Starting phenix.real_space_refine on Wed Mar 4 14:53:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ns3_12559/03_2026/7ns3_12559.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19 atoms to isotropic. 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 68 5.16 5 C 9386 2.51 5 N 2403 2.21 5 O 2588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14445 Number of models: 1 Model: "" Number of chains: 6 Chain: "5" Number of atoms: 5919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5919 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 23, 'TRANS': 738} Chain breaks: 4 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 26, 'GLN:plan1': 7, 'ASP:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 196 Chain: "8" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2597 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "1" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3272 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 8 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 14, 'ARG:plan': 4, 'GLU:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 115 Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain breaks: 3 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "4" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain breaks: 3 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "Fb" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Time building chain proxies: 2.99, per 1000 atoms: 0.21 Number of scatterers: 14445 At special positions: 0 Unit cell: (118.5, 121.66, 145.36, 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 68 16.00 O 2588 8.00 N 2403 7.00 C 9386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 656 " - pdb=" SG CYS 4 357 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 582.6 milliseconds 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 5 sheets defined 53.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain '5' and resid 7 through 16 Processing helix chain '5' and resid 21 through 28 removed outlier: 3.805A pdb=" N PHE 5 28 " --> pdb=" O LYS 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 39 removed outlier: 4.197A pdb=" N GLN 5 37 " --> pdb=" O CYS 5 33 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 61 Processing helix chain '5' and resid 66 through 72 Processing helix chain '5' and resid 74 through 85 Processing helix chain '5' and resid 92 through 96 Processing helix chain '5' and resid 98 through 114 Processing helix chain '5' and resid 123 through 137 Processing helix chain '5' and resid 145 through 160 removed outlier: 3.753A pdb=" N LEU 5 160 " --> pdb=" O LYS 5 156 " (cutoff:3.500A) Processing helix chain '5' and resid 188 through 206 removed outlier: 5.107A pdb=" N LYS 5 206 " --> pdb=" O LYS 5 202 " (cutoff:3.500A) Processing helix chain '5' and resid 255 through 271 Processing helix chain '5' and resid 285 through 296 removed outlier: 4.310A pdb=" N LYS 5 296 " --> pdb=" O LEU 5 292 " (cutoff:3.500A) Processing helix chain '5' and resid 300 through 316 Proline residue: 5 313 - end of helix Processing helix chain '5' and resid 324 through 338 Proline residue: 5 332 - end of helix removed outlier: 4.176A pdb=" N PHE 5 338 " --> pdb=" O LEU 5 334 " (cutoff:3.500A) Processing helix chain '5' and resid 349 through 363 Processing helix chain '5' and resid 369 through 377 removed outlier: 3.854A pdb=" N THR 5 377 " --> pdb=" O THR 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 379 through 391 Processing helix chain '5' and resid 398 through 414 Processing helix chain '5' and resid 419 through 428 removed outlier: 4.608A pdb=" N ASP 5 428 " --> pdb=" O LEU 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 431 through 451 Processing helix chain '5' and resid 453 through 459 Processing helix chain '5' and resid 474 through 489 removed outlier: 4.016A pdb=" N ARG 5 489 " --> pdb=" O LYS 5 485 " (cutoff:3.500A) Processing helix chain '5' and resid 491 through 496 Processing helix chain '5' and resid 501 through 520 Processing helix chain '5' and resid 526 through 546 Proline residue: 5 531 - end of helix removed outlier: 3.526A pdb=" N GLY 5 541 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN 5 545 " --> pdb=" O GLY 5 541 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE 5 546 " --> pdb=" O SER 5 542 " (cutoff:3.500A) Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 562 through 570 Processing helix chain '5' and resid 586 through 592 Processing helix chain '5' and resid 598 through 611 Processing helix chain '5' and resid 617 through 626 Processing helix chain '5' and resid 629 through 635 Processing helix chain '5' and resid 641 through 655 Processing helix chain '5' and resid 660 through 668 Processing helix chain '5' and resid 693 through 701 Processing helix chain '5' and resid 707 through 725 removed outlier: 3.944A pdb=" N ALA 5 725 " --> pdb=" O VAL 5 721 " (cutoff:3.500A) Processing helix chain '5' and resid 728 through 736 Processing helix chain '5' and resid 739 through 748 Processing helix chain '5' and resid 762 through 774 Processing helix chain '5' and resid 874 through 886 Processing helix chain '5' and resid 888 through 897 removed outlier: 3.725A pdb=" N ILE 5 896 " --> pdb=" O VAL 5 892 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR 5 897 " --> pdb=" O ARG 5 893 " (cutoff:3.500A) Processing helix chain '5' and resid 901 through 918 Processing helix chain '8' and resid 36 through 52 removed outlier: 3.982A pdb=" N TYR 8 46 " --> pdb=" O GLN 8 42 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA 8 48 " --> pdb=" O ALA 8 44 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET 8 49 " --> pdb=" O LYS 8 45 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY 8 50 " --> pdb=" O TYR 8 46 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU 8 51 " --> pdb=" O SER 8 47 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU 8 52 " --> pdb=" O ALA 8 48 " (cutoff:3.500A) Processing helix chain '8' and resid 89 through 99 Processing helix chain '8' and resid 103 through 112 Processing helix chain '8' and resid 119 through 129 Processing helix chain '8' and resid 131 through 142 Processing helix chain '8' and resid 147 through 156 Processing helix chain '8' and resid 159 through 163 Processing helix chain '8' and resid 194 through 209 Processing helix chain '8' and resid 221 through 239 removed outlier: 4.337A pdb=" N ALA 8 235 " --> pdb=" O GLN 8 231 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE 8 236 " --> pdb=" O ASN 8 232 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS 8 237 " --> pdb=" O LYS 8 233 " (cutoff:3.500A) Processing helix chain '8' and resid 243 through 256 Processing helix chain '8' and resid 274 through 278 Processing helix chain '8' and resid 281 through 307 Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 353 through 356 No H-bonds generated for 'chain '8' and resid 353 through 356' Processing helix chain '8' and resid 395 through 402 removed outlier: 3.817A pdb=" N GLU 8 401 " --> pdb=" O ASN 8 397 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU 8 402 " --> pdb=" O GLN 8 398 " (cutoff:3.500A) Processing helix chain '8' and resid 418 through 423 Processing helix chain '8' and resid 428 through 445 Processing helix chain '1' and resid 7 through 16 Processing helix chain '1' and resid 20 through 23 No H-bonds generated for 'chain '1' and resid 20 through 23' Processing helix chain '1' and resid 27 through 38 Processing helix chain '1' and resid 70 through 80 Processing helix chain '1' and resid 108 through 115 Processing helix chain '1' and resid 317 through 321 Processing helix chain '1' and resid 497 through 502 Processing helix chain '1' and resid 597 through 612 removed outlier: 3.692A pdb=" N TRP 1 604 " --> pdb=" O TYR 1 600 " (cutoff:3.500A) Processing helix chain '1' and resid 709 through 724 Processing helix chain '1' and resid 728 through 741 Processing helix chain '1' and resid 752 through 776 Processing helix chain '1' and resid 916 through 931 Processing helix chain '1' and resid 945 through 948 No H-bonds generated for 'chain '1' and resid 945 through 948' Processing helix chain '1' and resid 951 through 956 removed outlier: 3.894A pdb=" N LEU 1 956 " --> pdb=" O ASP 1 952 " (cutoff:3.500A) Processing helix chain '9' and resid 188 through 200 Processing helix chain '9' and resid 209 through 213 Processing helix chain '9' and resid 225 through 239 Processing helix chain '9' and resid 244 through 253 Processing helix chain '9' and resid 263 through 278 removed outlier: 3.661A pdb=" N ILE 9 273 " --> pdb=" O SER 9 269 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS 9 276 " --> pdb=" O LEU 9 272 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR 9 277 " --> pdb=" O ILE 9 273 " (cutoff:3.500A) Processing helix chain '9' and resid 304 through 313 Processing helix chain '9' and resid 345 through 350 Processing helix chain '9' and resid 354 through 370 Processing helix chain '4' and resid 196 through 200 removed outlier: 4.877A pdb=" N TRP 4 200 " --> pdb=" O LEU 4 196 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 196 through 200' Processing helix chain '4' and resid 206 through 210 removed outlier: 4.118A pdb=" N LYS 4 210 " --> pdb=" O LEU 4 206 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 206 through 210' Processing helix chain '4' and resid 213 through 221 Processing helix chain '4' and resid 224 through 229 removed outlier: 3.865A pdb=" N GLN 4 228 " --> pdb=" O PRO 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 278 removed outlier: 4.127A pdb=" N LYS 4 277 " --> pdb=" O PHE 4 273 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN 4 278 " --> pdb=" O SER 4 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 337 through 340 removed outlier: 6.113A pdb=" N HIS 1 346 " --> pdb=" O SER 1 340 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR 1 345 " --> pdb=" O THR 1 585 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR 1 585 " --> pdb=" O THR 1 345 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN 1 581 " --> pdb=" O PRO 1 349 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER 1 582 " --> pdb=" O LEU 1 409 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR 1 400 " --> pdb=" O PHE 1 545 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 1 404 " --> pdb=" O CYS 1 541 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 1 408 " --> pdb=" O ASP 1 537 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP 1 537 " --> pdb=" O VAL 1 408 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY 1 548 " --> pdb=" O ASP 1 565 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 386 through 390 removed outlier: 4.018A pdb=" N ILE 1 424 " --> pdb=" O TYR 1 512 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY 1 511 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 1 518 " --> pdb=" O CYS 1 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '5' and resid 213 through 219 removed outlier: 5.073A pdb=" N LEU 5 213 " --> pdb=" O PHE 1 104 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE 1 98 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '8' and resid 31 through 34 removed outlier: 3.785A pdb=" N LYS 8 32 " --> pdb=" O GLN 8 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 126 through 135 removed outlier: 4.681A pdb=" N MET 4 127 " --> pdb=" O LEU 4 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 4 146 " --> pdb=" O MET 4 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY 4 131 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 4 142 " --> pdb=" O GLY 4 131 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL 4 142 " --> pdb=" O ARG 4 170 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG 4 170 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL 4 144 " --> pdb=" O SER 4 168 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER 4 168 " --> pdb=" O VAL 4 144 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU 4 146 " --> pdb=" O PHE 4 166 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE 4 166 " --> pdb=" O LEU 4 146 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS 4 162 " --> pdb=" O ASP 4 150 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR 4 181 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE 4 289 " --> pdb=" O VAL 4 188 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ARG 4 286 " --> pdb=" O GLN 4 322 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP 4 292 " --> pdb=" O TYR 4 316 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU 4 294 " --> pdb=" O GLY 4 314 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY 4 314 " --> pdb=" O GLU 4 294 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE 4 330 " --> pdb=" O TYR 4 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN 4 326 " --> pdb=" O ASP 4 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 4 327 " --> pdb=" O LEU 4 344 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN 4 340 " --> pdb=" O TYR 4 331 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2082 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: 2.27 Time building geometry restraints manager: 1.60 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: 4547 1.34 - 1.46: 3291 1.46 - 1.58: 6804 1.58 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 14745 Sorted by residual: bond pdb=" CA PHE 4 339 " pdb=" CB PHE 4 339 " ideal model delta sigma weight residual 1.527 1.560 -0.033 2.48e-02 1.63e+03 1.72e+00 bond pdb=" CG1 ILE 1 539 " pdb=" CD1 ILE 1 539 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" C LEU 9 205 " pdb=" N PRO 9 206 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.30e+00 bond pdb=" CG GLU 8 249 " pdb=" CD GLU 8 249 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CG1 ILE 8 203 " pdb=" CD1 ILE 8 203 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.50e-01 ... (remaining 14740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19710 1.91 - 3.82: 249 3.82 - 5.73: 40 5.73 - 7.64: 4 7.64 - 9.55: 1 Bond angle restraints: 20004 Sorted by residual: angle pdb=" N VAL 5 48 " pdb=" CA VAL 5 48 " pdb=" C VAL 5 48 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" C LEU 8 248 " pdb=" N GLU 8 249 " pdb=" CA GLU 8 249 " ideal model delta sigma weight residual 121.14 115.08 6.06 1.75e+00 3.27e-01 1.20e+01 angle pdb=" N GLU 8 249 " pdb=" CA GLU 8 249 " pdb=" CB GLU 8 249 " ideal model delta sigma weight residual 110.40 115.68 -5.28 1.63e+00 3.76e-01 1.05e+01 angle pdb=" C LYS 5 202 " pdb=" N ILE 5 203 " pdb=" CA ILE 5 203 " ideal model delta sigma weight residual 122.35 118.67 3.68 1.18e+00 7.18e-01 9.71e+00 angle pdb=" CA GLU 4 192 " pdb=" CB GLU 4 192 " pdb=" CG GLU 4 192 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.09e+00 ... (remaining 19999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7859 17.69 - 35.39: 746 35.39 - 53.08: 132 53.08 - 70.78: 23 70.78 - 88.47: 9 Dihedral angle restraints: 8769 sinusoidal: 3293 harmonic: 5476 Sorted by residual: dihedral pdb=" CA PHE 8 423 " pdb=" C PHE 8 423 " pdb=" N PRO 8 424 " pdb=" CA PRO 8 424 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CB CYS 5 656 " pdb=" SG CYS 5 656 " pdb=" SG CYS 4 357 " pdb=" CB CYS 4 357 " ideal model delta sinusoidal sigma weight residual -86.00 -127.09 41.09 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 8766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1695 0.043 - 0.086: 517 0.086 - 0.130: 110 0.130 - 0.173: 8 0.173 - 0.216: 1 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CA GLU 8 249 " pdb=" N GLU 8 249 " pdb=" C GLU 8 249 " pdb=" CB GLU 8 249 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA TYR 5 360 " pdb=" N TYR 5 360 " pdb=" C TYR 5 360 " pdb=" CB TYR 5 360 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ILE 5 216 " pdb=" N ILE 5 216 " pdb=" C ILE 5 216 " pdb=" CB ILE 5 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 2328 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 8 423 " 0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO 8 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO 8 424 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO 8 424 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 8 89 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO 8 90 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO 8 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 8 90 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET 8 245 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" C MET 8 245 " 0.035 2.00e-02 2.50e+03 pdb=" O MET 8 245 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN 8 246 " -0.012 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 132 2.64 - 3.21: 13454 3.21 - 3.77: 20994 3.77 - 4.34: 28216 4.34 - 4.90: 47880 Nonbonded interactions: 110676 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 652 " pdb=" OG SER 4 358 " model vdw 2.079 3.120 nonbonded pdb=" OG1 THR 4 148 " pdb=" OG SER 4 164 " model vdw 2.158 3.040 nonbonded pdb=" OD1 ASP 4 216 " pdb=" OH TYR 4 317 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP 1 9 " pdb=" OH TYR 1 34 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR 1 529 " pdb=" O GLY 1 560 " model vdw 2.264 3.040 ... (remaining 110671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.520 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14746 Z= 0.169 Angle : 0.583 9.554 20006 Z= 0.322 Chirality : 0.042 0.216 2331 Planarity : 0.004 0.088 2500 Dihedral : 14.317 88.469 5190 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1787 helix: 1.55 (0.17), residues: 1010 sheet: -1.45 (0.46), residues: 124 loop : -1.88 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 609 TYR 0.014 0.001 TYR 4 182 PHE 0.027 0.002 PHE 8 423 TRP 0.009 0.001 TRP 9 210 HIS 0.009 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00399 (14745) covalent geometry : angle 0.58212 (20004) SS BOND : bond 0.00425 ( 1) SS BOND : angle 2.38551 ( 2) hydrogen bonds : bond 0.05587 ( 696) hydrogen bonds : angle 4.27792 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: 9 245 ASP cc_start: 0.8133 (m-30) cc_final: 0.7819 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0972 time to fit residues: 13.7273 Evaluate side-chains 71 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 715 ASN 9 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.066747 restraints weight = 37076.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068524 restraints weight = 21322.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069698 restraints weight = 14801.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.070419 restraints weight = 11588.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070993 restraints weight = 9870.437| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14746 Z= 0.111 Angle : 0.504 8.436 20006 Z= 0.264 Chirality : 0.039 0.138 2331 Planarity : 0.004 0.083 2500 Dihedral : 4.376 30.221 1958 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1787 helix: 1.79 (0.17), residues: 1013 sheet: -1.39 (0.46), residues: 125 loop : -1.74 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 609 TYR 0.009 0.001 TYR 5 333 PHE 0.025 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 5 272 Details of bonding type rmsd covalent geometry : bond 0.00253 (14745) covalent geometry : angle 0.50297 (20004) SS BOND : bond 0.00150 ( 1) SS BOND : angle 2.67302 ( 2) hydrogen bonds : bond 0.03828 ( 696) hydrogen bonds : angle 3.92483 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: 8 350 ASP cc_start: 0.7967 (t0) cc_final: 0.7662 (t0) REVERT: 9 245 ASP cc_start: 0.8271 (m-30) cc_final: 0.7880 (m-30) outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.0973 time to fit residues: 12.8307 Evaluate side-chains 75 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 0.0010 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.069620 restraints weight = 37699.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071276 restraints weight = 22307.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072418 restraints weight = 15880.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073192 restraints weight = 12551.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073570 restraints weight = 10642.851| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14746 Z= 0.107 Angle : 0.481 8.287 20006 Z= 0.252 Chirality : 0.039 0.137 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.202 30.182 1958 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.33 % Allowed : 8.17 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1787 helix: 1.93 (0.17), residues: 1012 sheet: -1.26 (0.47), residues: 124 loop : -1.68 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 609 TYR 0.009 0.001 TYR 5 333 PHE 0.023 0.001 PHE 8 423 TRP 0.008 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00248 (14745) covalent geometry : angle 0.48046 (20004) SS BOND : bond 0.00166 ( 1) SS BOND : angle 2.58622 ( 2) hydrogen bonds : bond 0.03621 ( 696) hydrogen bonds : angle 3.78218 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.370 Fit side-chains REVERT: 5 76 TYR cc_start: 0.8289 (t80) cc_final: 0.8068 (t80) REVERT: 9 245 ASP cc_start: 0.8211 (m-30) cc_final: 0.7831 (m-30) outliers start: 5 outliers final: 1 residues processed: 82 average time/residue: 0.0879 time to fit residues: 12.2756 Evaluate side-chains 75 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 723 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 220 ASN 1 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069825 restraints weight = 37261.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071423 restraints weight = 22752.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072386 restraints weight = 16360.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.073214 restraints weight = 13254.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073641 restraints weight = 11210.936| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14746 Z= 0.101 Angle : 0.468 8.116 20006 Z= 0.245 Chirality : 0.038 0.136 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.090 30.354 1958 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.79 % Allowed : 10.02 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1787 helix: 2.02 (0.17), residues: 1012 sheet: -1.25 (0.46), residues: 134 loop : -1.63 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.009 0.001 TYR 9 234 PHE 0.021 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00231 (14745) covalent geometry : angle 0.46764 (20004) SS BOND : bond 0.00161 ( 1) SS BOND : angle 2.40827 ( 2) hydrogen bonds : bond 0.03437 ( 696) hydrogen bonds : angle 3.69575 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.525 Fit side-chains REVERT: 5 76 TYR cc_start: 0.8250 (t80) cc_final: 0.8044 (t80) REVERT: 8 246 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8003 (mp10) outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 0.0925 time to fit residues: 13.7778 Evaluate side-chains 80 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 431 LEU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068890 restraints weight = 37253.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070486 restraints weight = 22754.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071475 restraints weight = 16352.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072224 restraints weight = 13199.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072720 restraints weight = 11286.013| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14746 Z= 0.126 Angle : 0.482 8.662 20006 Z= 0.252 Chirality : 0.039 0.145 2331 Planarity : 0.004 0.083 2500 Dihedral : 4.130 30.333 1958 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.73 % Allowed : 11.14 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1787 helix: 2.02 (0.17), residues: 1011 sheet: -1.22 (0.46), residues: 134 loop : -1.60 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 609 TYR 0.012 0.001 TYR 9 234 PHE 0.019 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00303 (14745) covalent geometry : angle 0.48186 (20004) SS BOND : bond 0.00313 ( 1) SS BOND : angle 2.34182 ( 2) hydrogen bonds : bond 0.03775 ( 696) hydrogen bonds : angle 3.73886 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.574 Fit side-chains REVERT: 5 76 TYR cc_start: 0.8342 (t80) cc_final: 0.8113 (t80) REVERT: 5 273 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7187 (t80) REVERT: 5 744 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8551 (mpp) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 0.0894 time to fit residues: 13.1158 Evaluate side-chains 83 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 431 LEU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 69 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067367 restraints weight = 37405.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068953 restraints weight = 22959.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069990 restraints weight = 16551.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070497 restraints weight = 13261.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071137 restraints weight = 11655.569| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14746 Z= 0.169 Angle : 0.523 9.632 20006 Z= 0.272 Chirality : 0.040 0.159 2331 Planarity : 0.004 0.083 2500 Dihedral : 4.316 30.020 1958 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.86 % Allowed : 11.80 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1787 helix: 1.93 (0.17), residues: 1011 sheet: -1.27 (0.45), residues: 133 loop : -1.60 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 5 609 TYR 0.014 0.001 TYR 9 234 PHE 0.017 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 1 558 Details of bonding type rmsd covalent geometry : bond 0.00414 (14745) covalent geometry : angle 0.52233 (20004) SS BOND : bond 0.00506 ( 1) SS BOND : angle 2.48635 ( 2) hydrogen bonds : bond 0.04384 ( 696) hydrogen bonds : angle 3.88367 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.621 Fit side-chains REVERT: 5 76 TYR cc_start: 0.8399 (t80) cc_final: 0.8122 (t80) REVERT: 5 273 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.6983 (t80) REVERT: 5 744 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8596 (mpp) REVERT: 8 246 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7996 (mp10) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.0881 time to fit residues: 12.9643 Evaluate side-chains 83 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 431 LEU Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 8 residue 205 MET Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 139 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069822 restraints weight = 37044.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071409 restraints weight = 22633.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072475 restraints weight = 16331.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073236 restraints weight = 13075.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073737 restraints weight = 11136.035| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14746 Z= 0.096 Angle : 0.459 8.477 20006 Z= 0.241 Chirality : 0.038 0.144 2331 Planarity : 0.004 0.081 2500 Dihedral : 4.065 30.357 1958 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.73 % Allowed : 12.20 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1787 helix: 2.07 (0.17), residues: 1011 sheet: -1.12 (0.46), residues: 134 loop : -1.54 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.026 0.001 TYR 9 234 PHE 0.019 0.001 PHE 8 423 TRP 0.009 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00216 (14745) covalent geometry : angle 0.45849 (20004) SS BOND : bond 0.00124 ( 1) SS BOND : angle 2.22311 ( 2) hydrogen bonds : bond 0.03345 ( 696) hydrogen bonds : angle 3.68039 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.537 Fit side-chains REVERT: 5 76 TYR cc_start: 0.8231 (t80) cc_final: 0.8001 (t80) REVERT: 5 273 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7074 (t80) REVERT: 5 744 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: 8 246 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8054 (mp10) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.0977 time to fit residues: 13.4359 Evaluate side-chains 81 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 145 ILE Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 377 THR Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 36 optimal weight: 1.9990 chunk 172 optimal weight: 0.0170 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 23 optimal weight: 3.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.069872 restraints weight = 36876.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071462 restraints weight = 22433.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072445 restraints weight = 16174.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073220 restraints weight = 13043.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073491 restraints weight = 11147.422| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14746 Z= 0.097 Angle : 0.454 8.166 20006 Z= 0.238 Chirality : 0.038 0.138 2331 Planarity : 0.004 0.081 2500 Dihedral : 3.969 30.581 1958 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.86 % Allowed : 12.33 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1787 helix: 2.12 (0.17), residues: 1011 sheet: -1.09 (0.46), residues: 134 loop : -1.52 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.025 0.001 TYR 9 234 PHE 0.019 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00220 (14745) covalent geometry : angle 0.45404 (20004) SS BOND : bond 0.00162 ( 1) SS BOND : angle 2.08074 ( 2) hydrogen bonds : bond 0.03317 ( 696) hydrogen bonds : angle 3.62451 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: 5 76 TYR cc_start: 0.8223 (t80) cc_final: 0.8005 (t80) REVERT: 5 273 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7015 (t80) REVERT: 5 744 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8607 (mpp) REVERT: 8 246 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: 8 257 PHE cc_start: 0.7169 (t80) cc_final: 0.6908 (t80) REVERT: 1 687 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: 4 221 ILE cc_start: 0.8810 (tp) cc_final: 0.8549 (tp) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0891 time to fit residues: 13.3438 Evaluate side-chains 89 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 84 TYR Chi-restraints excluded: chain 5 residue 145 ILE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 377 THR Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 8 residue 431 GLN Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.068989 restraints weight = 37524.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.070659 restraints weight = 22361.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.071783 restraints weight = 15939.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072571 restraints weight = 12619.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073091 restraints weight = 10689.581| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14746 Z= 0.125 Angle : 0.487 11.030 20006 Z= 0.253 Chirality : 0.039 0.201 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.046 30.719 1958 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.86 % Allowed : 12.59 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1787 helix: 2.10 (0.17), residues: 1011 sheet: -1.15 (0.46), residues: 133 loop : -1.51 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.024 0.001 TYR 9 234 PHE 0.017 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00299 (14745) covalent geometry : angle 0.48643 (20004) SS BOND : bond 0.00310 ( 1) SS BOND : angle 2.14456 ( 2) hydrogen bonds : bond 0.03706 ( 696) hydrogen bonds : angle 3.70138 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: 5 76 TYR cc_start: 0.8348 (t80) cc_final: 0.8093 (t80) REVERT: 5 273 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7031 (t80) REVERT: 5 744 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8671 (mpp) REVERT: 8 246 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: 8 257 PHE cc_start: 0.7316 (t80) cc_final: 0.7017 (t80) REVERT: 1 687 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: 1 717 MET cc_start: 0.8402 (mtp) cc_final: 0.8125 (mtt) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.0870 time to fit residues: 12.7584 Evaluate side-chains 86 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 8 residue 431 GLN Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 594 VAL Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 32 optimal weight: 0.0270 chunk 153 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.069111 restraints weight = 37223.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.070759 restraints weight = 22318.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.071893 restraints weight = 15980.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072668 restraints weight = 12700.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.073193 restraints weight = 10785.731| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14746 Z= 0.118 Angle : 0.474 8.721 20006 Z= 0.248 Chirality : 0.039 0.183 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.046 30.606 1958 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.92 % Allowed : 12.66 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1787 helix: 2.10 (0.17), residues: 1011 sheet: -1.08 (0.46), residues: 134 loop : -1.52 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.024 0.001 TYR 9 234 PHE 0.018 0.001 PHE 8 423 TRP 0.008 0.001 TRP 9 210 HIS 0.004 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00280 (14745) covalent geometry : angle 0.47325 (20004) SS BOND : bond 0.00265 ( 1) SS BOND : angle 2.15737 ( 2) hydrogen bonds : bond 0.03614 ( 696) hydrogen bonds : angle 3.69091 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: 5 76 TYR cc_start: 0.8338 (t80) cc_final: 0.8079 (t80) REVERT: 5 273 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7039 (t80) REVERT: 5 744 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (mpp) REVERT: 8 246 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: 8 257 PHE cc_start: 0.7324 (t80) cc_final: 0.6984 (t80) REVERT: 1 687 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6699 (m-10) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.0945 time to fit residues: 13.8311 Evaluate side-chains 88 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 145 ILE Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 273 TYR Chi-restraints excluded: chain 5 residue 377 THR Chi-restraints excluded: chain 5 residue 723 LEU Chi-restraints excluded: chain 5 residue 744 MET Chi-restraints excluded: chain 8 residue 246 GLN Chi-restraints excluded: chain 8 residue 431 GLN Chi-restraints excluded: chain 1 residue 383 VAL Chi-restraints excluded: chain 1 residue 594 VAL Chi-restraints excluded: chain 1 residue 687 PHE Chi-restraints excluded: chain 9 residue 235 ILE Chi-restraints excluded: chain 4 residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 102 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 0.0470 chunk 133 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070428 restraints weight = 37180.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072023 restraints weight = 22517.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073112 restraints weight = 16151.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073788 restraints weight = 12843.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074321 restraints weight = 11041.960| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14746 Z= 0.092 Angle : 0.447 8.452 20006 Z= 0.235 Chirality : 0.038 0.178 2331 Planarity : 0.003 0.081 2500 Dihedral : 3.887 30.736 1958 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.86 % Allowed : 12.79 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1787 helix: 2.18 (0.17), residues: 1013 sheet: -1.05 (0.46), residues: 134 loop : -1.46 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 609 TYR 0.020 0.001 TYR 9 234 PHE 0.019 0.001 PHE 8 423 TRP 0.007 0.001 TRP 9 210 HIS 0.004 0.001 HIS 4 333 Details of bonding type rmsd covalent geometry : bond 0.00207 (14745) covalent geometry : angle 0.44654 (20004) SS BOND : bond 0.00126 ( 1) SS BOND : angle 1.94877 ( 2) hydrogen bonds : bond 0.03085 ( 696) hydrogen bonds : angle 3.57527 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.04 seconds wall clock time: 33 minutes 19.99 seconds (1999.99 seconds total)