Starting phenix.real_space_refine on Fri Feb 6 11:25:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p97_71401/02_2026/9p97_71401_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p97_71401/02_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_71401/02_2026/9p97_71401_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p97_71401/02_2026/9p97_71401_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p97_71401/02_2026/9p97_71401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p97_71401/02_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-2.0-5952/lib/python3.9/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, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 1.49 Conformation dependent library (CDL) restraints added in 802.6 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: 0.71 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: 5.82 Time building geometry restraints manager: 2.06 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: 3.410 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: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.480 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:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 covalent geometry : bond 0.00436 (12506) covalent geometry : angle 0.59394 (16991) SS BOND : bond 0.00125 ( 5) SS BOND : angle 0.75676 ( 10) hydrogen bonds : bond 0.20505 ( 436) hydrogen bonds : angle 9.25834 ( 1209) link_ALPHA1-3 : bond 0.01447 ( 1) link_ALPHA1-3 : angle 0.97266 ( 3) link_ALPHA1-6 : bond 0.01318 ( 1) link_ALPHA1-6 : angle 1.74507 ( 3) link_BETA1-4 : bond 0.00811 ( 6) link_BETA1-4 : angle 2.93614 ( 18) link_NAG-ASN : bond 0.00754 ( 7) link_NAG-ASN : angle 2.30363 ( 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 : 0.548 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: 1.1916 time to fit residues: 337.9850 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 : 0.631 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125136 restraints weight = 50117.385| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.42 r_work: 0.3314 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0752 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= 0.261 Angle : 0.618 6.648 17046 Z= 0.320 Chirality : 0.047 0.368 1954 Planarity : 0.005 0.068 2193 Dihedral : 7.404 59.934 2023 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.58 % Allowed : 15.31 % Favored : 82.11 % 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: -0.34 (0.21), residues: 1560 helix: -0.25 (0.36), residues: 199 sheet: -0.07 (0.21), residues: 601 loop : -0.20 (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 covalent geometry : bond 0.00620 (12506) covalent geometry : angle 0.60914 (16991) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.15796 ( 10) hydrogen bonds : bond 0.04528 ( 436) hydrogen bonds : angle 6.70332 ( 1209) link_ALPHA1-3 : bond 0.01102 ( 1) link_ALPHA1-3 : angle 2.04755 ( 3) link_ALPHA1-6 : bond 0.01012 ( 1) link_ALPHA1-6 : angle 1.80905 ( 3) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 2.22663 ( 18) link_NAG-ASN : bond 0.00400 ( 7) link_NAG-ASN : angle 1.87763 ( 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 288 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.637 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: 0.8715 (p) cc_final: 0.8485 (m) REVERT: A 94 VAL cc_start: 0.8555 (t) cc_final: 0.8203 (p) REVERT: A 204 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7881 (mtpt) REVERT: A 208 SER cc_start: 0.8122 (t) cc_final: 0.7839 (p) REVERT: A 212 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8132 (mtt180) REVERT: A 217 LYS cc_start: 0.8328 (mttt) cc_final: 0.8053 (mttt) REVERT: A 268 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6572 (tp-100) REVERT: A 316 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (t) REVERT: A 334 ARG cc_start: 0.7294 (tmm-80) cc_final: 0.6961 (mmm-85) REVERT: A 349 PHE cc_start: 0.8174 (m-80) cc_final: 0.7870 (m-80) REVERT: A 382 GLN cc_start: 0.8153 (mp10) cc_final: 0.7872 (mp10) REVERT: A 480 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7234 (mp0) REVERT: A 538 GLN cc_start: 0.7803 (mp10) cc_final: 0.7222 (mp10) REVERT: B 108 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7200 (mmm-85) REVERT: B 110 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7430 (ttm170) REVERT: B 170 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 236 LEU cc_start: 0.8647 (tp) cc_final: 0.8379 (tt) REVERT: B 355 ASP cc_start: 0.7676 (t0) cc_final: 0.7378 (t0) REVERT: B 359 VAL cc_start: 0.8244 (t) cc_final: 0.7944 (m) REVERT: B 390 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6907 (tt0) REVERT: H 30 GLU cc_start: 0.6702 (pm20) cc_final: 0.6356 (pm20) REVERT: L 33 SER cc_start: 0.8469 (m) cc_final: 0.8057 (p) REVERT: L 182 MET cc_start: 0.5784 (pmm) cc_final: 0.5531 (pmm) outliers start: 34 outliers final: 19 residues processed: 267 average time/residue: 1.2097 time to fit residues: 351.9900 Evaluate side-chains 268 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 A residue 645 ILE 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: 0.9980 chunk 110 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.0270 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4224 r_free = 0.4224 target = 0.180110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125906 restraints weight = 50056.285| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.24 r_work: 0.3330 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1005 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= 0.177 Angle : 0.550 5.502 17046 Z= 0.285 Chirality : 0.045 0.366 1954 Planarity : 0.005 0.058 2193 Dihedral : 6.822 58.669 2017 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.20 % Allowed : 15.47 % Favored : 82.34 % 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: -0.20 (0.21), residues: 1560 helix: -0.10 (0.36), residues: 205 sheet: 0.00 (0.21), residues: 599 loop : -0.10 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.014 0.001 TYR A 215 PHE 0.014 0.001 PHE A 627 TRP 0.020 0.001 TRP L 42 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00418 (12506) covalent geometry : angle 0.54348 (16991) SS BOND : bond 0.00364 ( 5) SS BOND : angle 1.04920 ( 10) hydrogen bonds : bond 0.04052 ( 436) hydrogen bonds : angle 6.19120 ( 1209) link_ALPHA1-3 : bond 0.01050 ( 1) link_ALPHA1-3 : angle 1.86539 ( 3) link_ALPHA1-6 : bond 0.01114 ( 1) link_ALPHA1-6 : angle 1.82626 ( 3) link_BETA1-4 : bond 0.00543 ( 6) link_BETA1-4 : angle 1.81775 ( 18) link_NAG-ASN : bond 0.00458 ( 7) link_NAG-ASN : angle 1.46045 ( 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: 29 poor density : 240 time to evaluate : 0.676 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: 0.8711 (p) cc_final: 0.8491 (m) REVERT: A 204 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7852 (mtpt) REVERT: A 208 SER cc_start: 0.8109 (t) cc_final: 0.7837 (p) REVERT: A 212 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8107 (mtt180) REVERT: A 217 LYS cc_start: 0.8367 (mttt) cc_final: 0.8095 (mttt) REVERT: A 220 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 268 GLN cc_start: 0.6781 (tp-100) cc_final: 0.6477 (tp-100) REVERT: A 316 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 334 ARG cc_start: 0.7309 (tmm-80) cc_final: 0.6919 (mmm-85) REVERT: A 349 PHE cc_start: 0.8158 (m-80) cc_final: 0.7780 (m-80) REVERT: A 477 GLU cc_start: 0.6780 (mp0) cc_final: 0.6568 (mp0) REVERT: A 480 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7227 (mp0) REVERT: A 538 GLN cc_start: 0.7728 (mp10) cc_final: 0.7127 (mp10) REVERT: B 108 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7159 (mmm-85) REVERT: B 170 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 236 LEU cc_start: 0.8636 (tp) cc_final: 0.8376 (tt) REVERT: B 355 ASP cc_start: 0.7609 (t0) cc_final: 0.7257 (t0) REVERT: B 359 VAL cc_start: 0.8213 (t) cc_final: 0.7922 (m) REVERT: B 390 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6879 (tt0) REVERT: H 30 GLU cc_start: 0.6703 (pm20) cc_final: 0.6360 (pm20) REVERT: L 33 SER cc_start: 0.8498 (m) cc_final: 0.8070 (p) REVERT: L 182 MET cc_start: 0.5723 (pmm) cc_final: 0.5470 (pmm) outliers start: 29 outliers final: 20 residues processed: 252 average time/residue: 1.2632 time to fit residues: 344.4619 Evaluate side-chains 262 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 183 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125686 restraints weight = 49919.805| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.23 r_work: 0.3297 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12526 Z= 0.193 Angle : 0.545 6.826 17046 Z= 0.282 Chirality : 0.045 0.366 1954 Planarity : 0.005 0.069 2193 Dihedral : 6.416 55.863 2017 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.73 % Allowed : 15.31 % Favored : 81.96 % 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: -0.17 (0.21), residues: 1560 helix: 0.00 (0.36), residues: 205 sheet: 0.15 (0.21), residues: 593 loop : -0.22 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 546 TYR 0.014 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 covalent geometry : bond 0.00461 (12506) covalent geometry : angle 0.53900 (16991) SS BOND : bond 0.00216 ( 5) SS BOND : angle 1.01237 ( 10) hydrogen bonds : bond 0.03666 ( 436) hydrogen bonds : angle 5.86574 ( 1209) link_ALPHA1-3 : bond 0.00774 ( 1) link_ALPHA1-3 : angle 1.70387 ( 3) link_ALPHA1-6 : bond 0.01072 ( 1) link_ALPHA1-6 : angle 1.59533 ( 3) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 1.69689 ( 18) link_NAG-ASN : bond 0.00363 ( 7) link_NAG-ASN : angle 1.38664 ( 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 276 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.540 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: 0.8738 (p) cc_final: 0.8508 (m) REVERT: A 94 VAL cc_start: 0.8562 (t) cc_final: 0.8208 (p) REVERT: A 204 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7825 (mtpt) REVERT: A 208 SER cc_start: 0.8084 (t) cc_final: 0.7811 (p) REVERT: A 212 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8112 (mtt180) REVERT: A 217 LYS cc_start: 0.8345 (mttt) cc_final: 0.8060 (mttt) REVERT: A 268 GLN cc_start: 0.6724 (tp-100) cc_final: 0.6386 (tp-100) REVERT: A 316 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (t) REVERT: A 334 ARG cc_start: 0.7285 (tmm-80) cc_final: 0.6876 (mmm-85) REVERT: A 349 PHE cc_start: 0.8197 (m-80) cc_final: 0.7856 (m-80) REVERT: A 480 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7142 (mp0) REVERT: A 538 GLN cc_start: 0.7747 (mp10) cc_final: 0.7093 (mp10) REVERT: B 108 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7231 (mmm-85) REVERT: B 170 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 236 LEU cc_start: 0.8645 (tp) cc_final: 0.8421 (tt) REVERT: B 355 ASP cc_start: 0.7599 (t0) cc_final: 0.7251 (t0) REVERT: B 359 VAL cc_start: 0.8197 (t) cc_final: 0.7918 (m) REVERT: H 30 GLU cc_start: 0.6673 (pm20) cc_final: 0.6312 (pm20) REVERT: L 33 SER cc_start: 0.8491 (m) cc_final: 0.8063 (p) REVERT: L 182 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5547 (pmm) outliers start: 36 outliers final: 23 residues processed: 258 average time/residue: 1.1323 time to fit residues: 318.2742 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 140 optimal weight: 0.0370 chunk 4 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4225 r_free = 0.4225 target = 0.180108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126022 restraints weight = 49754.723| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.42 r_work: 0.3333 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1401 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= 0.159 Angle : 0.526 7.149 17046 Z= 0.272 Chirality : 0.044 0.368 1954 Planarity : 0.005 0.073 2193 Dihedral : 5.989 56.227 2017 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 15.77 % Favored : 81.88 % 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: -0.12 (0.21), residues: 1560 helix: 0.04 (0.36), residues: 205 sheet: 0.16 (0.21), residues: 594 loop : -0.18 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 546 TYR 0.014 0.001 TYR H 153 PHE 0.013 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 covalent geometry : bond 0.00379 (12506) covalent geometry : angle 0.52194 (16991) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.86177 ( 10) hydrogen bonds : bond 0.03388 ( 436) hydrogen bonds : angle 5.65328 ( 1209) link_ALPHA1-3 : bond 0.00893 ( 1) link_ALPHA1-3 : angle 1.64327 ( 3) link_ALPHA1-6 : bond 0.00844 ( 1) link_ALPHA1-6 : angle 1.36322 ( 3) link_BETA1-4 : bond 0.00609 ( 6) link_BETA1-4 : angle 1.54021 ( 18) link_NAG-ASN : bond 0.00192 ( 7) link_NAG-ASN : angle 1.20730 ( 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 270 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.724 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: 0.8722 (p) cc_final: 0.8506 (m) REVERT: A 94 VAL cc_start: 0.8550 (t) cc_final: 0.8215 (p) REVERT: A 208 SER cc_start: 0.8089 (t) cc_final: 0.7738 (p) REVERT: A 217 LYS cc_start: 0.8299 (mttt) cc_final: 0.8006 (mttt) REVERT: A 220 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 268 GLN cc_start: 0.6740 (tp-100) cc_final: 0.6402 (tp-100) REVERT: A 316 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8287 (t) REVERT: A 334 ARG cc_start: 0.7287 (tmm-80) cc_final: 0.6864 (mmm-85) REVERT: A 475 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 479 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6629 (ttm-80) REVERT: A 480 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7301 (mp0) REVERT: A 538 GLN cc_start: 0.7759 (mp10) cc_final: 0.7137 (mp10) REVERT: B 108 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7218 (mmm-85) REVERT: B 150 GLU cc_start: 0.7459 (tp30) cc_final: 0.7253 (tp30) REVERT: B 170 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 236 LEU cc_start: 0.8683 (tp) cc_final: 0.8462 (tt) REVERT: B 359 VAL cc_start: 0.8190 (t) cc_final: 0.7908 (m) REVERT: L 33 SER cc_start: 0.8522 (m) cc_final: 0.8094 (p) REVERT: L 182 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.5429 (pmm) outliers start: 31 outliers final: 22 residues processed: 254 average time/residue: 1.2770 time to fit residues: 351.7682 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 475 GLN 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 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 12 VAL Chi-restraints excluded: chain H residue 82 MET 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: 0.6980 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4225 r_free = 0.4225 target = 0.180101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126015 restraints weight = 49986.353| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.26 r_work: 0.3330 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12526 Z= 0.150 Angle : 0.519 7.885 17046 Z= 0.268 Chirality : 0.044 0.363 1954 Planarity : 0.005 0.075 2193 Dihedral : 5.666 56.345 2015 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.43 % Allowed : 16.30 % Favored : 81.27 % 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: -0.09 (0.21), residues: 1560 helix: 0.02 (0.36), residues: 206 sheet: 0.21 (0.21), residues: 593 loop : -0.17 (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 0.013 0.001 PHE A 627 TRP 0.010 0.001 TRP A 34 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00357 (12506) covalent geometry : angle 0.51373 (16991) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.88042 ( 10) hydrogen bonds : bond 0.03269 ( 436) hydrogen bonds : angle 5.51510 ( 1209) link_ALPHA1-3 : bond 0.00719 ( 1) link_ALPHA1-3 : angle 1.48196 ( 3) link_ALPHA1-6 : bond 0.00467 ( 1) link_ALPHA1-6 : angle 1.74476 ( 3) link_BETA1-4 : bond 0.00556 ( 6) link_BETA1-4 : angle 1.50514 ( 18) link_NAG-ASN : bond 0.00293 ( 7) link_NAG-ASN : angle 1.29744 ( 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 265 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.622 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 21 SER cc_start: 0.8721 (p) cc_final: 0.8501 (m) REVERT: A 94 VAL cc_start: 0.8555 (t) cc_final: 0.8217 (p) REVERT: A 208 SER cc_start: 0.8089 (t) cc_final: 0.7863 (p) REVERT: A 212 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8131 (mtt180) REVERT: A 217 LYS cc_start: 0.8349 (mttt) cc_final: 0.8057 (mttt) REVERT: A 220 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 316 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8263 (t) REVERT: A 334 ARG cc_start: 0.7267 (tmm-80) cc_final: 0.6883 (mmm-85) REVERT: A 475 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: A 479 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6635 (ttm-80) REVERT: A 480 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7236 (mp0) REVERT: A 538 GLN cc_start: 0.7763 (mp10) cc_final: 0.7112 (mp10) REVERT: B 108 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7234 (mmm-85) REVERT: B 170 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 236 LEU cc_start: 0.8706 (tp) cc_final: 0.8499 (tt) REVERT: B 359 VAL cc_start: 0.8181 (t) cc_final: 0.7895 (m) REVERT: B 439 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7805 (ptt180) REVERT: L 33 SER cc_start: 0.8543 (m) cc_final: 0.8112 (p) REVERT: L 182 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5476 (pmm) outliers start: 32 outliers final: 19 residues processed: 249 average time/residue: 1.2401 time to fit residues: 334.5169 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 331 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 138 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.180345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126699 restraints weight = 49768.039| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.26 r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12526 Z= 0.132 Angle : 0.510 7.433 17046 Z= 0.263 Chirality : 0.043 0.366 1954 Planarity : 0.005 0.095 2193 Dihedral : 5.471 56.393 2013 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.20 % Allowed : 16.83 % Favored : 80.97 % 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: -0.03 (0.21), residues: 1560 helix: 0.13 (0.37), residues: 206 sheet: 0.17 (0.21), residues: 603 loop : -0.08 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 546 TYR 0.011 0.001 TYR A 215 PHE 0.012 0.001 PHE A 627 TRP 0.009 0.001 TRP A 34 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00317 (12506) covalent geometry : angle 0.50571 (16991) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.81656 ( 10) hydrogen bonds : bond 0.03098 ( 436) hydrogen bonds : angle 5.38034 ( 1209) link_ALPHA1-3 : bond 0.00668 ( 1) link_ALPHA1-3 : angle 1.44493 ( 3) link_ALPHA1-6 : bond 0.00296 ( 1) link_ALPHA1-6 : angle 1.65869 ( 3) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.42088 ( 18) link_NAG-ASN : bond 0.00200 ( 7) link_NAG-ASN : angle 1.13020 ( 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 265 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.458 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 21 SER cc_start: 0.8724 (p) cc_final: 0.8497 (m) REVERT: A 94 VAL cc_start: 0.8543 (t) cc_final: 0.8206 (p) REVERT: A 208 SER cc_start: 0.8054 (t) cc_final: 0.7750 (p) REVERT: A 217 LYS cc_start: 0.8286 (mttt) cc_final: 0.7976 (mttt) REVERT: A 220 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 316 VAL cc_start: 0.8556 (t) cc_final: 0.8277 (p) REVERT: A 334 ARG cc_start: 0.7226 (tmm-80) cc_final: 0.6836 (mmm-85) REVERT: A 475 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: A 479 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6669 (ttm-80) REVERT: A 480 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7251 (mp0) REVERT: A 538 GLN cc_start: 0.7746 (mp10) cc_final: 0.7158 (mp10) REVERT: B 108 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.7211 (mmm-85) REVERT: B 170 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 236 LEU cc_start: 0.8712 (tp) cc_final: 0.8507 (tt) REVERT: B 359 VAL cc_start: 0.8184 (t) cc_final: 0.7902 (m) REVERT: L 33 SER cc_start: 0.8537 (m) cc_final: 0.8092 (p) REVERT: L 182 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.5428 (pmm) outliers start: 29 outliers final: 20 residues processed: 253 average time/residue: 1.3774 time to fit residues: 377.3802 Evaluate side-chains 263 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 182 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 0.0370 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4220 r_free = 0.4220 target = 0.179723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125147 restraints weight = 49839.447| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.44 r_work: 0.3330 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12526 Z= 0.191 Angle : 0.529 6.174 17046 Z= 0.275 Chirality : 0.044 0.363 1954 Planarity : 0.005 0.097 2193 Dihedral : 5.520 56.463 2013 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.50 % Allowed : 16.68 % Favored : 80.82 % 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: -0.04 (0.21), residues: 1560 helix: 0.01 (0.36), residues: 206 sheet: 0.20 (0.21), residues: 605 loop : -0.09 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 546 TYR 0.017 0.001 TYR H 153 PHE 0.015 0.002 PHE A 627 TRP 0.010 0.001 TRP A 34 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00458 (12506) covalent geometry : angle 0.52464 (16991) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.82344 ( 10) hydrogen bonds : bond 0.03372 ( 436) hydrogen bonds : angle 5.34258 ( 1209) link_ALPHA1-3 : bond 0.00569 ( 1) link_ALPHA1-3 : angle 1.35459 ( 3) link_ALPHA1-6 : bond 0.00277 ( 1) link_ALPHA1-6 : angle 1.68438 ( 3) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.51660 ( 18) link_NAG-ASN : bond 0.00265 ( 7) link_NAG-ASN : angle 1.34202 ( 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 274 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.632 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: 0.8746 (p) cc_final: 0.8492 (m) REVERT: A 94 VAL cc_start: 0.8548 (t) cc_final: 0.8210 (p) REVERT: A 208 SER cc_start: 0.8098 (t) cc_final: 0.7866 (p) REVERT: A 212 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8125 (mtt180) REVERT: A 217 LYS cc_start: 0.8318 (mttt) cc_final: 0.8010 (mttt) REVERT: A 261 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.5753 (t) REVERT: A 268 GLN cc_start: 0.6689 (tp-100) cc_final: 0.6372 (tp-100) REVERT: A 316 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 334 ARG cc_start: 0.7197 (tmm-80) cc_final: 0.6814 (mmm-85) REVERT: A 349 PHE cc_start: 0.8198 (m-80) cc_final: 0.7900 (m-80) REVERT: A 475 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: A 479 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6697 (ttm-80) REVERT: A 480 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 538 GLN cc_start: 0.7805 (mp10) cc_final: 0.7248 (mp10) REVERT: A 668 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5619 (mtp) REVERT: B 108 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7213 (mmm-85) REVERT: B 170 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 236 LEU cc_start: 0.8735 (tp) cc_final: 0.8505 (tt) REVERT: B 355 ASP cc_start: 0.7614 (t0) cc_final: 0.7284 (t0) REVERT: B 359 VAL cc_start: 0.8189 (t) cc_final: 0.7917 (m) REVERT: L 33 SER cc_start: 0.8559 (m) cc_final: 0.8118 (p) REVERT: L 182 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5553 (pmm) outliers start: 33 outliers final: 22 residues processed: 259 average time/residue: 1.3215 time to fit residues: 372.0838 Evaluate side-chains 268 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 506 ASP Chi-restraints excluded: chain A residue 668 MET 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 170 VAL Chi-restraints excluded: chain B residue 183 LEU 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 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 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: 0.8980 chunk 151 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4213 r_free = 0.4213 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125044 restraints weight = 49579.131| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.41 r_work: 0.3320 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12526 Z= 0.247 Angle : 0.563 7.927 17046 Z= 0.292 Chirality : 0.045 0.361 1954 Planarity : 0.006 0.092 2193 Dihedral : 5.606 56.881 2013 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.43 % Allowed : 16.76 % Favored : 80.82 % 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: -0.17 (0.36), residues: 205 sheet: 0.23 (0.21), residues: 597 loop : -0.24 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 546 TYR 0.011 0.001 TYR A 215 PHE 0.018 0.002 PHE A 627 TRP 0.012 0.001 TRP A 34 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00591 (12506) covalent geometry : angle 0.55792 (16991) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.81746 ( 10) hydrogen bonds : bond 0.03615 ( 436) hydrogen bonds : angle 5.35589 ( 1209) link_ALPHA1-3 : bond 0.00494 ( 1) link_ALPHA1-3 : angle 1.31637 ( 3) link_ALPHA1-6 : bond 0.00256 ( 1) link_ALPHA1-6 : angle 1.65167 ( 3) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 1.58454 ( 18) link_NAG-ASN : bond 0.00359 ( 7) link_NAG-ASN : angle 1.43096 ( 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 272 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.627 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: 0.8747 (p) cc_final: 0.8496 (m) REVERT: A 94 VAL cc_start: 0.8564 (t) cc_final: 0.8226 (p) REVERT: A 208 SER cc_start: 0.8153 (t) cc_final: 0.7900 (p) REVERT: A 212 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8137 (mtt180) REVERT: A 217 LYS cc_start: 0.8345 (mttt) cc_final: 0.8043 (mttt) REVERT: A 261 THR cc_start: 0.6332 (OUTLIER) cc_final: 0.5831 (t) REVERT: A 268 GLN cc_start: 0.6740 (tp-100) cc_final: 0.6489 (tp-100) REVERT: A 316 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8330 (t) REVERT: A 334 ARG cc_start: 0.7224 (tmm-80) cc_final: 0.6831 (mmm-85) REVERT: A 475 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: A 479 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6764 (ttm-80) REVERT: A 480 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7234 (mp0) REVERT: A 538 GLN cc_start: 0.7878 (mp10) cc_final: 0.7265 (mp10) REVERT: B 108 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7231 (mmm-85) REVERT: B 355 ASP cc_start: 0.7629 (t0) cc_final: 0.7339 (t0) REVERT: B 359 VAL cc_start: 0.8187 (t) cc_final: 0.7937 (m) REVERT: L 33 SER cc_start: 0.8546 (m) cc_final: 0.8115 (p) REVERT: L 182 MET cc_start: 0.5747 (OUTLIER) cc_final: 0.5518 (pmm) outliers start: 32 outliers final: 22 residues processed: 259 average time/residue: 1.2539 time to fit residues: 353.8625 Evaluate side-chains 264 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 506 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 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 199 THR 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 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: 0.8980 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4220 r_free = 0.4220 target = 0.180106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125853 restraints weight = 50014.557| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.43 r_work: 0.3306 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1988 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= 0.148 Angle : 0.519 7.315 17046 Z= 0.268 Chirality : 0.044 0.359 1954 Planarity : 0.005 0.094 2193 Dihedral : 5.456 57.183 2013 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.97 % Allowed : 17.36 % 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: -0.05 (0.21), residues: 1560 helix: 0.03 (0.37), residues: 206 sheet: 0.20 (0.21), residues: 603 loop : -0.10 (0.23), residues: 751 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 0.015 0.001 PHE A 627 TRP 0.012 0.001 TRP A 34 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00353 (12506) covalent geometry : angle 0.51512 (16991) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.74766 ( 10) hydrogen bonds : bond 0.03160 ( 436) hydrogen bonds : angle 5.23891 ( 1209) link_ALPHA1-3 : bond 0.00502 ( 1) link_ALPHA1-3 : angle 1.36812 ( 3) link_ALPHA1-6 : bond 0.00301 ( 1) link_ALPHA1-6 : angle 1.58105 ( 3) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.41458 ( 18) link_NAG-ASN : bond 0.00193 ( 7) link_NAG-ASN : angle 1.21109 ( 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 261 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.589 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: 0.8747 (p) cc_final: 0.8496 (m) REVERT: A 94 VAL cc_start: 0.8556 (t) cc_final: 0.8232 (p) REVERT: A 208 SER cc_start: 0.8100 (t) cc_final: 0.7820 (p) REVERT: A 212 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8135 (mtt180) REVERT: A 217 LYS cc_start: 0.8322 (mttt) cc_final: 0.8012 (mttt) REVERT: A 220 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 268 GLN cc_start: 0.6700 (tp-100) cc_final: 0.6363 (tp-100) REVERT: A 334 ARG cc_start: 0.7209 (tmm-80) cc_final: 0.6792 (mmm-85) REVERT: A 349 PHE cc_start: 0.8198 (m-80) cc_final: 0.7745 (m-80) REVERT: A 475 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: A 479 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6721 (ttm-80) REVERT: A 480 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7190 (mp0) REVERT: A 495 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.6443 (m-10) REVERT: A 538 GLN cc_start: 0.7837 (mp10) cc_final: 0.7215 (mp10) REVERT: B 108 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7198 (mmm-85) REVERT: B 355 ASP cc_start: 0.7612 (t0) cc_final: 0.7281 (t0) REVERT: B 359 VAL cc_start: 0.8185 (t) cc_final: 0.7926 (m) REVERT: L 33 SER cc_start: 0.8566 (m) cc_final: 0.8121 (p) REVERT: L 182 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5548 (pmm) outliers start: 26 outliers final: 19 residues processed: 251 average time/residue: 1.1889 time to fit residues: 325.3624 Evaluate side-chains 254 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 506 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 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 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 182 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4215 r_free = 0.4215 target = 0.179153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124943 restraints weight = 49622.723| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.42 r_work: 0.3324 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2084 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= 0.220 Angle : 0.550 8.868 17046 Z= 0.284 Chirality : 0.045 0.363 1954 Planarity : 0.005 0.087 2193 Dihedral : 5.526 57.224 2013 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 17.97 % 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: -0.11 (0.36), residues: 206 sheet: 0.17 (0.21), residues: 605 loop : -0.15 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 546 TYR 0.013 0.001 TYR A 215 PHE 0.017 0.002 PHE A 627 TRP 0.011 0.001 TRP A 34 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00529 (12506) covalent geometry : angle 0.54555 (16991) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.77836 ( 10) hydrogen bonds : bond 0.03487 ( 436) hydrogen bonds : angle 5.24453 ( 1209) link_ALPHA1-3 : bond 0.00505 ( 1) link_ALPHA1-3 : angle 1.35953 ( 3) link_ALPHA1-6 : bond 0.00281 ( 1) link_ALPHA1-6 : angle 1.60867 ( 3) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 1.52075 ( 18) link_NAG-ASN : bond 0.00320 ( 7) link_NAG-ASN : angle 1.41649 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10878.12 seconds wall clock time: 184 minutes 11.43 seconds (11051.43 seconds total)