Starting phenix.real_space_refine on Sat Aug 23 13:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqa_40700/08_2025/8sqa_40700.map" } resolution = 4.2 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= 0.005 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 7662 2.51 5 N 2079 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6052 Classifications: {'peptide': 765} Link IDs: {'CIS': 2, 'PTRANS': 28, 'TRANS': 734} Chain breaks: 4 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2776 Classifications: {'peptide': 369} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 53} 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: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1740 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "F" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 483 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 3.11, per 1000 atoms: 0.26 Number of scatterers: 12156 At special positions: 0 Unit cell: (100.44, 139.32, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 2381 8.00 N 2079 7.00 C 7662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS F1208 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 505.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 22 sheets defined 22.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.801A pdb=" N ARG A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.606A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 4.075A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.861A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.973A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.634A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.175A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 4.136A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.945A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.721A pdb=" N GLY D 129 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.953A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 Processing helix chain 'D' and resid 208 through 225 removed outlier: 4.209A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.543A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.718A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.626A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.571A pdb=" N LYS A 152 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 168 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183 removed outlier: 6.976A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLN A 178 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 12.830A pdb=" N VAL A 258 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N ILE A 180 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.059A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 342 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.059A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.764A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 401 removed outlier: 3.930A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 415 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 432 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.530A pdb=" N GLY A 457 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 473 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY A 516 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 525 through 526 removed outlier: 4.029A pdb=" N ARG A 526 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 618 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 596 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 610 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET A 711 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 718 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 737 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 736 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 773 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 772 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 743 through 744 removed outlier: 3.936A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 718 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 737 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 736 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 773 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 772 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 784 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 805 " --> pdb=" O VAL A 784 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.791A pdb=" N LYS B 82 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.723A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 123 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 132 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.650A pdb=" N LEU B 174 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.720A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.647A pdb=" N VAL B 254 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.935A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 307 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.685A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 338 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.812A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1223 through 1226 removed outlier: 3.620A pdb=" N GLU F1277 " --> pdb=" O ASN F1293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1266 through 1267 383 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4070 1.34 - 1.46: 2527 1.46 - 1.57: 5751 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 12413 Sorted by residual: bond pdb=" C ASP B 248 " pdb=" N THR B 249 " ideal model delta sigma weight residual 1.331 1.273 0.057 2.56e-02 1.53e+03 5.03e+00 bond pdb=" C THR A 722 " pdb=" N PRO A 723 " ideal model delta sigma weight residual 1.334 1.315 0.018 8.40e-03 1.42e+04 4.66e+00 bond pdb=" C TYR A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.326 1.299 0.027 1.44e-02 4.82e+03 3.50e+00 bond pdb=" CB VAL D 181 " pdb=" CG1 VAL D 181 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.21e+00 bond pdb=" N THR B 249 " pdb=" CA THR B 249 " ideal model delta sigma weight residual 1.460 1.426 0.034 2.12e-02 2.22e+03 2.60e+00 ... (remaining 12408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 16683 2.88 - 5.77: 156 5.77 - 8.65: 22 8.65 - 11.54: 1 11.54 - 14.42: 1 Bond angle restraints: 16863 Sorted by residual: angle pdb=" N ILE B 56 " pdb=" CA ILE B 56 " pdb=" C ILE B 56 " ideal model delta sigma weight residual 113.71 107.28 6.43 9.50e-01 1.11e+00 4.58e+01 angle pdb=" C ASP D 204 " pdb=" N TYR D 205 " pdb=" CA TYR D 205 " ideal model delta sigma weight residual 123.21 115.53 7.68 1.19e+00 7.06e-01 4.16e+01 angle pdb=" C TYR B 263 " pdb=" N ASN B 264 " pdb=" CA ASN B 264 " ideal model delta sigma weight residual 121.44 114.97 6.47 1.59e+00 3.96e-01 1.65e+01 angle pdb=" N ASP A 500 " pdb=" CA ASP A 500 " pdb=" C ASP A 500 " ideal model delta sigma weight residual 110.06 115.84 -5.78 1.43e+00 4.89e-01 1.63e+01 angle pdb=" C ALA A 499 " pdb=" N ASP A 500 " pdb=" CA ASP A 500 " ideal model delta sigma weight residual 122.62 116.66 5.96 1.63e+00 3.76e-01 1.34e+01 ... (remaining 16858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6519 17.65 - 35.30: 678 35.30 - 52.95: 96 52.95 - 70.61: 15 70.61 - 88.26: 13 Dihedral angle restraints: 7321 sinusoidal: 2842 harmonic: 4479 Sorted by residual: dihedral pdb=" CA ILE B 227 " pdb=" C ILE B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta harmonic sigma weight residual 180.00 133.96 46.04 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA SER B 285 " pdb=" C SER B 285 " pdb=" N VAL B 286 " pdb=" CA VAL B 286 " ideal model delta harmonic sigma weight residual -180.00 -143.28 -36.72 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA LEU A 158 " pdb=" C LEU A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 -147.55 -32.45 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 7318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1269 0.044 - 0.088: 437 0.088 - 0.132: 116 0.132 - 0.175: 18 0.175 - 0.219: 6 Chirality restraints: 1846 Sorted by residual: chirality pdb=" CA TRP D 191 " pdb=" N TRP D 191 " pdb=" C TRP D 191 " pdb=" CB TRP D 191 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE B 227 " pdb=" CA ILE B 227 " pdb=" CG1 ILE B 227 " pdb=" CG2 ILE B 227 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1843 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 199 " -0.036 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 200 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 541 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 520 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ASN A 520 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN A 520 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 521 " -0.010 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 391 2.63 - 3.19: 12811 3.19 - 3.76: 18599 3.76 - 4.33: 24626 4.33 - 4.90: 37947 Nonbonded interactions: 94374 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASN B 264 " model vdw 2.058 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" OD1 ASP D 162 " model vdw 2.141 3.040 nonbonded pdb=" O LEU A 501 " pdb=" OH TYR A 674 " model vdw 2.145 3.040 nonbonded pdb=" O ASN E 41 " pdb=" OG SER E 44 " model vdw 2.146 3.040 nonbonded pdb=" OD2 ASP B 363 " pdb=" OH TYR B 388 " model vdw 2.148 3.040 ... (remaining 94369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.007 0.083 12414 Z= 0.335 Angle : 0.807 14.424 16865 Z= 0.444 Chirality : 0.048 0.219 1846 Planarity : 0.004 0.053 2219 Dihedral : 14.346 88.257 4466 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 18.78 % Favored : 81.16 % Rotamer: Outliers : 0.39 % Allowed : 11.92 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -5.75 (0.16), residues: 1539 helix: -2.13 (0.23), residues: 304 sheet: -4.09 (0.20), residues: 411 loop : -4.47 (0.16), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 243 TYR 0.021 0.002 TYR D 205 PHE 0.023 0.002 PHE A 197 TRP 0.024 0.002 TRP D 191 HIS 0.007 0.002 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00709 (12413) covalent geometry : angle 0.80719 (16863) SS BOND : bond 0.00648 ( 1) SS BOND : angle 0.70615 ( 2) hydrogen bonds : bond 0.23579 ( 378) hydrogen bonds : angle 9.39743 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9484 (ttp) cc_final: 0.9172 (ttm) REVERT: A 372 MET cc_start: 0.9308 (mmm) cc_final: 0.9034 (mmp) REVERT: A 477 TYR cc_start: 0.9132 (m-80) cc_final: 0.8899 (m-80) REVERT: A 512 ASP cc_start: 0.8824 (p0) cc_final: 0.8589 (p0) REVERT: B 226 MET cc_start: 0.8758 (ppp) cc_final: 0.8445 (pmm) REVERT: B 278 MET cc_start: 0.9126 (mmt) cc_final: 0.8712 (mmm) REVERT: B 289 PHE cc_start: 0.9247 (p90) cc_final: 0.8860 (p90) REVERT: D 93 ASP cc_start: 0.8716 (t70) cc_final: 0.8460 (t70) REVERT: D 199 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8280 (tm-30) REVERT: E 52 GLN cc_start: 0.9246 (mt0) cc_final: 0.8931 (mt0) REVERT: E 63 LEU cc_start: 0.9715 (tp) cc_final: 0.9505 (tp) REVERT: F 1297 ARG cc_start: 0.8887 (ttt90) cc_final: 0.8650 (tpp80) REVERT: F 1298 TYR cc_start: 0.8596 (t80) cc_final: 0.8369 (t80) outliers start: 5 outliers final: 5 residues processed: 124 average time/residue: 0.0998 time to fit residues: 18.0315 Evaluate side-chains 92 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 264 ASN B 319 GLN B 359 GLN D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.050539 restraints weight = 51761.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052106 restraints weight = 29869.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053122 restraints weight = 20824.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.053864 restraints weight = 16469.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054286 restraints weight = 14059.525| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12414 Z= 0.152 Angle : 0.688 9.970 16865 Z= 0.361 Chirality : 0.047 0.197 1846 Planarity : 0.004 0.045 2219 Dihedral : 5.962 45.723 1703 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -4.27 (0.19), residues: 1539 helix: -0.04 (0.28), residues: 307 sheet: -3.38 (0.22), residues: 399 loop : -3.79 (0.17), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.016 0.001 TYR C 31 PHE 0.012 0.001 PHE F1296 TRP 0.022 0.001 TRP B 228 HIS 0.007 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00331 (12413) covalent geometry : angle 0.68773 (16863) SS BOND : bond 0.00737 ( 1) SS BOND : angle 1.16987 ( 2) hydrogen bonds : bond 0.04727 ( 378) hydrogen bonds : angle 6.00782 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9492 (ttp) cc_final: 0.9177 (ttm) REVERT: A 430 ILE cc_start: 0.8606 (mt) cc_final: 0.8396 (mp) REVERT: A 477 TYR cc_start: 0.9029 (m-80) cc_final: 0.8777 (m-80) REVERT: A 480 VAL cc_start: 0.9364 (m) cc_final: 0.8979 (p) REVERT: A 545 MET cc_start: 0.9076 (mtp) cc_final: 0.8024 (mtm) REVERT: B 80 LEU cc_start: 0.9185 (pt) cc_final: 0.8960 (pp) REVERT: B 221 MET cc_start: 0.8136 (ttt) cc_final: 0.7859 (ttt) REVERT: B 278 MET cc_start: 0.9006 (mmt) cc_final: 0.8672 (mmm) REVERT: B 289 PHE cc_start: 0.9159 (p90) cc_final: 0.8769 (p90) REVERT: B 306 MET cc_start: 0.8668 (ppp) cc_final: 0.8424 (ppp) REVERT: D 93 ASP cc_start: 0.9034 (t70) cc_final: 0.8803 (t0) REVERT: D 109 MET cc_start: 0.9017 (mmm) cc_final: 0.8188 (tpp) REVERT: D 199 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8427 (tm-30) REVERT: E 46 ILE cc_start: 0.9727 (pt) cc_final: 0.9490 (mp) REVERT: E 52 GLN cc_start: 0.9295 (mt0) cc_final: 0.8797 (mt0) REVERT: F 1296 PHE cc_start: 0.8357 (m-10) cc_final: 0.7845 (m-80) REVERT: F 1297 ARG cc_start: 0.8864 (ttt90) cc_final: 0.8584 (tpp80) REVERT: F 1298 TYR cc_start: 0.8609 (t80) cc_final: 0.8323 (t80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.0984 time to fit residues: 21.6758 Evaluate side-chains 109 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 276 GLN B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.049384 restraints weight = 53057.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.050965 restraints weight = 30095.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052022 restraints weight = 20880.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052716 restraints weight = 16396.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.053131 restraints weight = 14054.700| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12414 Z= 0.196 Angle : 0.685 10.775 16865 Z= 0.360 Chirality : 0.046 0.196 1846 Planarity : 0.005 0.061 2219 Dihedral : 5.856 46.329 1703 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.81 (0.19), residues: 1539 helix: 0.49 (0.29), residues: 305 sheet: -3.10 (0.22), residues: 409 loop : -3.54 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.015 0.001 TYR A 315 PHE 0.010 0.001 PHE B 289 TRP 0.020 0.001 TRP B 348 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00430 (12413) covalent geometry : angle 0.68505 (16863) SS BOND : bond 0.01239 ( 1) SS BOND : angle 0.98859 ( 2) hydrogen bonds : bond 0.04712 ( 378) hydrogen bonds : angle 5.61826 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.9224 (ptm) cc_final: 0.8828 (ptm) REVERT: A 304 MET cc_start: 0.9499 (ttp) cc_final: 0.9196 (ttm) REVERT: A 477 TYR cc_start: 0.9077 (m-80) cc_final: 0.8875 (m-80) REVERT: A 545 MET cc_start: 0.8910 (mtp) cc_final: 0.8311 (mtm) REVERT: A 711 MET cc_start: 0.8406 (ttp) cc_final: 0.8165 (tmm) REVERT: A 777 MET cc_start: 0.8847 (tpp) cc_final: 0.8643 (tpp) REVERT: B 80 LEU cc_start: 0.9136 (pt) cc_final: 0.8920 (pp) REVERT: B 221 MET cc_start: 0.8148 (ttt) cc_final: 0.7883 (ttt) REVERT: B 267 LEU cc_start: 0.8754 (tt) cc_final: 0.8453 (mp) REVERT: B 278 MET cc_start: 0.8977 (mmt) cc_final: 0.8733 (mmm) REVERT: B 306 MET cc_start: 0.8686 (ppp) cc_final: 0.8432 (ppp) REVERT: C 67 ILE cc_start: 0.8910 (tp) cc_final: 0.8545 (tp) REVERT: D 93 ASP cc_start: 0.9019 (t70) cc_final: 0.8720 (t70) REVERT: D 187 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8420 (tm-30) REVERT: D 199 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8376 (tm-30) REVERT: E 52 GLN cc_start: 0.9302 (mt0) cc_final: 0.8805 (mt0) REVERT: F 1297 ARG cc_start: 0.8883 (ttt90) cc_final: 0.8664 (tpp80) REVERT: F 1298 TYR cc_start: 0.8615 (t80) cc_final: 0.8368 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0882 time to fit residues: 17.6072 Evaluate side-chains 101 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 115 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 384 GLN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.048629 restraints weight = 52405.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.050193 restraints weight = 29886.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.051234 restraints weight = 20818.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051903 restraints weight = 16424.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.052296 restraints weight = 14090.844| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12414 Z= 0.243 Angle : 0.724 12.940 16865 Z= 0.377 Chirality : 0.047 0.212 1846 Planarity : 0.005 0.048 2219 Dihedral : 5.981 46.640 1703 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.61 (0.19), residues: 1539 helix: 0.57 (0.29), residues: 305 sheet: -2.87 (0.22), residues: 395 loop : -3.44 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.015 0.002 TYR A 649 PHE 0.025 0.002 PHE B 289 TRP 0.018 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00532 (12413) covalent geometry : angle 0.72395 (16863) SS BOND : bond 0.00724 ( 1) SS BOND : angle 1.09593 ( 2) hydrogen bonds : bond 0.04582 ( 378) hydrogen bonds : angle 5.68423 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9483 (ttp) cc_final: 0.9177 (ttm) REVERT: A 477 TYR cc_start: 0.9122 (m-80) cc_final: 0.8891 (m-80) REVERT: A 539 MET cc_start: 0.8596 (tpp) cc_final: 0.8389 (mmt) REVERT: A 545 MET cc_start: 0.8785 (mtp) cc_final: 0.8460 (mtp) REVERT: A 711 MET cc_start: 0.8409 (ttp) cc_final: 0.8146 (tmm) REVERT: B 80 LEU cc_start: 0.9091 (pt) cc_final: 0.8861 (pp) REVERT: B 267 LEU cc_start: 0.8766 (tt) cc_final: 0.8417 (mp) REVERT: B 278 MET cc_start: 0.8989 (mmt) cc_final: 0.8735 (mmm) REVERT: B 289 PHE cc_start: 0.9125 (p90) cc_final: 0.8680 (p90) REVERT: B 306 MET cc_start: 0.8683 (ppp) cc_final: 0.8456 (ppp) REVERT: D 74 ASP cc_start: 0.9405 (m-30) cc_final: 0.9205 (m-30) REVERT: D 93 ASP cc_start: 0.9008 (t70) cc_final: 0.8673 (t70) REVERT: D 187 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8521 (tm-30) REVERT: D 199 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 218 MET cc_start: 0.9354 (ttt) cc_final: 0.9118 (ttm) REVERT: E 52 GLN cc_start: 0.9290 (mt0) cc_final: 0.8779 (mt0) REVERT: F 1297 ARG cc_start: 0.9060 (ttt90) cc_final: 0.8854 (tpp80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0916 time to fit residues: 17.7993 Evaluate side-chains 96 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 117 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.049068 restraints weight = 52823.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.050624 restraints weight = 30586.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.051639 restraints weight = 21442.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052276 restraints weight = 17011.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052731 restraints weight = 14705.180| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12414 Z= 0.221 Angle : 0.711 13.116 16865 Z= 0.368 Chirality : 0.046 0.203 1846 Planarity : 0.005 0.051 2219 Dihedral : 5.901 46.329 1703 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.42 (0.20), residues: 1539 helix: 0.68 (0.29), residues: 306 sheet: -2.69 (0.23), residues: 399 loop : -3.33 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F1273 TYR 0.017 0.002 TYR C 31 PHE 0.021 0.002 PHE B 289 TRP 0.019 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00486 (12413) covalent geometry : angle 0.71053 (16863) SS BOND : bond 0.01171 ( 1) SS BOND : angle 1.14129 ( 2) hydrogen bonds : bond 0.04451 ( 378) hydrogen bonds : angle 5.48512 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9148 (t80) cc_final: 0.8910 (t80) REVERT: A 304 MET cc_start: 0.9492 (ttp) cc_final: 0.9188 (ttm) REVERT: A 477 TYR cc_start: 0.9141 (m-80) cc_final: 0.8877 (m-80) REVERT: A 539 MET cc_start: 0.8831 (tpp) cc_final: 0.8455 (tpp) REVERT: A 711 MET cc_start: 0.8502 (ttp) cc_final: 0.8198 (tmm) REVERT: A 777 MET cc_start: 0.8819 (tpp) cc_final: 0.8611 (tpp) REVERT: B 80 LEU cc_start: 0.9100 (pt) cc_final: 0.8858 (pp) REVERT: B 221 MET cc_start: 0.8283 (ttt) cc_final: 0.7983 (ttt) REVERT: B 267 LEU cc_start: 0.8770 (tt) cc_final: 0.8427 (mp) REVERT: B 278 MET cc_start: 0.8985 (mmt) cc_final: 0.8737 (mmm) REVERT: B 289 PHE cc_start: 0.9072 (p90) cc_final: 0.8668 (p90) REVERT: B 290 ILE cc_start: 0.9675 (pt) cc_final: 0.9441 (mp) REVERT: B 306 MET cc_start: 0.8718 (ppp) cc_final: 0.8287 (ppp) REVERT: D 74 ASP cc_start: 0.9411 (m-30) cc_final: 0.9207 (m-30) REVERT: D 93 ASP cc_start: 0.9038 (t70) cc_final: 0.8685 (t70) REVERT: D 109 MET cc_start: 0.9058 (mmt) cc_final: 0.8857 (tpt) REVERT: D 187 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 199 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 213 ASP cc_start: 0.8994 (m-30) cc_final: 0.8475 (t0) REVERT: E 52 GLN cc_start: 0.9299 (mt0) cc_final: 0.8786 (mt0) REVERT: F 1297 ARG cc_start: 0.9083 (ttt90) cc_final: 0.8846 (tpp80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0975 time to fit residues: 19.2397 Evaluate side-chains 102 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 6 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 207 ASN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.066189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.048299 restraints weight = 52589.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.049836 restraints weight = 30273.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.050839 restraints weight = 21066.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.051567 restraints weight = 16680.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051989 restraints weight = 14198.458| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12414 Z= 0.275 Angle : 0.761 13.967 16865 Z= 0.395 Chirality : 0.048 0.233 1846 Planarity : 0.005 0.056 2219 Dihedral : 6.095 46.631 1703 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.87 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.46 (0.19), residues: 1539 helix: 0.49 (0.29), residues: 305 sheet: -2.63 (0.23), residues: 399 loop : -3.33 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F1273 TYR 0.020 0.002 TYR D 79 PHE 0.020 0.002 PHE B 289 TRP 0.018 0.002 TRP B 228 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00599 (12413) covalent geometry : angle 0.76135 (16863) SS BOND : bond 0.00875 ( 1) SS BOND : angle 1.48028 ( 2) hydrogen bonds : bond 0.04680 ( 378) hydrogen bonds : angle 5.68082 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8477 (tp) cc_final: 0.8254 (tp) REVERT: A 140 PHE cc_start: 0.9168 (t80) cc_final: 0.8960 (t80) REVERT: A 304 MET cc_start: 0.9492 (ttp) cc_final: 0.9196 (ttm) REVERT: A 477 TYR cc_start: 0.9177 (m-80) cc_final: 0.8894 (m-80) REVERT: A 777 MET cc_start: 0.8836 (tpp) cc_final: 0.8633 (tpp) REVERT: A 808 LYS cc_start: 0.6669 (mmmm) cc_final: 0.5927 (mmpt) REVERT: B 80 LEU cc_start: 0.9092 (pt) cc_final: 0.8874 (pp) REVERT: B 221 MET cc_start: 0.8354 (ttt) cc_final: 0.8047 (ttt) REVERT: B 267 LEU cc_start: 0.8756 (tt) cc_final: 0.8405 (mp) REVERT: B 278 MET cc_start: 0.8956 (mmt) cc_final: 0.8718 (mmm) REVERT: B 289 PHE cc_start: 0.9094 (p90) cc_final: 0.8667 (p90) REVERT: B 306 MET cc_start: 0.8753 (ppp) cc_final: 0.8319 (ppp) REVERT: C 67 ILE cc_start: 0.9012 (tp) cc_final: 0.8802 (tp) REVERT: D 93 ASP cc_start: 0.9031 (t70) cc_final: 0.8633 (t0) REVERT: D 187 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8588 (tm-30) REVERT: D 199 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8246 (tm-30) REVERT: E 52 GLN cc_start: 0.9277 (mt0) cc_final: 0.8797 (mt0) REVERT: F 1297 ARG cc_start: 0.9011 (ttt90) cc_final: 0.8772 (tpp80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0950 time to fit residues: 18.5712 Evaluate side-chains 101 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 109 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 129 optimal weight: 0.0470 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 3.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.048764 restraints weight = 52039.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.050337 restraints weight = 29792.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.051415 restraints weight = 20710.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052080 restraints weight = 16226.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.052561 restraints weight = 13894.797| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12414 Z= 0.233 Angle : 0.732 13.707 16865 Z= 0.377 Chirality : 0.047 0.241 1846 Planarity : 0.005 0.058 2219 Dihedral : 5.976 46.288 1703 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.30 (0.20), residues: 1539 helix: 0.62 (0.29), residues: 306 sheet: -2.53 (0.23), residues: 399 loop : -3.23 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1273 TYR 0.019 0.002 TYR D 79 PHE 0.017 0.002 PHE B 289 TRP 0.019 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00512 (12413) covalent geometry : angle 0.73174 (16863) SS BOND : bond 0.00724 ( 1) SS BOND : angle 1.21987 ( 2) hydrogen bonds : bond 0.04526 ( 378) hydrogen bonds : angle 5.46069 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8424 (tp) cc_final: 0.8219 (tp) REVERT: A 304 MET cc_start: 0.9507 (ttp) cc_final: 0.9204 (ttm) REVERT: A 477 TYR cc_start: 0.9147 (m-80) cc_final: 0.8883 (m-80) REVERT: A 545 MET cc_start: 0.9023 (mtm) cc_final: 0.8375 (mtm) REVERT: A 711 MET cc_start: 0.8389 (ttp) cc_final: 0.7899 (tmm) REVERT: A 808 LYS cc_start: 0.6709 (mmmm) cc_final: 0.5920 (mmpt) REVERT: B 80 LEU cc_start: 0.9087 (pt) cc_final: 0.8853 (pp) REVERT: B 267 LEU cc_start: 0.8749 (tt) cc_final: 0.8410 (mp) REVERT: B 278 MET cc_start: 0.8937 (mmt) cc_final: 0.8683 (mmm) REVERT: B 289 PHE cc_start: 0.9103 (p90) cc_final: 0.8689 (p90) REVERT: B 290 ILE cc_start: 0.9686 (pt) cc_final: 0.9446 (mp) REVERT: B 306 MET cc_start: 0.8723 (ppp) cc_final: 0.8455 (ppp) REVERT: C 67 ILE cc_start: 0.8972 (tp) cc_final: 0.8642 (tp) REVERT: D 178 GLU cc_start: 0.8602 (pp20) cc_final: 0.8316 (pp20) REVERT: D 187 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8641 (tm-30) REVERT: D 199 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8279 (tm-30) REVERT: E 52 GLN cc_start: 0.9291 (mt0) cc_final: 0.8812 (mt0) REVERT: F 1297 ARG cc_start: 0.9016 (ttt90) cc_final: 0.8792 (tpp80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0905 time to fit residues: 17.5391 Evaluate side-chains 103 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS B 264 ASN B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051941 restraints weight = 51034.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.053640 restraints weight = 28643.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054763 restraints weight = 19573.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055434 restraints weight = 15216.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055974 restraints weight = 13009.135| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12414 Z= 0.121 Angle : 0.671 10.571 16865 Z= 0.346 Chirality : 0.046 0.247 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.457 44.273 1703 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.08 % Allowed : 1.47 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.87 (0.20), residues: 1539 helix: 1.15 (0.30), residues: 307 sheet: -2.29 (0.24), residues: 396 loop : -3.02 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1273 TYR 0.020 0.001 TYR C 31 PHE 0.016 0.001 PHE B 289 TRP 0.021 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00268 (12413) covalent geometry : angle 0.67106 (16863) SS BOND : bond 0.00641 ( 1) SS BOND : angle 1.34291 ( 2) hydrogen bonds : bond 0.04019 ( 378) hydrogen bonds : angle 4.93631 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8347 (tp) cc_final: 0.8077 (tt) REVERT: A 140 PHE cc_start: 0.9134 (t80) cc_final: 0.8900 (t80) REVERT: A 304 MET cc_start: 0.9505 (ttp) cc_final: 0.9198 (ttm) REVERT: A 477 TYR cc_start: 0.9038 (m-80) cc_final: 0.8722 (m-80) REVERT: A 550 TYR cc_start: 0.8462 (m-10) cc_final: 0.8193 (m-80) REVERT: B 80 LEU cc_start: 0.9032 (pt) cc_final: 0.8785 (pp) REVERT: B 267 LEU cc_start: 0.8725 (tt) cc_final: 0.8390 (mp) REVERT: B 289 PHE cc_start: 0.8960 (p90) cc_final: 0.8647 (p90) REVERT: B 306 MET cc_start: 0.8672 (ppp) cc_final: 0.8196 (ppp) REVERT: B 317 TRP cc_start: 0.8420 (p-90) cc_final: 0.8086 (p-90) REVERT: B 380 ILE cc_start: 0.9455 (tt) cc_final: 0.9193 (tt) REVERT: C 67 ILE cc_start: 0.8869 (tp) cc_final: 0.8546 (tp) REVERT: D 199 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 201 MET cc_start: 0.8648 (ttt) cc_final: 0.8442 (ttt) REVERT: E 52 GLN cc_start: 0.9297 (mt0) cc_final: 0.8785 (mt0) REVERT: E 80 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 1297 ARG cc_start: 0.9036 (ttt90) cc_final: 0.8802 (tpp80) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0821 time to fit residues: 18.8668 Evaluate side-chains 115 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 110 optimal weight: 0.0370 chunk 2 optimal weight: 0.0570 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.0578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 244 GLN B 319 GLN B 324 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.052717 restraints weight = 50663.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054403 restraints weight = 28335.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055500 restraints weight = 19349.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056225 restraints weight = 15077.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.056731 restraints weight = 12818.198| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12414 Z= 0.119 Angle : 0.661 9.441 16865 Z= 0.343 Chirality : 0.045 0.251 1846 Planarity : 0.004 0.059 2219 Dihedral : 5.247 46.488 1703 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.66 (0.21), residues: 1539 helix: 1.27 (0.30), residues: 307 sheet: -2.21 (0.24), residues: 400 loop : -2.82 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1273 TYR 0.023 0.001 TYR D 185 PHE 0.011 0.001 PHE A 738 TRP 0.028 0.001 TRP A 546 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00264 (12413) covalent geometry : angle 0.66119 (16863) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.86930 ( 2) hydrogen bonds : bond 0.03911 ( 378) hydrogen bonds : angle 4.83148 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8342 (tp) cc_final: 0.8062 (tt) REVERT: A 304 MET cc_start: 0.9509 (ttp) cc_final: 0.9207 (ttm) REVERT: A 477 TYR cc_start: 0.8964 (m-80) cc_final: 0.8643 (m-80) REVERT: A 545 MET cc_start: 0.9129 (mtm) cc_final: 0.8790 (mtm) REVERT: A 550 TYR cc_start: 0.8354 (m-10) cc_final: 0.8103 (m-80) REVERT: B 259 PHE cc_start: 0.8960 (m-80) cc_final: 0.8694 (m-80) REVERT: B 267 LEU cc_start: 0.8685 (tt) cc_final: 0.8373 (mp) REVERT: B 289 PHE cc_start: 0.8950 (p90) cc_final: 0.8509 (p90) REVERT: B 306 MET cc_start: 0.8688 (ppp) cc_final: 0.8243 (ppp) REVERT: B 317 TRP cc_start: 0.8423 (p-90) cc_final: 0.8103 (p-90) REVERT: C 67 ILE cc_start: 0.8850 (tp) cc_final: 0.8547 (tp) REVERT: D 93 ASP cc_start: 0.8920 (t70) cc_final: 0.8563 (t0) REVERT: D 187 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8609 (tm-30) REVERT: D 199 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8075 (tm-30) REVERT: E 52 GLN cc_start: 0.9303 (mt0) cc_final: 0.8817 (mt0) REVERT: E 80 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7969 (tm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0892 time to fit residues: 19.8687 Evaluate side-chains 113 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.069681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.051762 restraints weight = 51433.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053428 restraints weight = 28910.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054481 restraints weight = 19832.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055239 restraints weight = 15628.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055683 restraints weight = 13227.452| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12414 Z= 0.145 Angle : 0.680 10.592 16865 Z= 0.354 Chirality : 0.045 0.256 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.302 47.472 1703 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.64 (0.21), residues: 1539 helix: 1.10 (0.30), residues: 308 sheet: -2.16 (0.23), residues: 430 loop : -2.75 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1273 TYR 0.029 0.001 TYR D 79 PHE 0.011 0.001 PHE F1274 TRP 0.025 0.001 TRP A 546 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00322 (12413) covalent geometry : angle 0.67994 (16863) SS BOND : bond 0.00391 ( 1) SS BOND : angle 0.44444 ( 2) hydrogen bonds : bond 0.04136 ( 378) hydrogen bonds : angle 4.95547 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8512 (tp) cc_final: 0.8251 (tt) REVERT: A 140 PHE cc_start: 0.9130 (t80) cc_final: 0.8897 (t80) REVERT: A 304 MET cc_start: 0.9509 (ttp) cc_final: 0.9209 (ttm) REVERT: A 477 TYR cc_start: 0.8931 (m-80) cc_final: 0.8717 (m-80) REVERT: A 550 TYR cc_start: 0.8392 (m-10) cc_final: 0.8144 (m-80) REVERT: B 259 PHE cc_start: 0.8979 (m-80) cc_final: 0.8711 (m-80) REVERT: B 267 LEU cc_start: 0.8609 (tt) cc_final: 0.8286 (mp) REVERT: B 289 PHE cc_start: 0.8965 (p90) cc_final: 0.8467 (p90) REVERT: B 306 MET cc_start: 0.8653 (ppp) cc_final: 0.8236 (ppp) REVERT: B 381 GLN cc_start: 0.9185 (tt0) cc_final: 0.8884 (mt0) REVERT: C 67 ILE cc_start: 0.8905 (tp) cc_final: 0.8585 (tp) REVERT: D 93 ASP cc_start: 0.8729 (t70) cc_final: 0.8504 (t70) REVERT: D 109 MET cc_start: 0.9097 (tpt) cc_final: 0.8753 (tpt) REVERT: D 178 GLU cc_start: 0.8558 (pp20) cc_final: 0.7701 (pp20) REVERT: D 199 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8100 (tm-30) REVERT: E 52 GLN cc_start: 0.9292 (mt0) cc_final: 0.8802 (mt0) REVERT: E 80 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 104 ILE cc_start: 0.9379 (pt) cc_final: 0.9178 (mp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0782 time to fit residues: 16.7368 Evaluate side-chains 114 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 144 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 244 GLN A 805 ASN B 130 GLN B 319 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.052593 restraints weight = 50429.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054279 restraints weight = 28316.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055366 restraints weight = 19383.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.056104 restraints weight = 15156.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.056611 restraints weight = 12877.184| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12414 Z= 0.122 Angle : 0.655 9.808 16865 Z= 0.341 Chirality : 0.045 0.257 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.199 47.244 1703 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.49 (0.21), residues: 1539 helix: 1.20 (0.30), residues: 308 sheet: -2.06 (0.23), residues: 430 loop : -2.65 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F1273 TYR 0.026 0.001 TYR D 79 PHE 0.011 0.001 PHE F1274 TRP 0.023 0.001 TRP A 546 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00274 (12413) covalent geometry : angle 0.65516 (16863) SS BOND : bond 0.00363 ( 1) SS BOND : angle 0.47433 ( 2) hydrogen bonds : bond 0.03948 ( 378) hydrogen bonds : angle 4.83236 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.72 seconds wall clock time: 32 minutes 47.01 seconds (1967.01 seconds total)