Starting phenix.real_space_refine on Wed May 14 21:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqa_40700/05_2025/8sqa_40700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqa_40700/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqa_40700/05_2025/8sqa_40700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqa_40700/05_2025/8sqa_40700.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqa_40700/05_2025/8sqa_40700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqa_40700/05_2025/8sqa_40700.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.39, per 1000 atoms: 0.36 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.32 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: 3.69 Time building geometry restraints manager: 3.50 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: 16.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.660 ------------------------------------------------------------------------------- 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 : 26.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP D 191 HIS 0.007 0.002 HIS E 83 PHE 0.023 0.002 PHE A 197 TYR 0.021 0.002 TYR D 205 ARG 0.005 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.23579 ( 378) hydrogen bonds : angle 9.39743 ( 1044) SS BOND : bond 0.00648 ( 1) SS BOND : angle 0.70615 ( 2) covalent geometry : bond 0.00709 (12413) covalent geometry : angle 0.80719 (16863) *********************** 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 : 1.364 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: 0.2386 time to fit residues: 43.6035 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 : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 359 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.050137 restraints weight = 51563.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.051686 restraints weight = 29801.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.052731 restraints weight = 20851.679| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12414 Z= 0.173 Angle : 0.701 10.431 16865 Z= 0.369 Chirality : 0.047 0.197 1846 Planarity : 0.005 0.046 2219 Dihedral : 6.044 46.227 1703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.18), residues: 1539 helix: -0.17 (0.28), residues: 307 sheet: -3.41 (0.22), residues: 399 loop : -3.82 (0.17), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 228 HIS 0.007 0.001 HIS E 83 PHE 0.016 0.001 PHE F1296 TYR 0.015 0.001 TYR C 31 ARG 0.005 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 378) hydrogen bonds : angle 6.07386 ( 1044) SS BOND : bond 0.00736 ( 1) SS BOND : angle 1.12618 ( 2) covalent geometry : bond 0.00380 (12413) covalent geometry : angle 0.70142 (16863) *********************** 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 138 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9507 (ttp) cc_final: 0.9192 (ttm) REVERT: A 430 ILE cc_start: 0.8615 (mt) cc_final: 0.8401 (mp) REVERT: A 477 TYR cc_start: 0.9057 (m-80) cc_final: 0.8823 (m-80) REVERT: A 480 VAL cc_start: 0.9357 (m) cc_final: 0.8972 (p) REVERT: A 545 MET cc_start: 0.9070 (mtp) cc_final: 0.8064 (mtm) REVERT: B 80 LEU cc_start: 0.9171 (pt) cc_final: 0.8951 (pp) REVERT: B 221 MET cc_start: 0.8167 (ttt) cc_final: 0.7897 (ttt) REVERT: B 278 MET cc_start: 0.9043 (mmt) cc_final: 0.8734 (mmm) REVERT: B 289 PHE cc_start: 0.9164 (p90) cc_final: 0.8744 (p90) REVERT: B 306 MET cc_start: 0.8691 (ppp) cc_final: 0.8477 (ppp) REVERT: B 319 GLN cc_start: 0.8023 (tm130) cc_final: 0.7498 (tm130) REVERT: D 93 ASP cc_start: 0.9074 (t70) cc_final: 0.8829 (t0) REVERT: D 109 MET cc_start: 0.9019 (mmm) cc_final: 0.8239 (tpp) REVERT: D 199 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8452 (tm-30) REVERT: E 52 GLN cc_start: 0.9322 (mt0) cc_final: 0.8817 (mt0) REVERT: F 1296 PHE cc_start: 0.8357 (m-10) cc_final: 0.7870 (m-80) REVERT: F 1297 ARG cc_start: 0.8868 (ttt90) cc_final: 0.8592 (tpp80) REVERT: F 1298 TYR cc_start: 0.8617 (t80) cc_final: 0.8325 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2028 time to fit residues: 42.6418 Evaluate side-chains 106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 150 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 0.0000 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.049241 restraints weight = 53318.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.050845 restraints weight = 30218.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051917 restraints weight = 20902.971| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12414 Z= 0.195 Angle : 0.688 10.962 16865 Z= 0.361 Chirality : 0.046 0.196 1846 Planarity : 0.004 0.059 2219 Dihedral : 5.897 46.310 1703 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.19), residues: 1539 helix: 0.41 (0.28), residues: 305 sheet: -3.12 (0.22), residues: 404 loop : -3.57 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 228 HIS 0.006 0.001 HIS E 83 PHE 0.010 0.001 PHE B 289 TYR 0.013 0.001 TYR A 315 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 378) hydrogen bonds : angle 5.67921 ( 1044) SS BOND : bond 0.01681 ( 1) SS BOND : angle 0.95536 ( 2) covalent geometry : bond 0.00428 (12413) covalent geometry : angle 0.68788 (16863) *********************** 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 133 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9507 (ttp) cc_final: 0.9204 (ttm) REVERT: A 477 TYR cc_start: 0.9083 (m-80) cc_final: 0.8859 (m-80) REVERT: A 545 MET cc_start: 0.8920 (mtp) cc_final: 0.8221 (mtm) REVERT: A 552 MET cc_start: 0.8726 (mmm) cc_final: 0.8469 (mtp) REVERT: A 711 MET cc_start: 0.8461 (ttp) cc_final: 0.8189 (tmm) REVERT: A 777 MET cc_start: 0.8828 (tpp) cc_final: 0.8626 (tpp) REVERT: B 80 LEU cc_start: 0.9140 (pt) cc_final: 0.8922 (pp) REVERT: B 221 MET cc_start: 0.8214 (ttt) cc_final: 0.8009 (ttt) REVERT: B 267 LEU cc_start: 0.8779 (tt) cc_final: 0.8429 (mp) REVERT: B 278 MET cc_start: 0.8996 (mmt) cc_final: 0.8740 (mmm) REVERT: B 306 MET cc_start: 0.8605 (ppp) cc_final: 0.8273 (ppp) REVERT: C 67 ILE cc_start: 0.8912 (tp) cc_final: 0.8565 (tp) REVERT: D 93 ASP cc_start: 0.9075 (t70) cc_final: 0.8780 (t70) REVERT: D 187 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8445 (tm-30) REVERT: D 199 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 52 GLN cc_start: 0.9317 (mt0) cc_final: 0.8811 (mt0) REVERT: F 1297 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8671 (tpp80) REVERT: F 1298 TYR cc_start: 0.8628 (t80) cc_final: 0.8419 (t80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2184 time to fit residues: 44.2182 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 : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3208 r_free = 0.3208 target = 0.066806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.048898 restraints weight = 51624.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.050468 restraints weight = 29504.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.051480 restraints weight = 20538.009| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12414 Z= 0.234 Angle : 0.718 12.891 16865 Z= 0.374 Chirality : 0.047 0.211 1846 Planarity : 0.005 0.048 2219 Dihedral : 5.953 46.573 1703 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.19), residues: 1539 helix: 0.55 (0.29), residues: 306 sheet: -2.90 (0.22), residues: 396 loop : -3.45 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 228 HIS 0.006 0.001 HIS E 83 PHE 0.026 0.002 PHE B 289 TYR 0.015 0.002 TYR A 649 ARG 0.005 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 378) hydrogen bonds : angle 5.64184 ( 1044) SS BOND : bond 0.00679 ( 1) SS BOND : angle 1.14085 ( 2) covalent geometry : bond 0.00514 (12413) covalent geometry : angle 0.71827 (16863) *********************** 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 123 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9500 (ttp) cc_final: 0.9195 (ttm) REVERT: A 477 TYR cc_start: 0.9119 (m-80) cc_final: 0.8872 (m-80) REVERT: A 539 MET cc_start: 0.8560 (mmm) cc_final: 0.8350 (mmt) REVERT: A 545 MET cc_start: 0.8863 (mtp) cc_final: 0.8252 (mtp) REVERT: A 552 MET cc_start: 0.8764 (mmm) cc_final: 0.8422 (mtp) REVERT: A 711 MET cc_start: 0.8476 (ttp) cc_final: 0.8198 (tmm) REVERT: B 80 LEU cc_start: 0.9098 (pt) cc_final: 0.8864 (pp) REVERT: B 267 LEU cc_start: 0.8779 (tt) cc_final: 0.8415 (mp) REVERT: B 278 MET cc_start: 0.9006 (mmt) cc_final: 0.8747 (mmm) REVERT: B 289 PHE cc_start: 0.9126 (p90) cc_final: 0.8658 (p90) REVERT: B 306 MET cc_start: 0.8670 (ppp) cc_final: 0.8463 (ppp) REVERT: D 93 ASP cc_start: 0.9067 (t70) cc_final: 0.8728 (t70) REVERT: D 187 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 199 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8430 (tm-30) REVERT: E 52 GLN cc_start: 0.9306 (mt0) cc_final: 0.8787 (mt0) REVERT: F 1297 ARG cc_start: 0.9058 (ttt90) cc_final: 0.8856 (tpp80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1970 time to fit residues: 37.8913 Evaluate side-chains 95 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 319 GLN D 54 GLN D 70 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.050240 restraints weight = 51200.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051856 restraints weight = 29026.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.052931 restraints weight = 20095.742| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12414 Z= 0.164 Angle : 0.672 11.869 16865 Z= 0.348 Chirality : 0.045 0.207 1846 Planarity : 0.004 0.051 2219 Dihedral : 5.702 45.308 1703 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.20), residues: 1539 helix: 0.88 (0.30), residues: 306 sheet: -2.65 (0.23), residues: 391 loop : -3.24 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.021 0.001 PHE B 289 TYR 0.018 0.001 TYR C 31 ARG 0.011 0.000 ARG F1273 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 378) hydrogen bonds : angle 5.27668 ( 1044) SS BOND : bond 0.00851 ( 1) SS BOND : angle 1.26670 ( 2) covalent geometry : bond 0.00364 (12413) covalent geometry : angle 0.67153 (16863) *********************** 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 135 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8496 (tp) cc_final: 0.8291 (tp) REVERT: A 304 MET cc_start: 0.9502 (ttp) cc_final: 0.9194 (ttm) REVERT: A 477 TYR cc_start: 0.9090 (m-80) cc_final: 0.8829 (m-80) REVERT: A 539 MET cc_start: 0.8528 (mmm) cc_final: 0.8264 (mmt) REVERT: A 545 MET cc_start: 0.8833 (mtp) cc_final: 0.8140 (mtp) REVERT: A 552 MET cc_start: 0.8753 (mmm) cc_final: 0.8428 (mtp) REVERT: A 777 MET cc_start: 0.8834 (tpp) cc_final: 0.8633 (tpp) REVERT: B 80 LEU cc_start: 0.9096 (pt) cc_final: 0.8847 (pp) REVERT: B 221 MET cc_start: 0.8287 (ttt) cc_final: 0.8020 (ttt) REVERT: B 267 LEU cc_start: 0.8758 (tt) cc_final: 0.8402 (mp) REVERT: B 278 MET cc_start: 0.8945 (mmt) cc_final: 0.8716 (mmm) REVERT: B 289 PHE cc_start: 0.9081 (p90) cc_final: 0.8601 (p90) REVERT: B 290 ILE cc_start: 0.9645 (pt) cc_final: 0.9441 (mp) REVERT: B 306 MET cc_start: 0.8715 (ppp) cc_final: 0.8264 (ppp) REVERT: B 380 ILE cc_start: 0.9438 (tt) cc_final: 0.9212 (tt) REVERT: D 74 ASP cc_start: 0.9346 (m-30) cc_final: 0.9123 (m-30) REVERT: D 93 ASP cc_start: 0.9076 (t70) cc_final: 0.8731 (t70) REVERT: D 187 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 199 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8368 (tm-30) REVERT: E 52 GLN cc_start: 0.9310 (mt0) cc_final: 0.8795 (mt0) REVERT: E 104 ILE cc_start: 0.9422 (pt) cc_final: 0.9154 (mp) REVERT: F 1297 ARG cc_start: 0.9086 (ttt90) cc_final: 0.8849 (tpp80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2143 time to fit residues: 44.7065 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 : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 79 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 0.0870 chunk 139 optimal weight: 9.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.052605 restraints weight = 51487.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054238 restraints weight = 29361.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055312 restraints weight = 20352.604| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12414 Z= 0.116 Angle : 0.646 8.928 16865 Z= 0.336 Chirality : 0.045 0.207 1846 Planarity : 0.004 0.055 2219 Dihedral : 5.401 43.889 1703 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1539 helix: 1.21 (0.31), residues: 308 sheet: -2.43 (0.23), residues: 396 loop : -3.03 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.017 0.001 PHE B 289 TYR 0.019 0.001 TYR D 79 ARG 0.009 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 378) hydrogen bonds : angle 4.98006 ( 1044) SS BOND : bond 0.00912 ( 1) SS BOND : angle 1.36029 ( 2) covalent geometry : bond 0.00255 (12413) covalent geometry : angle 0.64622 (16863) *********************** 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 150 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8507 (tp) cc_final: 0.8248 (tt) REVERT: A 304 MET cc_start: 0.9522 (ttp) cc_final: 0.9193 (ttm) REVERT: A 477 TYR cc_start: 0.9017 (m-80) cc_final: 0.8663 (m-80) REVERT: A 552 MET cc_start: 0.8732 (mmm) cc_final: 0.8498 (mtp) REVERT: B 80 LEU cc_start: 0.8996 (pt) cc_final: 0.8735 (pp) REVERT: B 189 MET cc_start: 0.8644 (ppp) cc_final: 0.8383 (ppp) REVERT: B 221 MET cc_start: 0.8371 (ttt) cc_final: 0.8158 (ttt) REVERT: B 267 LEU cc_start: 0.8762 (tt) cc_final: 0.8422 (mp) REVERT: B 306 MET cc_start: 0.8606 (ppp) cc_final: 0.8226 (ppp) REVERT: B 317 TRP cc_start: 0.8368 (p-90) cc_final: 0.7984 (p-90) REVERT: C 67 ILE cc_start: 0.8741 (tp) cc_final: 0.8461 (tp) REVERT: D 93 ASP cc_start: 0.9084 (t70) cc_final: 0.8707 (t0) REVERT: D 187 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 199 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 52 GLN cc_start: 0.9322 (mt0) cc_final: 0.8809 (mt0) REVERT: E 80 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 104 ILE cc_start: 0.9359 (pt) cc_final: 0.9094 (mp) REVERT: F 1297 ARG cc_start: 0.9096 (ttt90) cc_final: 0.8872 (tpp80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1917 time to fit residues: 45.0688 Evaluate side-chains 112 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 71 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN D 54 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.052578 restraints weight = 51084.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054267 restraints weight = 28618.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055386 restraints weight = 19573.732| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12414 Z= 0.116 Angle : 0.643 8.441 16865 Z= 0.332 Chirality : 0.045 0.202 1846 Planarity : 0.004 0.057 2219 Dihedral : 5.281 45.407 1703 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.21), residues: 1539 helix: 1.31 (0.30), residues: 306 sheet: -2.25 (0.23), residues: 412 loop : -2.92 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 228 HIS 0.003 0.001 HIS E 83 PHE 0.014 0.001 PHE B 289 TYR 0.016 0.001 TYR A 315 ARG 0.006 0.000 ARG F1273 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 378) hydrogen bonds : angle 4.88613 ( 1044) SS BOND : bond 0.00515 ( 1) SS BOND : angle 1.12390 ( 2) covalent geometry : bond 0.00258 (12413) covalent geometry : angle 0.64312 (16863) *********************** 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 145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8519 (tp) cc_final: 0.8266 (tt) REVERT: A 304 MET cc_start: 0.9529 (ttp) cc_final: 0.9205 (ttm) REVERT: A 477 TYR cc_start: 0.9036 (m-80) cc_final: 0.8698 (m-80) REVERT: A 550 TYR cc_start: 0.8388 (m-10) cc_final: 0.8168 (m-80) REVERT: A 552 MET cc_start: 0.8714 (mmm) cc_final: 0.8468 (mtp) REVERT: A 711 MET cc_start: 0.8306 (tmm) cc_final: 0.7438 (tmm) REVERT: B 267 LEU cc_start: 0.8727 (tt) cc_final: 0.8388 (mp) REVERT: B 306 MET cc_start: 0.8666 (ppp) cc_final: 0.8315 (ppp) REVERT: B 317 TRP cc_start: 0.8297 (p-90) cc_final: 0.8000 (p-90) REVERT: B 370 GLU cc_start: 0.9324 (pt0) cc_final: 0.8586 (pm20) REVERT: C 67 ILE cc_start: 0.8753 (tp) cc_final: 0.8473 (tp) REVERT: D 93 ASP cc_start: 0.9120 (t70) cc_final: 0.8713 (t0) REVERT: D 178 GLU cc_start: 0.8474 (pp20) cc_final: 0.7642 (pp20) REVERT: D 187 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8478 (tm-30) REVERT: D 199 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8044 (tm-30) REVERT: E 52 GLN cc_start: 0.9302 (mt0) cc_final: 0.8811 (mt0) REVERT: E 80 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8007 (tm-30) REVERT: F 1297 ARG cc_start: 0.9083 (ttt90) cc_final: 0.8872 (tpp80) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1946 time to fit residues: 44.4316 Evaluate side-chains 116 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 0.0020 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 B 319 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3268 r_free = 0.3268 target = 0.069522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.051517 restraints weight = 52066.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.053187 restraints weight = 29273.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054293 restraints weight = 20036.205| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12414 Z= 0.148 Angle : 0.665 10.008 16865 Z= 0.346 Chirality : 0.045 0.199 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.293 46.657 1703 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1539 helix: 1.23 (0.30), residues: 306 sheet: -2.19 (0.23), residues: 403 loop : -2.84 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 228 HIS 0.003 0.001 HIS E 83 PHE 0.017 0.001 PHE B 289 TYR 0.018 0.001 TYR A 504 ARG 0.006 0.000 ARG F1273 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 378) hydrogen bonds : angle 5.00742 ( 1044) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.35518 ( 2) covalent geometry : bond 0.00328 (12413) covalent geometry : angle 0.66455 (16863) *********************** 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 141 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8525 (tp) cc_final: 0.8282 (tt) REVERT: A 140 PHE cc_start: 0.9086 (t80) cc_final: 0.8883 (t80) REVERT: A 304 MET cc_start: 0.9520 (ttp) cc_final: 0.9231 (ttm) REVERT: A 477 TYR cc_start: 0.9049 (m-80) cc_final: 0.8732 (m-80) REVERT: A 550 TYR cc_start: 0.8420 (m-10) cc_final: 0.8199 (m-80) REVERT: A 552 MET cc_start: 0.8749 (mmm) cc_final: 0.8414 (mtp) REVERT: A 711 MET cc_start: 0.8354 (tmm) cc_final: 0.7519 (tmm) REVERT: B 267 LEU cc_start: 0.8689 (tt) cc_final: 0.8353 (mp) REVERT: B 306 MET cc_start: 0.8672 (ppp) cc_final: 0.8273 (ppp) REVERT: B 317 TRP cc_start: 0.8384 (p-90) cc_final: 0.8056 (p-90) REVERT: B 381 GLN cc_start: 0.9164 (tt0) cc_final: 0.8882 (mt0) REVERT: C 67 ILE cc_start: 0.8849 (tp) cc_final: 0.8547 (tp) REVERT: D 178 GLU cc_start: 0.8600 (pp20) cc_final: 0.7774 (pp20) REVERT: D 187 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 199 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 201 MET cc_start: 0.8371 (ttt) cc_final: 0.7931 (ttt) REVERT: E 52 GLN cc_start: 0.9329 (mt0) cc_final: 0.8840 (mt0) REVERT: E 80 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 104 ILE cc_start: 0.9351 (pt) cc_final: 0.9090 (mp) REVERT: E 107 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8871 (mmtt) REVERT: F 1297 ARG cc_start: 0.9100 (ttt90) cc_final: 0.8888 (tpp80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1936 time to fit residues: 42.8973 Evaluate side-chains 118 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 466 GLN A 563 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3207 r_free = 0.3207 target = 0.066786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.048751 restraints weight = 52427.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.050322 restraints weight = 30150.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.051355 restraints weight = 20999.122| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 12414 Z= 0.274 Angle : 0.763 13.614 16865 Z= 0.396 Chirality : 0.048 0.264 1846 Planarity : 0.005 0.057 2219 Dihedral : 5.851 50.182 1703 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1539 helix: 0.85 (0.29), residues: 308 sheet: -2.26 (0.23), residues: 393 loop : -2.90 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 205 HIS 0.005 0.001 HIS D 102 PHE 0.018 0.002 PHE B 289 TYR 0.023 0.002 TYR A 649 ARG 0.009 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 378) hydrogen bonds : angle 5.49771 ( 1044) SS BOND : bond 0.00390 ( 1) SS BOND : angle 0.55441 ( 2) covalent geometry : bond 0.00601 (12413) covalent geometry : angle 0.76351 (16863) *********************** 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 127 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9496 (ttp) cc_final: 0.9202 (ttm) REVERT: A 477 TYR cc_start: 0.9185 (m-80) cc_final: 0.8849 (m-80) REVERT: A 552 MET cc_start: 0.8797 (mmm) cc_final: 0.8409 (mtp) REVERT: B 80 LEU cc_start: 0.9065 (pt) cc_final: 0.8813 (pp) REVERT: B 267 LEU cc_start: 0.8659 (tt) cc_final: 0.8301 (mp) REVERT: B 306 MET cc_start: 0.8716 (ppp) cc_final: 0.8506 (ppp) REVERT: B 381 GLN cc_start: 0.9225 (tt0) cc_final: 0.8816 (mt0) REVERT: C 67 ILE cc_start: 0.8975 (tp) cc_final: 0.8755 (tp) REVERT: D 199 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 201 MET cc_start: 0.8547 (ttt) cc_final: 0.8228 (ttt) REVERT: E 52 GLN cc_start: 0.9326 (mt0) cc_final: 0.8851 (mt0) REVERT: F 1297 ARG cc_start: 0.9053 (ttt90) cc_final: 0.8842 (tpp80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1934 time to fit residues: 38.6727 Evaluate side-chains 100 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 119 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 D 54 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 = 0.3262 r_free = 0.3262 target = 0.069278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.051340 restraints weight = 50508.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053003 restraints weight = 28499.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054110 restraints weight = 19611.942| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12414 Z= 0.143 Angle : 0.682 10.335 16865 Z= 0.351 Chirality : 0.046 0.259 1846 Planarity : 0.004 0.057 2219 Dihedral : 5.434 48.386 1703 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1539 helix: 1.17 (0.30), residues: 307 sheet: -2.16 (0.23), residues: 404 loop : -2.75 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.013 0.001 PHE B 289 TYR 0.025 0.001 TYR D 79 ARG 0.005 0.000 ARG F1273 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 378) hydrogen bonds : angle 5.04363 ( 1044) SS BOND : bond 0.00368 ( 1) SS BOND : angle 0.55736 ( 2) covalent geometry : bond 0.00319 (12413) covalent geometry : angle 0.68162 (16863) ********************** 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 130 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8614 (tp) cc_final: 0.8290 (tt) REVERT: A 304 MET cc_start: 0.9506 (ttp) cc_final: 0.9209 (ttm) REVERT: A 477 TYR cc_start: 0.9052 (m-80) cc_final: 0.8761 (m-80) REVERT: A 539 MET cc_start: 0.8446 (mmm) cc_final: 0.8242 (mmm) REVERT: A 552 MET cc_start: 0.8739 (mmm) cc_final: 0.8488 (mtp) REVERT: B 80 LEU cc_start: 0.8993 (pt) cc_final: 0.8719 (pp) REVERT: B 259 PHE cc_start: 0.8915 (m-80) cc_final: 0.8706 (m-80) REVERT: B 267 LEU cc_start: 0.8677 (tt) cc_final: 0.8329 (mp) REVERT: B 306 MET cc_start: 0.8737 (ppp) cc_final: 0.8220 (ppp) REVERT: B 317 TRP cc_start: 0.8401 (p-90) cc_final: 0.8034 (p-90) REVERT: B 381 GLN cc_start: 0.9147 (tt0) cc_final: 0.8857 (mt0) REVERT: C 67 ILE cc_start: 0.8893 (tp) cc_final: 0.8591 (tp) REVERT: D 199 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 201 MET cc_start: 0.8531 (ttt) cc_final: 0.8291 (ttt) REVERT: D 213 ASP cc_start: 0.8984 (m-30) cc_final: 0.8455 (t0) REVERT: E 52 GLN cc_start: 0.9301 (mt0) cc_final: 0.8827 (mt0) REVERT: E 80 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 104 ILE cc_start: 0.9388 (pt) cc_final: 0.9138 (mp) REVERT: F 1297 ARG cc_start: 0.9029 (ttt90) cc_final: 0.8829 (tpp80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2072 time to fit residues: 41.8643 Evaluate side-chains 110 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 93 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 83 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 466 GLN A 538 ASN A 805 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053472 restraints weight = 50097.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055201 restraints weight = 27958.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056329 restraints weight = 19021.266| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12414 Z= 0.109 Angle : 0.648 9.866 16865 Z= 0.331 Chirality : 0.045 0.260 1846 Planarity : 0.004 0.058 2219 Dihedral : 5.093 47.135 1703 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.21), residues: 1539 helix: 1.48 (0.30), residues: 307 sheet: -1.94 (0.24), residues: 410 loop : -2.61 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.011 0.001 PHE A 648 TYR 0.023 0.001 TYR D 79 ARG 0.005 0.000 ARG F1273 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 378) hydrogen bonds : angle 4.76519 ( 1044) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.59301 ( 2) covalent geometry : bond 0.00241 (12413) covalent geometry : angle 0.64773 (16863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.92 seconds wall clock time: 62 minutes 59.37 seconds (3779.37 seconds total)