Starting phenix.real_space_refine on Thu Sep 18 06:45:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0n_10356/09_2025/6t0n_10356.map" } resolution = 2.54 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8940 2.51 5 N 2496 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14598 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5741 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 2 Chain: "B" Number of atoms: 5972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5972 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 1 Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2016 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 292 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 3.99, per 1000 atoms: 0.27 Number of scatterers: 14598 At special positions: 0 Unit cell: (106.464, 119.467, 118.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 29 15.00 Mg 2 11.99 O 3039 8.00 N 2496 7.00 C 8940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.25 Conformation dependent library (CDL) restraints added in 656.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 18 sheets defined 52.4% alpha, 14.0% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.645A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.590A pdb=" N TYR A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.783A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.928A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.648A pdb=" N SER A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.514A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.528A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.982A pdb=" N LEU A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.238A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.695A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.504A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.653A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.504A pdb=" N ASN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.723A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.805A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.732A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.525A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.515A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.626A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.519A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.529A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN B 679 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.070A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.718A pdb=" N THR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.566A pdb=" N GLU B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 757 Processing helix chain 'C' and resid 1 through 13 removed outlier: 3.516A pdb=" N LYS C 5 " --> pdb=" O MET C 1 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.881A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.842A pdb=" N ARG C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 removed outlier: 3.715A pdb=" N VAL C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.700A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 123 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.700A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.855A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.480A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.254A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.364A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.342A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.352A pdb=" N GLY A 626 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 188 Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.720A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB6, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB7, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.457A pdb=" N THR B 667 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 81 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.460A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 146 700 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3658 1.33 - 1.45: 2874 1.45 - 1.57: 7926 1.57 - 1.69: 56 1.69 - 1.81: 160 Bond restraints: 14674 Sorted by residual: bond pdb=" N ARG B 723 " pdb=" CA ARG B 723 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.11e+00 bond pdb=" CB THR B 141 " pdb=" CG2 THR B 141 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB MET A 570 " pdb=" CG MET A 570 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" C GLU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.19e+00 bond pdb=" CB ARG A 561 " pdb=" CG ARG A 561 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 ... (remaining 14669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 19107 1.53 - 3.06: 699 3.06 - 4.58: 95 4.58 - 6.11: 15 6.11 - 7.64: 5 Bond angle restraints: 19921 Sorted by residual: angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 111.62 108.35 3.27 7.90e-01 1.60e+00 1.72e+01 angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 113.97 109.81 4.16 1.28e+00 6.10e-01 1.06e+01 angle pdb=" C ALA B 291 " pdb=" N LYS B 292 " pdb=" CA LYS B 292 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 angle pdb=" C2' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " ideal model delta sigma weight residual 112.00 116.60 -4.60 1.50e+00 4.44e-01 9.40e+00 angle pdb=" C3' A V 7 " pdb=" C2' A V 7 " pdb=" O2' A V 7 " ideal model delta sigma weight residual 114.60 118.88 -4.28 1.50e+00 4.44e-01 8.15e+00 ... (remaining 19916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8104 17.98 - 35.97: 581 35.97 - 53.95: 190 53.95 - 71.93: 74 71.93 - 89.92: 24 Dihedral angle restraints: 8973 sinusoidal: 4005 harmonic: 4968 Sorted by residual: dihedral pdb=" CA THR C 35 " pdb=" C THR C 35 " pdb=" N SER C 36 " pdb=" CA SER C 36 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA VAL A 512 " pdb=" C VAL A 512 " pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TYR A 535 " pdb=" C TYR A 535 " pdb=" N CYS A 536 " pdb=" CA CYS A 536 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 8970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1509 0.044 - 0.087: 541 0.087 - 0.131: 127 0.131 - 0.174: 15 0.174 - 0.218: 4 Chirality restraints: 2196 Sorted by residual: chirality pdb=" C1' U R 9 " pdb=" O4' U R 9 " pdb=" C2' U R 9 " pdb=" N1 U R 9 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 2193 not shown) Planarity restraints: 2462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U R 9 " -0.036 2.00e-02 2.50e+03 1.79e-02 7.24e+00 pdb=" N1 U R 9 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U R 9 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U R 9 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U R 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U R 9 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U R 9 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U R 9 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U R 9 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.87e+00 pdb=" N PRO A 620 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.031 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 A V 7 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.017 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.010 2.00e-02 2.50e+03 ... (remaining 2459 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 379 2.66 - 3.22: 12487 3.22 - 3.78: 25091 3.78 - 4.34: 35812 4.34 - 4.90: 54945 Nonbonded interactions: 128714 Sorted by model distance: nonbonded pdb=" OP2 A V 4 " pdb="MG MG V 101 " model vdw 2.105 2.170 nonbonded pdb="MG MG V 101 " pdb=" O HOH V 201 " model vdw 2.146 2.170 nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 801 " model vdw 2.161 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.274 3.040 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.297 3.040 ... (remaining 128709 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.100 Find NCS groups from input model: 0.100 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.005 0.062 14674 Z= 0.242 Angle : 0.688 7.641 19921 Z= 0.397 Chirality : 0.046 0.218 2196 Planarity : 0.006 0.061 2462 Dihedral : 15.615 89.915 5759 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.45 % Rotamer: Outliers : 4.90 % Allowed : 6.75 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: -2.43 (0.16), residues: 1691 helix: -1.63 (0.14), residues: 792 sheet: -1.24 (0.34), residues: 188 loop : -1.50 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 672 TYR 0.016 0.002 TYR B 380 PHE 0.021 0.002 PHE A 211 TRP 0.023 0.003 TRP B 438 HIS 0.010 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00545 (14674) covalent geometry : angle 0.68762 (19921) hydrogen bonds : bond 0.15343 ( 705) hydrogen bonds : angle 6.00502 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 272 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4684 (OUTLIER) cc_final: 0.4179 (pp20) REVERT: A 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 356 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8136 (tttt) REVERT: A 372 GLU cc_start: 0.7707 (tt0) cc_final: 0.7481 (tt0) REVERT: A 455 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7253 (mpm) REVERT: A 616 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 700 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.9005 (p) REVERT: A 713 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7287 (mtp) REVERT: B 108 GLN cc_start: 0.7894 (tp40) cc_final: 0.7470 (tm-30) REVERT: B 135 ARG cc_start: 0.8144 (ptp-170) cc_final: 0.7902 (mtp85) REVERT: B 429 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7306 (mtm180) REVERT: B 534 MET cc_start: 0.9089 (mtp) cc_final: 0.8463 (mtp) REVERT: B 563 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (ttp80) REVERT: B 577 LYS cc_start: 0.8741 (tptt) cc_final: 0.8378 (tppt) REVERT: B 635 MET cc_start: 0.7380 (mtm) cc_final: 0.7042 (mtm) REVERT: B 679 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7383 (mm110) REVERT: B 680 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6996 (ptp90) REVERT: C 185 ILE cc_start: 0.8527 (mt) cc_final: 0.8230 (mm) outliers start: 74 outliers final: 21 residues processed: 325 average time/residue: 0.8788 time to fit residues: 306.4754 Evaluate side-chains 237 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 153 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 369 GLN A 387 GLN A 425 ASN A 490 GLN A 612 ASN B 115 GLN B 184 HIS B 312 ASN B 413 ASN B 694 GLN C 236 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106059 restraints weight = 14889.840| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.42 r_work: 0.2774 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14674 Z= 0.123 Angle : 0.487 8.048 19921 Z= 0.266 Chirality : 0.039 0.208 2196 Planarity : 0.004 0.051 2462 Dihedral : 11.683 75.166 2356 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.31 % Allowed : 12.32 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: -0.51 (0.19), residues: 1691 helix: 0.47 (0.17), residues: 800 sheet: -0.95 (0.34), residues: 193 loop : -1.01 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 608 TYR 0.017 0.001 TYR B 555 PHE 0.012 0.001 PHE B 551 TRP 0.014 0.001 TRP B 438 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00263 (14674) covalent geometry : angle 0.48712 (19921) hydrogen bonds : bond 0.04395 ( 705) hydrogen bonds : angle 4.31235 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4274 (OUTLIER) cc_final: 0.3581 (pp20) REVERT: A 356 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8277 (tttt) REVERT: A 594 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7797 (tp30) REVERT: A 711 LEU cc_start: 0.8688 (mp) cc_final: 0.8465 (mm) REVERT: B 108 GLN cc_start: 0.8207 (tp40) cc_final: 0.7675 (tm-30) REVERT: B 290 MET cc_start: 0.7804 (mtp) cc_final: 0.7467 (mmm) REVERT: B 481 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.7752 (mptt) REVERT: B 563 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8531 (mtp85) REVERT: B 635 MET cc_start: 0.7555 (mtm) cc_final: 0.7048 (mtm) REVERT: B 679 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7346 (mm110) REVERT: B 680 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6921 (ptp90) REVERT: C 28 MET cc_start: 0.9072 (ttp) cc_final: 0.8791 (ttp) REVERT: C 185 ILE cc_start: 0.7887 (mt) cc_final: 0.7531 (mm) REVERT: C 210 GLU cc_start: 0.8044 (tt0) cc_final: 0.7783 (tt0) REVERT: C 241 GLU cc_start: 0.8657 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 243 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7287 (tm130) outliers start: 50 outliers final: 15 residues processed: 236 average time/residue: 0.8603 time to fit residues: 219.0690 Evaluate side-chains 221 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 425 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.098111 restraints weight = 14549.750| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.41 r_work: 0.2706 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14674 Z= 0.235 Angle : 0.575 9.002 19921 Z= 0.308 Chirality : 0.044 0.224 2196 Planarity : 0.005 0.049 2462 Dihedral : 11.625 74.042 2322 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.51 % Allowed : 12.58 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.01 (0.19), residues: 1691 helix: 0.97 (0.18), residues: 803 sheet: -0.77 (0.35), residues: 193 loop : -0.83 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 608 TYR 0.015 0.002 TYR B 555 PHE 0.019 0.002 PHE A 211 TRP 0.017 0.002 TRP B 438 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00541 (14674) covalent geometry : angle 0.57473 (19921) hydrogen bonds : bond 0.05299 ( 705) hydrogen bonds : angle 4.32006 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5634 (mtp) cc_final: 0.5289 (mtp) REVERT: A 26 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.3626 (pp20) REVERT: A 351 LYS cc_start: 0.8789 (mttp) cc_final: 0.8541 (mttm) REVERT: A 356 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8328 (tttt) REVERT: A 544 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7110 (mp0) REVERT: A 616 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8811 (pp) REVERT: A 713 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: B 108 GLN cc_start: 0.8241 (tp40) cc_final: 0.7723 (tm-30) REVERT: B 277 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: B 290 MET cc_start: 0.7781 (mtp) cc_final: 0.7449 (mmm) REVERT: B 350 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8412 (mtt-85) REVERT: B 563 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8508 (mtp85) REVERT: B 635 MET cc_start: 0.7716 (mtm) cc_final: 0.7495 (mtm) REVERT: B 679 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7485 (mm110) REVERT: B 680 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7147 (ptp90) REVERT: C 156 SER cc_start: 0.7100 (m) cc_final: 0.6546 (p) REVERT: C 165 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: C 194 LYS cc_start: 0.7621 (tttt) cc_final: 0.7326 (ttmm) REVERT: C 210 GLU cc_start: 0.8124 (tt0) cc_final: 0.7865 (tt0) REVERT: C 241 GLU cc_start: 0.8717 (tt0) cc_final: 0.8508 (tm-30) REVERT: C 243 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7325 (tm130) outliers start: 53 outliers final: 22 residues processed: 232 average time/residue: 0.8790 time to fit residues: 219.3440 Evaluate side-chains 227 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 127 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 129 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 425 ASN A 490 GLN B 115 GLN B 413 ASN B 454 HIS B 694 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106457 restraints weight = 14961.207| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.32 r_work: 0.2801 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14674 Z= 0.097 Angle : 0.455 7.299 19921 Z= 0.245 Chirality : 0.038 0.204 2196 Planarity : 0.003 0.044 2462 Dihedral : 11.057 75.150 2318 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.52 % Allowed : 14.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.54 (0.20), residues: 1691 helix: 1.50 (0.18), residues: 804 sheet: -0.52 (0.36), residues: 184 loop : -0.69 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 608 TYR 0.015 0.001 TYR B 555 PHE 0.010 0.001 PHE A 211 TRP 0.011 0.001 TRP B 438 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00199 (14674) covalent geometry : angle 0.45469 (19921) hydrogen bonds : bond 0.03706 ( 705) hydrogen bonds : angle 4.05373 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5719 (mtp) cc_final: 0.5384 (mtp) REVERT: A 26 GLU cc_start: 0.4445 (OUTLIER) cc_final: 0.3679 (pp20) REVERT: A 356 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8263 (tttt) REVERT: A 711 LEU cc_start: 0.8704 (mp) cc_final: 0.8490 (mm) REVERT: B 1 MET cc_start: 0.8419 (tmm) cc_final: 0.8192 (tmm) REVERT: B 108 GLN cc_start: 0.8221 (tp40) cc_final: 0.7751 (tp40) REVERT: B 135 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7955 (ptm-80) REVERT: B 199 MET cc_start: 0.0872 (OUTLIER) cc_final: 0.0617 (tpt) REVERT: B 290 MET cc_start: 0.7761 (mtp) cc_final: 0.7451 (mmm) REVERT: B 480 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8505 (mtpm) REVERT: B 481 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.7722 (mptt) REVERT: B 635 MET cc_start: 0.7561 (mtm) cc_final: 0.7171 (mtm) REVERT: B 674 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7937 (pp) REVERT: B 679 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7361 (mm110) REVERT: B 680 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6918 (ptp90) REVERT: C 51 MET cc_start: 0.9315 (mmm) cc_final: 0.9076 (mmm) REVERT: C 156 SER cc_start: 0.7171 (m) cc_final: 0.6699 (p) REVERT: C 165 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: C 210 GLU cc_start: 0.8064 (tt0) cc_final: 0.7815 (tt0) REVERT: C 241 GLU cc_start: 0.8673 (tt0) cc_final: 0.8444 (tm-30) REVERT: C 243 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7263 (tm130) outliers start: 38 outliers final: 12 residues processed: 227 average time/residue: 0.8752 time to fit residues: 214.2335 Evaluate side-chains 214 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 160 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 119 optimal weight: 0.0050 chunk 64 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS C 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096862 restraints weight = 14464.743| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.43 r_work: 0.2683 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14674 Z= 0.225 Angle : 0.555 8.801 19921 Z= 0.296 Chirality : 0.043 0.223 2196 Planarity : 0.004 0.047 2462 Dihedral : 11.235 74.202 2308 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.05 % Allowed : 14.17 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.53 (0.20), residues: 1691 helix: 1.43 (0.18), residues: 804 sheet: -0.44 (0.36), residues: 186 loop : -0.65 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 608 TYR 0.014 0.002 TYR B 555 PHE 0.018 0.002 PHE A 211 TRP 0.016 0.002 TRP B 438 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00522 (14674) covalent geometry : angle 0.55523 (19921) hydrogen bonds : bond 0.04945 ( 705) hydrogen bonds : angle 4.19908 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5805 (mtp) cc_final: 0.5574 (mtp) REVERT: A 26 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.3744 (pp20) REVERT: A 356 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8347 (tttt) REVERT: A 616 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8717 (pp) REVERT: A 711 LEU cc_start: 0.8781 (mp) cc_final: 0.8566 (mm) REVERT: A 713 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7824 (mtp) REVERT: B 108 GLN cc_start: 0.8345 (tp40) cc_final: 0.7862 (tm-30) REVERT: B 277 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 290 MET cc_start: 0.7901 (mtp) cc_final: 0.7501 (mmm) REVERT: B 635 MET cc_start: 0.7735 (mtm) cc_final: 0.7519 (mtm) REVERT: B 674 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8223 (pp) REVERT: B 679 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7506 (mm110) REVERT: B 680 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7148 (ptp90) REVERT: B 706 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7969 (ttm170) REVERT: C 51 MET cc_start: 0.9378 (mmm) cc_final: 0.9106 (mmm) REVERT: C 156 SER cc_start: 0.7154 (m) cc_final: 0.6662 (p) REVERT: C 160 GLN cc_start: 0.8018 (tt0) cc_final: 0.7797 (tt0) REVERT: C 165 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: C 194 LYS cc_start: 0.7669 (tttt) cc_final: 0.7355 (ttmm) REVERT: C 241 GLU cc_start: 0.8835 (tt0) cc_final: 0.8608 (tm-30) REVERT: C 243 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7408 (tm130) outliers start: 46 outliers final: 18 residues processed: 229 average time/residue: 0.8175 time to fit residues: 201.8261 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 7 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.0010 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 454 HIS B 694 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103246 restraints weight = 14436.662| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.55 r_work: 0.2768 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14674 Z= 0.102 Angle : 0.459 8.248 19921 Z= 0.245 Chirality : 0.038 0.203 2196 Planarity : 0.003 0.045 2462 Dihedral : 10.845 75.036 2308 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 14.70 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.84 (0.20), residues: 1691 helix: 1.74 (0.18), residues: 804 sheet: -0.29 (0.36), residues: 184 loop : -0.56 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 608 TYR 0.015 0.001 TYR B 555 PHE 0.012 0.001 PHE B 357 TRP 0.012 0.001 TRP B 438 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00214 (14674) covalent geometry : angle 0.45942 (19921) hydrogen bonds : bond 0.03688 ( 705) hydrogen bonds : angle 4.00643 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.3763 (pp20) REVERT: A 356 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8298 (tttt) REVERT: A 372 GLU cc_start: 0.8628 (tt0) cc_final: 0.8343 (tt0) REVERT: A 608 ARG cc_start: 0.8278 (mmt90) cc_final: 0.7924 (mmt-90) REVERT: A 711 LEU cc_start: 0.8699 (mp) cc_final: 0.8493 (mm) REVERT: B 1 MET cc_start: 0.8473 (tmm) cc_final: 0.8258 (tmm) REVERT: B 108 GLN cc_start: 0.8278 (tp40) cc_final: 0.7788 (tp40) REVERT: B 135 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8017 (ptm-80) REVERT: B 148 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: B 277 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: B 290 MET cc_start: 0.7806 (mtp) cc_final: 0.7442 (mmm) REVERT: B 480 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8558 (mtpm) REVERT: B 481 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7793 (mptt) REVERT: B 577 LYS cc_start: 0.9011 (tptt) cc_final: 0.8521 (ttmp) REVERT: B 635 MET cc_start: 0.7590 (mtm) cc_final: 0.7369 (mtm) REVERT: B 674 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8013 (pp) REVERT: B 679 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7344 (mm110) REVERT: B 680 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6909 (ptp90) REVERT: C 51 MET cc_start: 0.9363 (mmm) cc_final: 0.9144 (mmm) REVERT: C 156 SER cc_start: 0.7138 (m) cc_final: 0.6684 (p) REVERT: C 165 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: C 241 GLU cc_start: 0.8741 (tt0) cc_final: 0.8524 (tm-30) REVERT: C 243 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7336 (tm130) outliers start: 39 outliers final: 12 residues processed: 224 average time/residue: 0.8558 time to fit residues: 206.5216 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 104 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 454 HIS B 694 GLN C 110 HIS C 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105580 restraints weight = 14816.875| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.36 r_work: 0.2762 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14674 Z= 0.130 Angle : 0.488 9.442 19921 Z= 0.258 Chirality : 0.039 0.207 2196 Planarity : 0.003 0.046 2462 Dihedral : 10.893 74.988 2308 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.78 % Allowed : 14.77 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.90 (0.20), residues: 1691 helix: 1.77 (0.18), residues: 803 sheet: -0.20 (0.36), residues: 184 loop : -0.52 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 608 TYR 0.015 0.001 TYR B 555 PHE 0.014 0.001 PHE B 357 TRP 0.014 0.001 TRP B 438 HIS 0.006 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00290 (14674) covalent geometry : angle 0.48841 (19921) hydrogen bonds : bond 0.04035 ( 705) hydrogen bonds : angle 4.02168 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5757 (mtp) cc_final: 0.4758 (mtm) REVERT: A 26 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.3648 (pp20) REVERT: A 315 TRP cc_start: 0.7365 (m100) cc_final: 0.7024 (m-90) REVERT: A 356 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8242 (tttt) REVERT: A 608 ARG cc_start: 0.8279 (mmt90) cc_final: 0.7953 (mmt-90) REVERT: A 616 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 711 LEU cc_start: 0.8678 (mp) cc_final: 0.8470 (mm) REVERT: B 1 MET cc_start: 0.8483 (tmm) cc_final: 0.8167 (tmm) REVERT: B 108 GLN cc_start: 0.8248 (tp40) cc_final: 0.7750 (tp40) REVERT: B 135 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7831 (ptm-80) REVERT: B 290 MET cc_start: 0.7750 (mtp) cc_final: 0.7338 (mmm) REVERT: B 480 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8433 (mtpm) REVERT: B 481 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7704 (mptt) REVERT: B 577 LYS cc_start: 0.8978 (tptt) cc_final: 0.8462 (ttmp) REVERT: B 635 MET cc_start: 0.7597 (mtm) cc_final: 0.7364 (mtm) REVERT: B 674 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7991 (pp) REVERT: B 679 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7263 (mm110) REVERT: B 680 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6811 (ptp90) REVERT: B 706 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7888 (ttm170) REVERT: C 8 MET cc_start: 0.8252 (tpt) cc_final: 0.7736 (tpt) REVERT: C 156 SER cc_start: 0.7098 (m) cc_final: 0.6641 (p) REVERT: C 165 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 241 GLU cc_start: 0.8720 (tt0) cc_final: 0.8501 (tm-30) REVERT: C 243 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7284 (tm130) outliers start: 42 outliers final: 17 residues processed: 223 average time/residue: 0.8459 time to fit residues: 203.3827 Evaluate side-chains 219 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 490 GLN B 115 GLN B 394 HIS B 413 ASN B 694 GLN C 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097945 restraints weight = 14480.517| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.39 r_work: 0.2772 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14674 Z= 0.214 Angle : 0.561 11.489 19921 Z= 0.296 Chirality : 0.043 0.220 2196 Planarity : 0.004 0.049 2462 Dihedral : 11.172 74.050 2308 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.58 % Allowed : 15.23 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.73 (0.20), residues: 1691 helix: 1.58 (0.18), residues: 805 sheet: -0.23 (0.37), residues: 186 loop : -0.56 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 608 TYR 0.014 0.002 TYR B 555 PHE 0.017 0.002 PHE A 211 TRP 0.016 0.002 TRP B 438 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00495 (14674) covalent geometry : angle 0.56056 (19921) hydrogen bonds : bond 0.04852 ( 705) hydrogen bonds : angle 4.15780 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5817 (mtp) cc_final: 0.5338 (mtp) REVERT: A 26 GLU cc_start: 0.4457 (OUTLIER) cc_final: 0.3586 (pp20) REVERT: A 356 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8345 (tttt) REVERT: A 608 ARG cc_start: 0.8327 (mmt90) cc_final: 0.8006 (mmt-90) REVERT: B 1 MET cc_start: 0.8644 (tmm) cc_final: 0.8305 (tmm) REVERT: B 108 GLN cc_start: 0.8352 (tp40) cc_final: 0.7885 (tm-30) REVERT: B 290 MET cc_start: 0.7904 (mtp) cc_final: 0.7555 (mmm) REVERT: B 481 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.7940 (mptt) REVERT: B 577 LYS cc_start: 0.9065 (tptt) cc_final: 0.8670 (ttmp) REVERT: B 674 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 679 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7486 (mm-40) REVERT: B 680 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7101 (ptp90) REVERT: B 691 LYS cc_start: 0.8678 (tttm) cc_final: 0.8459 (ttpp) REVERT: B 706 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7920 (ttm170) REVERT: C 8 MET cc_start: 0.8454 (tpt) cc_final: 0.7989 (tpt) REVERT: C 156 SER cc_start: 0.7062 (m) cc_final: 0.6622 (p) REVERT: C 165 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 194 LYS cc_start: 0.7749 (tttt) cc_final: 0.7430 (ttmm) REVERT: C 241 GLU cc_start: 0.8804 (tt0) cc_final: 0.8600 (tm-30) REVERT: C 243 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7456 (tm130) outliers start: 39 outliers final: 18 residues processed: 223 average time/residue: 0.8397 time to fit residues: 202.1175 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 142 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 454 HIS B 694 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102684 restraints weight = 14516.182| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.45 r_work: 0.2738 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14674 Z= 0.121 Angle : 0.500 12.141 19921 Z= 0.262 Chirality : 0.039 0.209 2196 Planarity : 0.003 0.046 2462 Dihedral : 10.949 74.943 2308 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.32 % Allowed : 15.63 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.94 (0.20), residues: 1691 helix: 1.77 (0.18), residues: 805 sheet: -0.13 (0.37), residues: 184 loop : -0.48 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 608 TYR 0.014 0.001 TYR B 555 PHE 0.015 0.001 PHE B 357 TRP 0.013 0.001 TRP B 438 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00267 (14674) covalent geometry : angle 0.50039 (19921) hydrogen bonds : bond 0.03975 ( 705) hydrogen bonds : angle 4.05009 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TRP cc_start: 0.7379 (m100) cc_final: 0.7027 (m-90) REVERT: A 356 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8271 (tttt) REVERT: A 608 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7979 (mmt-90) REVERT: B 108 GLN cc_start: 0.8267 (tp40) cc_final: 0.7780 (tp40) REVERT: B 135 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7897 (ptm-80) REVERT: B 290 MET cc_start: 0.7839 (mtp) cc_final: 0.7377 (mmm) REVERT: B 362 MET cc_start: 0.7693 (mpp) cc_final: 0.7447 (mpt) REVERT: B 481 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.7747 (mptt) REVERT: B 577 LYS cc_start: 0.9015 (tptt) cc_final: 0.8503 (ttmp) REVERT: B 674 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 679 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7328 (mm110) REVERT: B 680 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6853 (ptp90) REVERT: B 691 LYS cc_start: 0.8458 (tttm) cc_final: 0.8199 (ttpp) REVERT: B 706 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7840 (ttm170) REVERT: C 1 MET cc_start: 0.7062 (mmm) cc_final: 0.6749 (tmm) REVERT: C 156 SER cc_start: 0.7139 (m) cc_final: 0.6686 (p) REVERT: C 165 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 241 GLU cc_start: 0.8739 (tt0) cc_final: 0.8512 (tm-30) REVERT: C 243 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7342 (tm130) outliers start: 35 outliers final: 16 residues processed: 218 average time/residue: 0.8246 time to fit residues: 193.5712 Evaluate side-chains 214 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 15 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 161 optimal weight: 0.0070 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097893 restraints weight = 14474.454| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.39 r_work: 0.2696 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14674 Z= 0.186 Angle : 0.557 12.600 19921 Z= 0.291 Chirality : 0.042 0.215 2196 Planarity : 0.004 0.048 2462 Dihedral : 11.087 74.123 2305 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.99 % Allowed : 15.89 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.80 (0.20), residues: 1691 helix: 1.64 (0.18), residues: 805 sheet: -0.19 (0.37), residues: 186 loop : -0.53 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.014 0.002 TYR B 555 PHE 0.016 0.001 PHE B 357 TRP 0.015 0.002 TRP B 438 HIS 0.009 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00426 (14674) covalent geometry : angle 0.55738 (19921) hydrogen bonds : bond 0.04611 ( 705) hydrogen bonds : angle 4.15068 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5829 (mtp) cc_final: 0.5534 (ptm) REVERT: A 315 TRP cc_start: 0.7489 (m100) cc_final: 0.7167 (m-90) REVERT: A 356 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8340 (tttt) REVERT: A 608 ARG cc_start: 0.8317 (mmt90) cc_final: 0.8013 (mmt-90) REVERT: B 108 GLN cc_start: 0.8336 (tp40) cc_final: 0.7896 (tp40) REVERT: B 290 MET cc_start: 0.7892 (mtp) cc_final: 0.7501 (mmm) REVERT: B 362 MET cc_start: 0.7831 (mpp) cc_final: 0.7597 (mpt) REVERT: B 481 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.7796 (mptt) REVERT: B 577 LYS cc_start: 0.9058 (tptt) cc_final: 0.8603 (ttmp) REVERT: B 674 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 679 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7418 (mm-40) REVERT: B 680 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7029 (ptp90) REVERT: B 691 LYS cc_start: 0.8634 (tttm) cc_final: 0.8322 (ttpm) REVERT: B 706 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7931 (ttm170) REVERT: C 1 MET cc_start: 0.7052 (mmm) cc_final: 0.6637 (tmm) REVERT: C 2 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: C 156 SER cc_start: 0.7147 (m) cc_final: 0.6700 (p) REVERT: C 165 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: C 241 GLU cc_start: 0.8830 (tt0) cc_final: 0.8613 (tm-30) REVERT: C 243 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7421 (tm130) outliers start: 30 outliers final: 20 residues processed: 213 average time/residue: 0.8480 time to fit residues: 194.9279 Evaluate side-chains 216 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 160 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 454 HIS B 694 GLN C 13 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.142577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.098866 restraints weight = 14289.365| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.44 r_work: 0.2745 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14674 Z= 0.128 Angle : 0.512 12.471 19921 Z= 0.267 Chirality : 0.040 0.209 2196 Planarity : 0.003 0.046 2462 Dihedral : 10.930 75.023 2305 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 15.83 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 aren not related in a simple way. whole: 0.95 (0.20), residues: 1691 helix: 1.78 (0.18), residues: 805 sheet: -0.08 (0.37), residues: 184 loop : -0.49 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.014 0.001 TYR B 555 PHE 0.015 0.001 PHE B 357 TRP 0.013 0.001 TRP B 438 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00285 (14674) covalent geometry : angle 0.51219 (19921) hydrogen bonds : bond 0.04027 ( 705) hydrogen bonds : angle 4.06605 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6995.24 seconds wall clock time: 119 minutes 56.90 seconds (7196.90 seconds total)