " pdb=" H ALA A 181 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ARG B 81 " pdb=" CA ARG B 81 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N ARG B 81 " pdb=" H ARG B 81 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N PHE A 1 " pdb=" H PHE A 1 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 24299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 43733 7.10 - 14.19: 3 14.19 - 21.29: 0 21.29 - 28.39: 0 28.39 - 35.49: 3 Bond angle restraints: 43739 Sorted by residual: angle pdb=" C ASN A 303 " pdb=" CA ASN A 303 " pdb=" HA ASN A 303 " ideal model delta sigma weight residual 109.00 73.51 35.49 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ASN A 303 " pdb=" CA ASN A 303 " pdb=" HA ASN A 303 " ideal model delta sigma weight residual 110.00 75.72 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB ASN A 303 " pdb=" CA ASN A 303 " pdb=" HA ASN A 303 " ideal model delta sigma weight residual 109.00 74.74 34.26 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C ASP A 589 " pdb=" CA ASP A 589 " pdb=" CB ASP A 589 " ideal model delta sigma weight residual 116.34 111.03 5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" C1 NAG B2003 " pdb=" C2 NAG B2003 " pdb=" N2 NAG B2003 " ideal model delta sigma weight residual 110.79 121.96 -11.17 3.00e+00 1.11e-01 1.39e+01 ... (remaining 43734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10523 17.94 - 35.88: 851 35.88 - 53.82: 291 53.82 - 71.76: 84 71.76 - 89.70: 30 Dihedral angle restraints: 11779 sinusoidal: 6527 harmonic: 5252 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 96 " pdb=" CB CYS L 96 " ideal model delta sinusoidal sigma weight residual 93.00 172.97 -79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA CYS L 96 " pdb=" C CYS L 96 " pdb=" N ARG L 97 " pdb=" CA ARG L 97 " ideal model delta harmonic sigma weight residual 180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ILE A 232 " pdb=" C ILE A 232 " pdb=" N GLN A 233 " pdb=" CA GLN A 233 " ideal model delta harmonic sigma weight residual 180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 11776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.365: 1953 0.365 - 0.730: 0 0.730 - 1.095: 0 1.095 - 1.460: 0 1.460 - 1.825: 1 Chirality restraints: 1954 Sorted by residual: chirality pdb=" C2 NAG B2003 " pdb=" C1 NAG B2003 " pdb=" C3 NAG B2003 " pdb=" N2 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.49 -0.67 -1.83 2.00e-01 2.50e+01 8.33e+01 chirality pdb=" CA ASN A 303 " pdb=" N ASN A 303 " pdb=" C ASN A 303 " pdb=" CB ASN A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA VAL B 189 " pdb=" N VAL B 189 " pdb=" C VAL B 189 " pdb=" CB VAL B 189 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 1951 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 415 " 0.025 2.00e-02 2.50e+03 2.32e-02 6.74e+00 pdb=" CG ASN B 415 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 415 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 415 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG B2003 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 229 " -0.216 9.50e-02 1.11e+02 7.25e-02 6.20e+00 pdb=" NE ARG B 229 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 229 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 229 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 229 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 229 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG B 229 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 229 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 229 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 7 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 8 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " -0.026 5.00e-02 4.00e+02 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 989 2.18 - 2.78: 47224 2.78 - 3.39: 63774 3.39 - 3.99: 86552 3.99 - 4.60: 133260 Nonbonded interactions: 331799 Sorted by model distance: nonbonded pdb=" H ASN A 303 " pdb=" HA ASN A 303 " model vdw 1.571 1.816 nonbonded pdb=" HA ASN A 303 " pdb=" HB3 ASN A 303 " model vdw 1.628 1.952 nonbonded pdb="HD22 ASN B 415 " pdb=" O5 NAG B2003 " model vdw 1.675 1.960 nonbonded pdb=" HG3 ARG B 229 " pdb="HH11 ARG B 229 " model vdw 1.795 2.270 nonbonded pdb="HE21 GLN L 98 " pdb=" HG1 THR L 106 " model vdw 1.824 2.100 ... (remaining 331794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 0.037 12526 Z= 0.193 Angle : 0.607 11.165 17046 Z= 0.322 Chirality : 0.061 1.825 1954 Planarity : 0.005 0.095 2193 Dihedral : 15.124 89.698 4765 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.14 % Allowed : 15.16 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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 (0.22), residues: 1560 helix: 0.13 (0.38), residues: 183 sheet: -0.40 (0.21), residues: 592 loop : -0.07 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 229 TYR 0.013 0.001 TYR A 366 PHE 0.015 0.001 PHE A 627 TRP 0.009 0.001 TRP A 34 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (12506) covalent geometry : angle 0.59394 / 0.32 (16991) SS BOND : bond 0.00125 / 0.07 ( 5) SS BOND : angle 0.75676 / 0.44 ( 10) hydrogen bonds : bond 0.20505 / 13.42 ( 436) hydrogen bonds : angle 9.25834 / 6.44 ( 1209) link_ALPHA1-3 : bond 0.01447 / 0.76 ( 1) link_ALPHA1-3 : angle 0.97266 / 0.56 ( 3) link_ALPHA1-6 : bond 0.01318 / 0.69 ( 1) link_ALPHA1-6 : angle 1.74507 / 1.16 ( 3) link_BETA1-4 : bond 0.00811 / 0.41 ( 6) link_BETA1-4 : angle 2.93614 / 1.63 ( 18) link_NAG-ASN : bond 0.00754 / 0.36 ( 7) link_NAG-ASN : angle 2.30363 / 1.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8705 (t) cc_final: 0.8411 (p) REVERT: A 127 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 204 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7804 (mtpt) REVERT: A 208 SER cc_start: 0.8141 (t) cc_final: 0.7854 (p) REVERT: A 212 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8098 (mtt180) REVERT: A 217 LYS cc_start: 0.8375 (mttt) cc_final: 0.8130 (mttt) REVERT: A 268 GLN cc_start: 0.6860 (tp-100) cc_final: 0.6156 (tp-100) REVERT: A 272 ASP cc_start: 0.7655 (m-30) cc_final: 0.6871 (m-30) REVERT: A 334 ARG cc_start: 0.7213 (tmm-80) cc_final: 0.6929 (mmm-85) REVERT: A 349 PHE cc_start: 0.8053 (m-80) cc_final: 0.7699 (m-80) REVERT: A 538 GLN cc_start: 0.7713 (mp10) cc_final: 0.7159 (mp10) REVERT: B 236 LEU cc_start: 0.8614 (tp) cc_final: 0.8313 (tt) REVERT: B 355 ASP cc_start: 0.7612 (t0) cc_final: 0.7299 (t0) REVERT: B 359 VAL cc_start: 0.8304 (t) cc_final: 0.7958 (m) REVERT: B 390 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6948 (tt0) REVERT: B 439 ARG cc_start: 0.8313 (ptt-90) cc_final: 0.8033 (ptt-90) REVERT: B 446 GLU cc_start: 0.7436 (tt0) cc_final: 0.7177 (tt0) REVERT: H 30 GLU cc_start: 0.6769 (pm20) cc_final: 0.6438 (pm20) REVERT: L 33 SER cc_start: 0.8456 (m) cc_final: 0.8027 (p) REVERT: L 123 SER cc_start: 0.6751 (m) cc_final: 0.6507 (t) REVERT: L 182 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5472 (pmm) outliers start: 15 outliers final: 9 residues processed: 261 average time/residue: 1.1796 time to fit residues: 337.9202 Evaluate side-chains 257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.0010 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 0.9908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.179436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125181 restraints weight = 50095.670| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.27 r_work: 0.3296 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12526 Z= 0.259 Angle : 0.619 7.405 17046 Z= 0.321 Chirality : 0.047 0.368 1954 Planarity : 0.005 0.066 2193 Dihedral : 7.335 59.941 2023 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.50 % Allowed : 15.24 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: -0.38 (0.21), residues: 1560 helix: -0.23 (0.36), residues: 199 sheet: -0.08 (0.21), residues: 601 loop : -0.26 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.012 0.002 TYR B 337 PHE 0.018 0.002 PHE A 627 TRP 0.012 0.002 TRP A 34 HIS 0.006 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (12506) covalent geometry : angle 0.61010 / 0.32 (16991) SS BOND : bond 0.00326 / 0.16 ( 5) SS BOND : angle 1.12933 / 0.65 ( 10) hydrogen bonds : bond 0.04371 / 2.83 ( 436) hydrogen bonds : angle 6.66033 / 4.62 ( 1209) link_ALPHA1-3 : bond 0.01260 / 0.66 ( 1) link_ALPHA1-3 : angle 2.11393 / 1.18 ( 3) link_ALPHA1-6 : bond 0.01246 / 0.66 ( 1) link_ALPHA1-6 : angle 1.96180 / 1.39 ( 3) link_BETA1-4 : bond 0.00599 / 0.31 ( 6) link_BETA1-4 : angle 2.20017 / 1.22 ( 18) link_NAG-ASN : bond 0.00392 / 0.22 ( 7) link_NAG-ASN : angle 1.87808 / 1.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8703 (p) cc_final: 0.8465 (m) REVERT: A 94 VAL cc_start: 0.8545 (t) cc_final: 0.8194 (p) REVERT: A 204 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7859 (mtpt) REVERT: A 208 SER cc_start: 0.8115 (t) cc_final: 0.7828 (p) REVERT: A 212 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8119 (mtt180) REVERT: A 217 LYS cc_start: 0.8337 (mttt) cc_final: 0.8056 (mttt) REVERT: A 268 GLN cc_start: 0.6862 (tp-100) cc_final: 0.6559 (tp-100) REVERT: A 316 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8301 (t) REVERT: A 334 ARG cc_start: 0.7278 (tmm-80) cc_final: 0.6945 (mmm-85) REVERT: A 349 PHE cc_start: 0.8168 (m-80) cc_final: 0.7865 (m-80) REVERT: A 382 GLN cc_start: 0.8113 (mp10) cc_final: 0.7848 (mp10) REVERT: A 480 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7226 (mp0) REVERT: A 538 GLN cc_start: 0.7794 (mp10) cc_final: 0.7215 (mp10) REVERT: B 108 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7188 (mmm-85) REVERT: B 110 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: B 170 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 236 LEU cc_start: 0.8504 (tp) cc_final: 0.8242 (tt) REVERT: B 355 ASP cc_start: 0.7637 (t0) cc_final: 0.7332 (t0) REVERT: B 359 VAL cc_start: 0.8224 (t) cc_final: 0.7929 (m) REVERT: B 390 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6883 (tt0) REVERT: H 30 GLU cc_start: 0.6681 (pm20) cc_final: 0.6333 (pm20) REVERT: L 33 SER cc_start: 0.8476 (m) cc_final: 0.8060 (p) REVERT: L 182 MET cc_start: 0.5775 (pmm) cc_final: 0.5520 (pmm) outliers start: 33 outliers final: 18 residues processed: 262 average time/residue: 1.1526 time to fit residues: 331.0408 Evaluate side-chains 262 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 227 GLN A 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126403 restraints weight = 50179.094| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.26 r_work: 0.3345 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12526 Z= 0.174 Angle : 0.549 5.533 17046 Z= 0.285 Chirality : 0.045 0.366 1954 Planarity : 0.005 0.056 2193 Dihedral : 6.916 58.842 2017 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 15.24 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: -0.25 (0.21), residues: 1560 helix: -0.11 (0.36), residues: 205 sheet: 0.01 (0.21), residues: 599 loop : -0.19 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.013 0.001 TYR A 215 PHE 0.014 0.001 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (12506) covalent geometry : angle 0.54247 / 0.28 (16991) SS BOND : bond 0.00245 / 0.12 ( 5) SS BOND : angle 0.99744 / 0.58 ( 10) hydrogen bonds : bond 0.04074 / 2.62 ( 436) hydrogen bonds : angle 6.22707 / 4.33 ( 1209) link_ALPHA1-3 : bond 0.01019 / 0.54 ( 1) link_ALPHA1-3 : angle 1.88679 / 1.06 ( 3) link_ALPHA1-6 : bond 0.01187 / 0.62 ( 1) link_ALPHA1-6 : angle 1.90270 / 1.35 ( 3) link_BETA1-4 : bond 0.00551 / 0.28 ( 6) link_BETA1-4 : angle 1.84220 / 1.03 ( 18) link_NAG-ASN : bond 0.00385 / 0.19 ( 7) link_NAG-ASN : angle 1.37922 / 0.84 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8686 (p) cc_final: 0.8472 (m) REVERT: A 204 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7854 (mtpt) REVERT: A 208 SER cc_start: 0.8115 (t) cc_final: 0.7842 (p) REVERT: A 212 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8099 (mtt180) REVERT: A 217 LYS cc_start: 0.8319 (mttt) cc_final: 0.8051 (mttt) REVERT: A 268 GLN cc_start: 0.6787 (tp-100) cc_final: 0.6487 (tp-100) REVERT: A 316 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 334 ARG cc_start: 0.7279 (tmm-80) cc_final: 0.6910 (mmm-85) REVERT: A 349 PHE cc_start: 0.8159 (m-80) cc_final: 0.7866 (m-80) REVERT: A 480 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7373 (mp0) REVERT: A 538 GLN cc_start: 0.7783 (mp10) cc_final: 0.7224 (mp10) REVERT: B 108 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7173 (mmm-85) REVERT: B 170 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 236 LEU cc_start: 0.8553 (tp) cc_final: 0.8307 (tt) REVERT: B 355 ASP cc_start: 0.7645 (t0) cc_final: 0.7284 (t0) REVERT: B 359 VAL cc_start: 0.8211 (t) cc_final: 0.7914 (m) REVERT: B 390 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6901 (tt0) REVERT: H 30 GLU cc_start: 0.6713 (pm20) cc_final: 0.6367 (pm20) REVERT: L 33 SER cc_start: 0.8512 (m) cc_final: 0.8085 (p) REVERT: L 182 MET cc_start: 0.5709 (pmm) cc_final: 0.5459 (pmm) outliers start: 30 outliers final: 21 residues processed: 252 average time/residue: 1.1759 time to fit residues: 324.1290 Evaluate side-chains 256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 15 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125846 restraints weight = 50061.696| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.26 r_work: 0.3343 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12526 Z= 0.176 Angle : 0.537 6.699 17046 Z= 0.278 Chirality : 0.045 0.366 1954 Planarity : 0.005 0.065 2193 Dihedral : 6.475 56.467 2017 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.58 % Allowed : 15.24 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1560 helix: 0.03 (0.36), residues: 205 sheet: 0.11 (0.21), residues: 596 loop : -0.25 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.013 0.001 TYR A 215 PHE 0.015 0.001 PHE A 627 TRP 0.010 0.001 TRP A 34 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (12506) covalent geometry : angle 0.53152 / 0.28 (16991) SS BOND : bond 0.00219 / 0.11 ( 5) SS BOND : angle 0.94125 / 0.55 ( 10) hydrogen bonds : bond 0.03642 / 2.33 ( 436) hydrogen bonds : angle 5.90548 / 4.10 ( 1209) link_ALPHA1-3 : bond 0.00921 / 0.48 ( 1) link_ALPHA1-3 : angle 1.80532 / 1.02 ( 3) link_ALPHA1-6 : bond 0.01083 / 0.57 ( 1) link_ALPHA1-6 : angle 1.64696 / 1.23 ( 3) link_BETA1-4 : bond 0.00527 / 0.26 ( 6) link_BETA1-4 : angle 1.69613 / 0.95 ( 18) link_NAG-ASN : bond 0.00309 / 0.16 ( 7) link_NAG-ASN : angle 1.41232 / 0.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8704 (p) cc_final: 0.8492 (m) REVERT: A 94 VAL cc_start: 0.8574 (t) cc_final: 0.8226 (p) REVERT: A 204 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7829 (mtpt) REVERT: A 208 SER cc_start: 0.8089 (t) cc_final: 0.7844 (p) REVERT: A 212 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8089 (mtt180) REVERT: A 217 LYS cc_start: 0.8298 (mttt) cc_final: 0.8036 (mttt) REVERT: A 268 GLN cc_start: 0.6735 (tp-100) cc_final: 0.6397 (tp-100) REVERT: A 316 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8291 (t) REVERT: A 334 ARG cc_start: 0.7262 (tmm-80) cc_final: 0.6871 (mmm-85) REVERT: A 349 PHE cc_start: 0.8182 (m-80) cc_final: 0.7807 (m-80) REVERT: A 480 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7326 (mp0) REVERT: A 538 GLN cc_start: 0.7758 (mp10) cc_final: 0.7187 (mp10) REVERT: B 108 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7224 (mmm-85) REVERT: B 170 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 236 LEU cc_start: 0.8570 (tp) cc_final: 0.8334 (tt) REVERT: B 355 ASP cc_start: 0.7604 (t0) cc_final: 0.7235 (t0) REVERT: B 359 VAL cc_start: 0.8203 (t) cc_final: 0.7911 (m) REVERT: B 439 ARG cc_start: 0.8018 (ptt-90) cc_final: 0.7750 (ptt180) REVERT: H 30 GLU cc_start: 0.6678 (pm20) cc_final: 0.6310 (pm20) REVERT: L 33 SER cc_start: 0.8512 (m) cc_final: 0.8081 (p) REVERT: L 182 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5522 (pmm) outliers start: 34 outliers final: 24 residues processed: 250 average time/residue: 1.1585 time to fit residues: 317.8633 Evaluate side-chains 262 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 269 HIS A 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.179255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125417 restraints weight = 49733.210| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.26 r_work: 0.3340 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12526 Z= 0.223 Angle : 0.556 7.089 17046 Z= 0.288 Chirality : 0.045 0.368 1954 Planarity : 0.005 0.070 2193 Dihedral : 6.177 56.150 2017 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.81 % Allowed : 15.39 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: 1560 helix: -0.11 (0.36), residues: 205 sheet: 0.13 (0.21), residues: 594 loop : -0.35 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 546 TYR 0.014 0.001 TYR H 153 PHE 0.017 0.002 PHE A 627 TRP 0.012 0.001 TRP A 34 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (12506) covalent geometry : angle 0.55054 / 0.29 (16991) SS BOND : bond 0.00219 / 0.12 ( 5) SS BOND : angle 0.88550 / 0.52 ( 10) hydrogen bonds : bond 0.03730 / 2.39 ( 436) hydrogen bonds : angle 5.72107 / 3.97 ( 1209) link_ALPHA1-3 : bond 0.00877 / 0.46 ( 1) link_ALPHA1-3 : angle 1.59894 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00888 / 0.47 ( 1) link_ALPHA1-6 : angle 1.24968 / 1.20 ( 3) link_BETA1-4 : bond 0.00644 / 0.32 ( 6) link_BETA1-4 : angle 1.67667 / 0.95 ( 18) link_NAG-ASN : bond 0.00299 / 0.16 ( 7) link_NAG-ASN : angle 1.38424 / 0.79 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8709 (p) cc_final: 0.8486 (m) REVERT: A 94 VAL cc_start: 0.8574 (t) cc_final: 0.8237 (p) REVERT: A 208 SER cc_start: 0.8149 (t) cc_final: 0.7772 (p) REVERT: A 217 LYS cc_start: 0.8365 (mttt) cc_final: 0.8087 (mttt) REVERT: A 268 GLN cc_start: 0.6759 (tp-100) cc_final: 0.6438 (tp-100) REVERT: A 316 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 334 ARG cc_start: 0.7294 (tmm-80) cc_final: 0.6872 (mmm-85) REVERT: A 475 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: A 479 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6790 (ttm-80) REVERT: A 480 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7405 (mp0) REVERT: A 538 GLN cc_start: 0.7740 (mp10) cc_final: 0.7105 (mp10) REVERT: B 108 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7269 (mmm-85) REVERT: B 110 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (ttm170) REVERT: B 170 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8662 (p) REVERT: B 355 ASP cc_start: 0.7558 (t0) cc_final: 0.7248 (t0) REVERT: B 359 VAL cc_start: 0.8203 (t) cc_final: 0.7922 (m) REVERT: B 377 GLU cc_start: 0.7604 (tt0) cc_final: 0.7347 (tt0) REVERT: H 30 GLU cc_start: 0.6727 (pm20) cc_final: 0.6372 (pm20) REVERT: L 33 SER cc_start: 0.8548 (m) cc_final: 0.8128 (p) REVERT: L 182 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.5446 (pmm) outliers start: 37 outliers final: 25 residues processed: 254 average time/residue: 1.2020 time to fit residues: 334.9896 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 428 HIS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125710 restraints weight = 50029.121| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.25 r_work: 0.3340 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12526 Z= 0.179 Angle : 0.533 7.392 17046 Z= 0.277 Chirality : 0.044 0.363 1954 Planarity : 0.005 0.076 2193 Dihedral : 5.817 56.531 2017 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 16.30 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1560 helix: -0.03 (0.36), residues: 205 sheet: 0.16 (0.21), residues: 594 loop : -0.29 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 546 TYR 0.012 0.001 TYR A 215 PHE 0.016 0.001 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (12506) covalent geometry : angle 0.52814 / 0.28 (16991) SS BOND : bond 0.00207 / 0.11 ( 5) SS BOND : angle 0.82701 / 0.48 ( 10) hydrogen bonds : bond 0.03462 / 2.22 ( 436) hydrogen bonds : angle 5.57227 / 3.87 ( 1209) link_ALPHA1-3 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-3 : angle 1.48365 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00450 / 0.24 ( 1) link_ALPHA1-6 : angle 1.74245 / 1.55 ( 3) link_BETA1-4 : bond 0.00568 / 0.29 ( 6) link_BETA1-4 : angle 1.56062 / 0.88 ( 18) link_NAG-ASN : bond 0.00235 / 0.12 ( 7) link_NAG-ASN : angle 1.29754 / 0.79 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8704 (p) cc_final: 0.8480 (m) REVERT: A 94 VAL cc_start: 0.8552 (t) cc_final: 0.8214 (p) REVERT: A 208 SER cc_start: 0.8102 (t) cc_final: 0.7865 (p) REVERT: A 212 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8140 (mtt180) REVERT: A 217 LYS cc_start: 0.8364 (mttt) cc_final: 0.8069 (mttt) REVERT: A 220 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 268 GLN cc_start: 0.6729 (tp-100) cc_final: 0.6403 (tp-100) REVERT: A 316 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 334 ARG cc_start: 0.7301 (tmm-80) cc_final: 0.6872 (mmm-85) REVERT: A 479 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6685 (ttm-80) REVERT: A 480 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 538 GLN cc_start: 0.7777 (mp10) cc_final: 0.7114 (mp10) REVERT: B 108 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7214 (mmm-85) REVERT: B 170 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 355 ASP cc_start: 0.7577 (t0) cc_final: 0.7236 (t0) REVERT: B 359 VAL cc_start: 0.8195 (t) cc_final: 0.7914 (m) REVERT: L 33 SER cc_start: 0.8547 (m) cc_final: 0.8118 (p) REVERT: L 182 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5411 (pmm) outliers start: 31 outliers final: 20 residues processed: 249 average time/residue: 1.2368 time to fit residues: 336.9614 Evaluate side-chains 256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 72 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125803 restraints weight = 49733.281| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.25 r_work: 0.3319 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12526 Z= 0.183 Angle : 0.532 7.484 17046 Z= 0.276 Chirality : 0.044 0.366 1954 Planarity : 0.005 0.078 2193 Dihedral : 5.653 56.769 2015 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.65 % Allowed : 16.68 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1560 helix: -0.04 (0.36), residues: 205 sheet: 0.17 (0.21), residues: 595 loop : -0.30 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 546 TYR 0.014 0.001 TYR H 153 PHE 0.015 0.002 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (12506) covalent geometry : angle 0.52711 / 0.27 (16991) SS BOND : bond 0.00192 / 0.11 ( 5) SS BOND : angle 0.81552 / 0.47 ( 10) hydrogen bonds : bond 0.03418 / 2.19 ( 436) hydrogen bonds : angle 5.47483 / 3.80 ( 1209) link_ALPHA1-3 : bond 0.00614 / 0.32 ( 1) link_ALPHA1-3 : angle 1.39844 / 0.98 ( 3) link_ALPHA1-6 : bond 0.00275 / 0.14 ( 1) link_ALPHA1-6 : angle 1.68676 / 1.53 ( 3) link_BETA1-4 : bond 0.00512 / 0.26 ( 6) link_BETA1-4 : angle 1.52035 / 0.85 ( 18) link_NAG-ASN : bond 0.00234 / 0.12 ( 7) link_NAG-ASN : angle 1.28662 / 0.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8695 (p) cc_final: 0.8475 (m) REVERT: A 94 VAL cc_start: 0.8552 (t) cc_final: 0.8212 (p) REVERT: A 208 SER cc_start: 0.8087 (t) cc_final: 0.7856 (p) REVERT: A 212 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8101 (mtt180) REVERT: A 213 ASN cc_start: 0.8403 (t0) cc_final: 0.8126 (t0) REVERT: A 217 LYS cc_start: 0.8290 (mttt) cc_final: 0.7967 (mttt) REVERT: A 220 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 261 THR cc_start: 0.6294 (OUTLIER) cc_final: 0.5726 (t) REVERT: A 268 GLN cc_start: 0.6771 (tp-100) cc_final: 0.6457 (tp-100) REVERT: A 316 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8298 (t) REVERT: A 334 ARG cc_start: 0.7204 (tmm-80) cc_final: 0.6822 (mmm-85) REVERT: A 475 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7764 (mp10) REVERT: A 479 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6653 (ttm-80) REVERT: A 480 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7369 (mp0) REVERT: A 538 GLN cc_start: 0.7821 (mp10) cc_final: 0.7218 (mp10) REVERT: B 108 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7202 (mmm-85) REVERT: B 110 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7321 (ttm170) REVERT: B 170 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 355 ASP cc_start: 0.7617 (t0) cc_final: 0.7290 (t0) REVERT: B 359 VAL cc_start: 0.8172 (t) cc_final: 0.7895 (m) REVERT: L 33 SER cc_start: 0.8557 (m) cc_final: 0.8118 (p) REVERT: L 87 LYS cc_start: 0.6329 (OUTLIER) cc_final: 0.6116 (mptp) REVERT: L 182 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5405 (pmm) outliers start: 35 outliers final: 23 residues processed: 256 average time/residue: 1.1698 time to fit residues: 328.7806 Evaluate side-chains 270 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 428 HIS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS B 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125625 restraints weight = 49614.357| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.25 r_work: 0.3336 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12526 Z= 0.189 Angle : 0.528 7.045 17046 Z= 0.275 Chirality : 0.044 0.365 1954 Planarity : 0.005 0.085 2193 Dihedral : 5.613 57.022 2015 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.73 % Allowed : 16.76 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: -0.16 (0.21), residues: 1560 helix: -0.07 (0.36), residues: 205 sheet: 0.23 (0.21), residues: 599 loop : -0.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 546 TYR 0.013 0.001 TYR A 215 PHE 0.016 0.002 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (12506) covalent geometry : angle 0.52393 / 0.27 (16991) SS BOND : bond 0.00206 / 0.12 ( 5) SS BOND : angle 0.77344 / 0.45 ( 10) hydrogen bonds : bond 0.03416 / 2.20 ( 436) hydrogen bonds : angle 5.38890 / 3.74 ( 1209) link_ALPHA1-3 : bond 0.00580 / 0.31 ( 1) link_ALPHA1-3 : angle 1.34745 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00271 / 0.14 ( 1) link_ALPHA1-6 : angle 1.66512 / 1.48 ( 3) link_BETA1-4 : bond 0.00481 / 0.24 ( 6) link_BETA1-4 : angle 1.50268 / 0.84 ( 18) link_NAG-ASN : bond 0.00246 / 0.13 ( 7) link_NAG-ASN : angle 1.31203 / 0.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8715 (p) cc_final: 0.8473 (m) REVERT: A 90 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 94 VAL cc_start: 0.8542 (t) cc_final: 0.8204 (p) REVERT: A 208 SER cc_start: 0.8087 (t) cc_final: 0.7852 (p) REVERT: A 212 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8152 (mtt180) REVERT: A 217 LYS cc_start: 0.8335 (mttt) cc_final: 0.8031 (mttt) REVERT: A 220 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 261 THR cc_start: 0.6236 (OUTLIER) cc_final: 0.5743 (t) REVERT: A 268 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6491 (tp-100) REVERT: A 316 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8300 (t) REVERT: A 334 ARG cc_start: 0.7223 (tmm-80) cc_final: 0.6826 (mmm-85) REVERT: A 475 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: A 479 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: A 480 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7264 (mp0) REVERT: A 538 GLN cc_start: 0.7811 (mp10) cc_final: 0.7259 (mp10) REVERT: B 108 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7212 (mmm-85) REVERT: B 110 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7362 (ttm170) REVERT: B 355 ASP cc_start: 0.7572 (t0) cc_final: 0.7245 (t0) REVERT: B 359 VAL cc_start: 0.8181 (t) cc_final: 0.7906 (m) REVERT: B 377 GLU cc_start: 0.7563 (tt0) cc_final: 0.7309 (tt0) REVERT: L 33 SER cc_start: 0.8582 (m) cc_final: 0.8137 (p) REVERT: L 87 LYS cc_start: 0.6369 (OUTLIER) cc_final: 0.6132 (mptp) REVERT: L 182 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5525 (pmm) outliers start: 36 outliers final: 20 residues processed: 255 average time/residue: 1.1527 time to fit residues: 322.0686 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 428 HIS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS B 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.178707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124682 restraints weight = 49598.164| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.25 r_work: 0.3326 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12526 Z= 0.254 Angle : 0.567 6.046 17046 Z= 0.295 Chirality : 0.046 0.360 1954 Planarity : 0.006 0.084 2193 Dihedral : 5.710 57.376 2015 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.20 % Allowed : 17.51 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1560 helix: -0.29 (0.35), residues: 205 sheet: 0.21 (0.21), residues: 602 loop : -0.35 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 546 TYR 0.013 0.001 TYR A 215 PHE 0.019 0.002 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (12506) covalent geometry : angle 0.56211 / 0.29 (16991) SS BOND : bond 0.00221 / 0.12 ( 5) SS BOND : angle 0.77195 / 0.45 ( 10) hydrogen bonds : bond 0.03714 / 2.40 ( 436) hydrogen bonds : angle 5.41102 / 3.75 ( 1209) link_ALPHA1-3 : bond 0.00492 / 0.26 ( 1) link_ALPHA1-3 : angle 1.31957 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00274 / 0.14 ( 1) link_ALPHA1-6 : angle 1.67216 / 1.49 ( 3) link_BETA1-4 : bond 0.00485 / 0.24 ( 6) link_BETA1-4 : angle 1.60567 / 0.90 ( 18) link_NAG-ASN : bond 0.00383 / 0.20 ( 7) link_NAG-ASN : angle 1.50967 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8734 (p) cc_final: 0.8485 (m) REVERT: A 94 VAL cc_start: 0.8565 (t) cc_final: 0.8227 (p) REVERT: A 208 SER cc_start: 0.8115 (t) cc_final: 0.7836 (p) REVERT: A 212 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8135 (mtt180) REVERT: A 217 LYS cc_start: 0.8321 (mttt) cc_final: 0.8014 (mttt) REVERT: A 261 THR cc_start: 0.6322 (OUTLIER) cc_final: 0.5786 (t) REVERT: A 268 GLN cc_start: 0.6720 (tp-100) cc_final: 0.6436 (tp-100) REVERT: A 316 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8284 (t) REVERT: A 334 ARG cc_start: 0.7197 (tmm-80) cc_final: 0.6807 (mmm-85) REVERT: A 475 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: A 479 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6707 (ttm-80) REVERT: A 480 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7221 (mp0) REVERT: A 538 GLN cc_start: 0.7862 (mp10) cc_final: 0.7231 (mp10) REVERT: B 110 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7404 (ttm170) REVERT: B 355 ASP cc_start: 0.7639 (t0) cc_final: 0.7338 (t0) REVERT: B 359 VAL cc_start: 0.8186 (t) cc_final: 0.7938 (m) REVERT: B 377 GLU cc_start: 0.7607 (tt0) cc_final: 0.7387 (tt0) REVERT: H 60 LYS cc_start: 0.7725 (tttp) cc_final: 0.7276 (ttmm) REVERT: L 33 SER cc_start: 0.8580 (m) cc_final: 0.8149 (p) REVERT: L 182 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.5516 (pmm) outliers start: 29 outliers final: 20 residues processed: 247 average time/residue: 1.1520 time to fit residues: 310.6622 Evaluate side-chains 255 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.179217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125441 restraints weight = 49990.394| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.27 r_work: 0.3324 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12526 Z= 0.194 Angle : 0.538 6.007 17046 Z= 0.279 Chirality : 0.045 0.358 1954 Planarity : 0.005 0.092 2193 Dihedral : 5.612 57.751 2015 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 17.66 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: -0.22 (0.21), residues: 1560 helix: -0.19 (0.36), residues: 205 sheet: 0.18 (0.21), residues: 606 loop : -0.28 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 546 TYR 0.014 0.001 TYR A 215 PHE 0.016 0.002 PHE A 627 TRP 0.012 0.001 TRP A 34 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (12506) covalent geometry : angle 0.53327 / 0.28 (16991) SS BOND : bond 0.00196 / 0.12 ( 5) SS BOND : angle 0.71542 / 0.42 ( 10) hydrogen bonds : bond 0.03413 / 2.19 ( 436) hydrogen bonds : angle 5.30588 / 3.68 ( 1209) link_ALPHA1-3 : bond 0.00513 / 0.27 ( 1) link_ALPHA1-3 : angle 1.35534 / 0.98 ( 3) link_ALPHA1-6 : bond 0.00278 / 0.15 ( 1) link_ALPHA1-6 : angle 1.60382 / 1.41 ( 3) link_BETA1-4 : bond 0.00477 / 0.24 ( 6) link_BETA1-4 : angle 1.46846 / 0.82 ( 18) link_NAG-ASN : bond 0.00260 / 0.13 ( 7) link_NAG-ASN : angle 1.32940 / 0.84 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8717 (p) cc_final: 0.8476 (m) REVERT: A 90 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 94 VAL cc_start: 0.8545 (t) cc_final: 0.8210 (p) REVERT: A 208 SER cc_start: 0.8100 (t) cc_final: 0.7851 (p) REVERT: A 212 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8114 (mtt180) REVERT: A 217 LYS cc_start: 0.8290 (mttt) cc_final: 0.7980 (mttt) REVERT: A 220 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 261 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5811 (t) REVERT: A 268 GLN cc_start: 0.6768 (tp-100) cc_final: 0.6491 (tp-100) REVERT: A 316 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8286 (t) REVERT: A 334 ARG cc_start: 0.7177 (tmm-80) cc_final: 0.6787 (mmm-85) REVERT: A 475 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: A 479 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6666 (ttm-80) REVERT: A 480 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7356 (mp0) REVERT: A 495 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: A 538 GLN cc_start: 0.7901 (mp10) cc_final: 0.7313 (mp10) REVERT: B 355 ASP cc_start: 0.7624 (t0) cc_final: 0.7333 (t0) REVERT: B 359 VAL cc_start: 0.8176 (t) cc_final: 0.7921 (m) REVERT: B 377 GLU cc_start: 0.7616 (tt0) cc_final: 0.7395 (tt0) REVERT: L 33 SER cc_start: 0.8590 (m) cc_final: 0.8153 (p) REVERT: L 182 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5509 (pmm) outliers start: 28 outliers final: 19 residues processed: 243 average time/residue: 1.2212 time to fit residues: 324.7195 Evaluate side-chains 250 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 428 HIS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 182 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125517 restraints weight = 49823.403| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.42 r_work: 0.3344 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12526 Z= 0.152 Angle : 0.522 8.994 17046 Z= 0.269 Chirality : 0.044 0.360 1954 Planarity : 0.005 0.091 2193 Dihedral : 5.504 57.733 2015 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.05 % Allowed : 17.74 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.41 % 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: -0.13 (0.21), residues: 1560 helix: -0.01 (0.37), residues: 205 sheet: 0.17 (0.21), residues: 609 loop : -0.18 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 546 TYR 0.014 0.001 TYR A 215 PHE 0.014 0.001 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (12506) covalent geometry : angle 0.51750 / 0.27 (16991) SS BOND : bond 0.00174 / 0.10 ( 5) SS BOND : angle 0.68454 / 0.40 ( 10) hydrogen bonds : bond 0.03182 / 2.04 ( 436) hydrogen bonds : angle 5.21514 / 3.62 ( 1209) link_ALPHA1-3 : bond 0.00493 / 0.26 ( 1) link_ALPHA1-3 : angle 1.37848 / 1.01 ( 3) link_ALPHA1-6 : bond 0.00308 / 0.16 ( 1) link_ALPHA1-6 : angle 1.56778 / 1.37 ( 3) link_BETA1-4 : bond 0.00454 / 0.23 ( 6) link_BETA1-4 : angle 1.40638 / 0.78 ( 18) link_NAG-ASN : bond 0.00196 / 0.10 ( 7) link_NAG-ASN : angle 1.26206 / 0.77 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10380.37 seconds wall clock time: 175 minutes 56.00 seconds (10556.00 seconds total)