Starting phenix.real_space_refine on Thu Aug 6 07:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g7v_29825/08_2026/8g7v_29825.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 Zn 2 6.06 5 P 48 5.49 5 S 78 5.16 5 C 8762 2.51 5 N 2393 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14007 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5005 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 24, 'TRANS': 593} Chain breaks: 4 Chain: "D" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 501 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 22, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 487 Classifications: {'RNAv2': 23} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 21} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4741 SG CYS A 864 96.663 76.558 85.552 1.00 44.09 S ATOM 4780 SG CYS A 869 93.580 76.262 83.569 1.00 47.18 S ATOM 10817 SG CYS C 810 84.696 25.785 72.262 1.00 61.51 S ATOM 10843 SG CYS C 813 88.128 24.213 72.341 1.00 69.91 S ATOM 11155 SG CYS C 864 88.208 27.375 74.808 1.00 60.77 S ATOM 11194 SG CYS C 869 87.723 27.618 71.176 1.00 66.05 S Time building chain proxies: 2.16, per 1000 atoms: 0.15 Number of scatterers: 14007 At special positions: 0 Unit cell: (119.138, 115.782, 153.537, 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) Zn 2 29.99 S 78 16.00 P 48 15.00 O 2724 8.00 N 2393 7.00 C 8762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 402 " distance=2.04 Simple disulfide: pdb=" SG CYS D 347 " - pdb=" SG CYS D 402 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 458.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 810 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 813 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " Number of angles added : 6 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 16 sheets defined 37.7% alpha, 10.1% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.790A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.814A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 removed outlier: 4.057A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.044A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.885A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.924A pdb=" N ASN A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.774A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 506 through 520 removed outlier: 4.002A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 4.163A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 4.302A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.681A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.615A pdb=" N PHE A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.615A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 4.125A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 removed outlier: 3.695A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.768A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.778A pdb=" N ALA C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 4.270A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.664A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.962A pdb=" N LEU C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.592A pdb=" N ILE C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 366 " --> pdb=" O LEU C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 366' Processing helix chain 'C' and resid 373 through 377 Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 469 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 4.029A pdb=" N SER C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.804A pdb=" N MET C 521 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 558 removed outlier: 3.564A pdb=" N HIS C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 removed outlier: 3.710A pdb=" N ALA C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 602 removed outlier: 3.910A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 Processing helix chain 'C' and resid 636 through 649 Processing helix chain 'C' and resid 746 through 769 Processing helix chain 'C' and resid 773 through 792 Processing helix chain 'C' and resid 837 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.600A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 3.837A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.468A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.512A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 843 Processing sheet with id=AA6, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.248A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 280 through 282 removed outlier: 4.327A pdb=" N VAL B 317 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 376 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 302 removed outlier: 4.257A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 260 through 263 removed outlier: 3.801A pdb=" N LEU C 408 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 294 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 457 through 462 removed outlier: 3.736A pdb=" N CYS C 738 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.255A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 823 through 824 Processing sheet with id=AB4, first strand: chain 'C' and resid 843 through 844 Processing sheet with id=AB5, first strand: chain 'C' and resid 874 through 876 Processing sheet with id=AB6, first strand: chain 'D' and resid 280 through 282 removed outlier: 3.564A pdb=" N LEU D 425 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 426 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.427A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 351 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 327 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 349 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 352 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2226 1.32 - 1.44: 4088 1.44 - 1.57: 7893 1.57 - 1.70: 96 1.70 - 1.82: 104 Bond restraints: 14407 Sorted by residual: bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sigma weight residual 1.410 1.618 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 GTP X 1 " pdb=" C6 GTP X 1 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C4 GTP X 1 " pdb=" N3 GTP X 1 " ideal model delta sigma weight residual 1.355 1.493 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C2 GTP X 1 " pdb=" N2 GTP X 1 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 14402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19287 2.59 - 5.18: 362 5.18 - 7.77: 37 7.77 - 10.36: 1 10.36 - 12.95: 4 Bond angle restraints: 19691 Sorted by residual: angle pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" C VAL C 332 " ideal model delta sigma weight residual 108.88 120.51 -11.63 2.16e+00 2.14e-01 2.90e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.98 5.58 1.27e+00 6.20e-01 1.93e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 110.80 101.71 9.09 2.13e+00 2.20e-01 1.82e+01 angle pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " pdb=" CG1 VAL C 332 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 angle pdb=" C ALA A 733 " pdb=" N ARG A 734 " pdb=" CA ARG A 734 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 ... (remaining 19686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 8102 26.36 - 52.72: 429 52.72 - 79.08: 54 79.08 - 105.44: 11 105.44 - 131.80: 2 Dihedral angle restraints: 8598 sinusoidal: 3832 harmonic: 4766 Sorted by residual: dihedral pdb=" C4' C Y 2 " pdb=" C3' C Y 2 " pdb=" C2' C Y 2 " pdb=" C1' C Y 2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.86 74.20 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" O4' C Y 2 " pdb=" C4' C Y 2 " pdb=" C3' C Y 2 " pdb=" C2' C Y 2 " ideal model delta sinusoidal sigma weight residual -35.15 26.40 -61.55 1 4.00e+00 6.25e-02 3.14e+02 dihedral pdb=" O4' C Y 2 " pdb=" C2' C Y 2 " pdb=" C1' C Y 2 " pdb=" C3' C Y 2 " ideal model delta sinusoidal sigma weight residual -94.41 -37.20 -57.21 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1883 0.078 - 0.156: 266 0.156 - 0.234: 53 0.234 - 0.312: 14 0.312 - 0.390: 1 Chirality restraints: 2217 Sorted by residual: chirality pdb=" CA VAL C 332 " pdb=" N VAL C 332 " pdb=" C VAL C 332 " pdb=" CB VAL C 332 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C2' C Y 2 " pdb=" C3' C Y 2 " pdb=" O2' C Y 2 " pdb=" C1' C Y 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' C Y 2 " pdb=" C4' C Y 2 " pdb=" O3' C Y 2 " pdb=" C2' C Y 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2214 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " -0.100 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO C 333 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 712 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C VAL C 712 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE C 713 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 382 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.041 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2927 2.78 - 3.31: 12346 3.31 - 3.84: 23231 3.84 - 4.37: 25761 4.37 - 4.90: 43828 Nonbonded interactions: 108093 Sorted by model distance: nonbonded pdb=" CD LYS A 806 " pdb=" OD1 ASP A 896 " model vdw 2.246 3.440 nonbonded pdb=" O SER B 300 " pdb=" OG SER B 300 " model vdw 2.286 3.040 nonbonded pdb=" O LEU C 538 " pdb=" OG1 THR C 542 " model vdw 2.301 3.040 nonbonded pdb=" OG SER D 300 " pdb=" O LEU D 416 " model vdw 2.316 3.040 nonbonded pdb=" O LEU C 597 " pdb=" OG SER C 601 " model vdw 2.318 3.040 ... (remaining 108088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 241 through 661 or resid 690 through 699 or resid 709 thro \ ugh 718 or resid 734 through 845 or resid 858 through 921 or resid 1001)) selection = (chain 'C' and resid 241 through 1001) } ncs_group { reference = (chain 'B' and (resid 252 through 335 or (resid 336 and (name N or name CA or na \ me C or name O or name CB )) or resid 337 through 382 or (resid 383 through 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 through 43 \ 0)) selection = (chain 'D' and (resid 252 through 394 or (resid 395 through 399 and (name N or n \ ame CA or name C or name O or name CB )) or resid 400 through 430)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.008 0.232 14416 Z= 0.354 Angle : 0.921 33.534 19701 Z= 0.462 Chirality : 0.062 0.390 2217 Planarity : 0.007 0.151 2330 Dihedral : 15.774 131.797 5490 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.42 % Allowed : 9.09 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.16), residues: 1595 helix: -2.06 (0.17), residues: 569 sheet: -2.89 (0.28), residues: 253 loop : -3.13 (0.17), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 502 TYR 0.022 0.002 TYR C 879 PHE 0.024 0.002 PHE A 853 TRP 0.012 0.002 TRP D 379 HIS 0.010 0.002 HIS C 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.33 (14407) covalent geometry : angle 0.87349 / 0.46 (19691) SS BOND : bond 0.00362 / 0.18 ( 2) SS BOND : angle 0.38745 / 0.26 ( 4) hydrogen bonds : bond 0.16021 / 10.22 ( 536) hydrogen bonds : angle 6.57758 / 4.48 ( 1501) metal coordination : bond 0.13347 / 7.05 ( 6) metal coordination : angle 16.68953 / 9.28 ( 6) Misc. bond : bond 0.09817 / 5.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8800 (mmm) cc_final: 0.8510 (mtp) REVERT: A 387 MET cc_start: 0.8649 (mmm) cc_final: 0.8386 (mmp) REVERT: A 573 ASN cc_start: 0.8260 (t0) cc_final: 0.8022 (t0) REVERT: A 828 GLU cc_start: 0.7165 (mp0) cc_final: 0.6905 (mp0) REVERT: A 890 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 266 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7758 (mttm) REVERT: B 400 TYR cc_start: 0.6077 (t80) cc_final: 0.5526 (t80) REVERT: C 300 ILE cc_start: 0.9143 (mm) cc_final: 0.8901 (mt) REVERT: C 419 ASN cc_start: 0.8873 (p0) cc_final: 0.8617 (p0) REVERT: C 598 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 624 LEU cc_start: 0.8703 (tt) cc_final: 0.8358 (mp) REVERT: D 357 LEU cc_start: 0.5726 (tp) cc_final: 0.5306 (pp) outliers start: 6 outliers final: 5 residues processed: 204 average time/residue: 0.1116 time to fit residues: 32.4531 Evaluate side-chains 138 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 282 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 336 GLN A 353 ASN A 375 HIS A 393 GLN A 404 GLN A 445 ASN A 595 GLN A 623 HIS A 625 ASN A 645 ASN A 805 ASN B 301 GLN B 338 GLN B 394 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN C 349 GLN C 354 ASN C 389 ASN C 595 GLN C 692 ASN C 830 HIS D 381 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094632 restraints weight = 36406.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.094674 restraints weight = 25628.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.094749 restraints weight = 22931.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095119 restraints weight = 18653.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095193 restraints weight = 17069.733| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14416 Z= 0.189 Angle : 0.685 13.236 19701 Z= 0.331 Chirality : 0.049 0.633 2217 Planarity : 0.005 0.102 2330 Dihedral : 9.541 101.350 2285 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.22 % Allowed : 13.60 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.19), residues: 1595 helix: -0.30 (0.20), residues: 585 sheet: -2.50 (0.30), residues: 248 loop : -2.76 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 533 TYR 0.016 0.002 TYR C 541 PHE 0.022 0.002 PHE A 853 TRP 0.025 0.001 TRP B 379 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (14407) covalent geometry : angle 0.68338 / 0.33 (19691) SS BOND : bond 0.00488 / 0.26 ( 2) SS BOND : angle 0.51729 / 0.33 ( 4) hydrogen bonds : bond 0.04345 / 2.77 ( 536) hydrogen bonds : angle 4.96377 / 3.36 ( 1501) metal coordination : bond 0.01175 / 0.56 ( 6) metal coordination : angle 2.91205 / 1.77 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8873 (mmm) cc_final: 0.8519 (mtp) REVERT: A 387 MET cc_start: 0.8837 (mmm) cc_final: 0.8628 (mmp) REVERT: A 573 ASN cc_start: 0.8440 (t0) cc_final: 0.8197 (t0) REVERT: A 828 GLU cc_start: 0.7376 (mp0) cc_final: 0.7044 (mp0) REVERT: B 257 TRP cc_start: 0.6431 (m100) cc_final: 0.6189 (m100) REVERT: B 337 ASP cc_start: 0.8170 (m-30) cc_final: 0.7918 (m-30) REVERT: B 379 TRP cc_start: 0.7198 (t-100) cc_final: 0.6782 (t-100) REVERT: C 300 ILE cc_start: 0.9206 (mm) cc_final: 0.8743 (mt) REVERT: C 419 ASN cc_start: 0.8879 (p0) cc_final: 0.8424 (p0) REVERT: C 560 MET cc_start: 0.8148 (mmt) cc_final: 0.7905 (mmt) REVERT: C 598 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8207 (mp0) REVERT: C 624 LEU cc_start: 0.8705 (tt) cc_final: 0.8374 (mp) outliers start: 32 outliers final: 22 residues processed: 173 average time/residue: 0.0966 time to fit residues: 25.1880 Evaluate side-chains 149 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 25 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093023 restraints weight = 36828.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094899 restraints weight = 25698.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094672 restraints weight = 20278.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095266 restraints weight = 17394.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095363 restraints weight = 14896.616| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14416 Z= 0.191 Angle : 0.654 14.120 19701 Z= 0.316 Chirality : 0.047 0.402 2217 Planarity : 0.004 0.093 2330 Dihedral : 9.281 88.850 2282 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.12 % Allowed : 14.85 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.20), residues: 1595 helix: 0.33 (0.21), residues: 586 sheet: -2.22 (0.31), residues: 259 loop : -2.61 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 559 TYR 0.017 0.002 TYR C 313 PHE 0.021 0.002 PHE C 471 TRP 0.020 0.001 TRP B 315 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (14407) covalent geometry : angle 0.65227 / 0.32 (19691) SS BOND : bond 0.00103 / 0.05 ( 2) SS BOND : angle 0.28079 / 0.19 ( 4) hydrogen bonds : bond 0.04153 / 2.67 ( 536) hydrogen bonds : angle 4.77133 / 3.24 ( 1501) metal coordination : bond 0.00863 / 0.41 ( 6) metal coordination : angle 2.82377 / 1.72 ( 6) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8910 (mmm) cc_final: 0.8570 (mtp) REVERT: A 434 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9033 (tt) REVERT: A 573 ASN cc_start: 0.8410 (t0) cc_final: 0.8165 (t0) REVERT: A 828 GLU cc_start: 0.7414 (mp0) cc_final: 0.7102 (mp0) REVERT: B 337 ASP cc_start: 0.8172 (m-30) cc_final: 0.7911 (m-30) REVERT: B 379 TRP cc_start: 0.7341 (t-100) cc_final: 0.6544 (t-100) REVERT: C 300 ILE cc_start: 0.9149 (mm) cc_final: 0.8702 (mt) REVERT: C 419 ASN cc_start: 0.8784 (p0) cc_final: 0.8281 (p0) REVERT: C 560 MET cc_start: 0.8119 (mmt) cc_final: 0.7902 (mmt) REVERT: C 598 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 716 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7082 (tm-30) outliers start: 45 outliers final: 34 residues processed: 176 average time/residue: 0.0834 time to fit residues: 22.8615 Evaluate side-chains 158 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 50 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 0.0050 chunk 53 optimal weight: 4.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 GLN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.122319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096494 restraints weight = 36004.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097292 restraints weight = 23669.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097649 restraints weight = 17314.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098186 restraints weight = 16434.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098267 restraints weight = 14950.907| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14416 Z= 0.110 Angle : 0.566 10.810 19701 Z= 0.275 Chirality : 0.044 0.258 2217 Planarity : 0.004 0.079 2330 Dihedral : 8.973 92.731 2282 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.91 % Allowed : 17.00 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.21), residues: 1595 helix: 0.92 (0.22), residues: 585 sheet: -1.98 (0.33), residues: 247 loop : -2.38 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 559 TYR 0.015 0.001 TYR C 313 PHE 0.020 0.001 PHE C 471 TRP 0.021 0.001 TRP B 315 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14407) covalent geometry : angle 0.56441 / 0.27 (19691) SS BOND : bond 0.00334 / 0.18 ( 2) SS BOND : angle 0.32161 / 0.22 ( 4) hydrogen bonds : bond 0.03364 / 2.21 ( 536) hydrogen bonds : angle 4.36672 / 2.96 ( 1501) metal coordination : bond 0.00504 / 0.24 ( 6) metal coordination : angle 2.25563 / 1.27 ( 6) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8926 (mmm) cc_final: 0.8713 (mmm) REVERT: A 525 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7168 (tmm) REVERT: A 573 ASN cc_start: 0.8483 (t0) cc_final: 0.8269 (t0) REVERT: A 828 GLU cc_start: 0.7371 (mp0) cc_final: 0.7065 (mp0) REVERT: B 257 TRP cc_start: 0.6295 (m100) cc_final: 0.5998 (m100) REVERT: B 277 ASP cc_start: 0.8089 (p0) cc_final: 0.7808 (p0) REVERT: B 337 ASP cc_start: 0.8178 (m-30) cc_final: 0.7909 (m-30) REVERT: B 379 TRP cc_start: 0.7088 (t-100) cc_final: 0.6575 (t-100) REVERT: C 385 MET cc_start: 0.8578 (mmm) cc_final: 0.8284 (mmp) REVERT: C 419 ASN cc_start: 0.8823 (p0) cc_final: 0.8423 (p0) REVERT: C 598 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8232 (mt-10) REVERT: C 624 LEU cc_start: 0.8611 (tt) cc_final: 0.8318 (mp) REVERT: C 716 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7054 (tm-30) outliers start: 42 outliers final: 37 residues processed: 180 average time/residue: 0.0843 time to fit residues: 23.8273 Evaluate side-chains 166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 151 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096692 restraints weight = 36789.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095144 restraints weight = 34087.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096275 restraints weight = 32421.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096485 restraints weight = 22593.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096689 restraints weight = 21901.203| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14416 Z= 0.227 Angle : 0.689 14.510 19701 Z= 0.330 Chirality : 0.048 0.271 2217 Planarity : 0.004 0.084 2330 Dihedral : 9.136 88.058 2281 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.68 % Allowed : 18.18 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1595 helix: 0.86 (0.22), residues: 588 sheet: -2.14 (0.32), residues: 265 loop : -2.36 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 559 TYR 0.022 0.002 TYR C 313 PHE 0.025 0.002 PHE C 471 TRP 0.020 0.001 TRP B 315 HIS 0.005 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (14407) covalent geometry : angle 0.68776 / 0.33 (19691) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.21525 / 0.13 ( 4) hydrogen bonds : bond 0.04220 / 2.71 ( 536) hydrogen bonds : angle 4.63828 / 3.16 ( 1501) metal coordination : bond 0.01114 / 0.55 ( 6) metal coordination : angle 2.15239 / 1.49 ( 6) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8876 (mmm) cc_final: 0.8465 (mtp) REVERT: A 434 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 573 ASN cc_start: 0.8316 (t0) cc_final: 0.8076 (t0) REVERT: A 828 GLU cc_start: 0.7438 (mp0) cc_final: 0.7099 (mp0) REVERT: B 337 ASP cc_start: 0.8109 (m-30) cc_final: 0.7825 (m-30) REVERT: C 419 ASN cc_start: 0.8809 (p0) cc_final: 0.8421 (p0) REVERT: C 598 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8146 (mt-10) REVERT: C 711 LEU cc_start: 0.7323 (tp) cc_final: 0.6980 (tp) REVERT: C 716 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 53 outliers final: 44 residues processed: 178 average time/residue: 0.0838 time to fit residues: 23.5212 Evaluate side-chains 168 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097470 restraints weight = 36773.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096131 restraints weight = 33671.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097406 restraints weight = 31705.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097550 restraints weight = 21791.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097768 restraints weight = 20660.401| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14416 Z= 0.178 Angle : 0.644 13.309 19701 Z= 0.308 Chirality : 0.046 0.255 2217 Planarity : 0.004 0.081 2330 Dihedral : 9.046 88.384 2281 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.68 % Allowed : 19.78 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1595 helix: 0.94 (0.22), residues: 587 sheet: -2.01 (0.34), residues: 245 loop : -2.22 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 559 TYR 0.019 0.002 TYR C 313 PHE 0.023 0.001 PHE C 471 TRP 0.021 0.001 TRP B 315 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (14407) covalent geometry : angle 0.64350 / 0.31 (19691) SS BOND : bond 0.00135 / 0.07 ( 2) SS BOND : angle 0.24782 / 0.15 ( 4) hydrogen bonds : bond 0.03853 / 2.51 ( 536) hydrogen bonds : angle 4.49808 / 3.06 ( 1501) metal coordination : bond 0.00868 / 0.43 ( 6) metal coordination : angle 1.96656 / 1.31 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ASN cc_start: 0.8346 (t0) cc_final: 0.8135 (t0) REVERT: A 828 GLU cc_start: 0.7427 (mp0) cc_final: 0.7090 (mp0) REVERT: B 257 TRP cc_start: 0.6139 (m100) cc_final: 0.5840 (m100) REVERT: B 337 ASP cc_start: 0.8121 (m-30) cc_final: 0.7819 (m-30) REVERT: B 400 TYR cc_start: 0.5782 (t80) cc_final: 0.5433 (t80) REVERT: C 247 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: C 598 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 716 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6883 (tm-30) outliers start: 53 outliers final: 45 residues processed: 172 average time/residue: 0.0834 time to fit residues: 22.6121 Evaluate side-chains 168 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 0.0370 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.0980 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN B 321 ASN B 423 ASN D 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100047 restraints weight = 36709.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100624 restraints weight = 32947.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101450 restraints weight = 23309.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101531 restraints weight = 18050.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101675 restraints weight = 17148.974| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14416 Z= 0.095 Angle : 0.578 9.565 19701 Z= 0.278 Chirality : 0.044 0.234 2217 Planarity : 0.004 0.068 2330 Dihedral : 8.754 93.647 2281 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.26 % Allowed : 20.40 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1595 helix: 1.28 (0.22), residues: 588 sheet: -1.75 (0.35), residues: 241 loop : -2.06 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 342 TYR 0.017 0.001 TYR C 541 PHE 0.019 0.001 PHE C 471 TRP 0.024 0.001 TRP B 315 HIS 0.002 0.000 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (14407) covalent geometry : angle 0.57792 / 0.28 (19691) SS BOND : bond 0.00068 / 0.04 ( 2) SS BOND : angle 0.25547 / 0.17 ( 4) hydrogen bonds : bond 0.03152 / 2.08 ( 536) hydrogen bonds : angle 4.15812 / 2.82 ( 1501) metal coordination : bond 0.00406 / 0.19 ( 6) metal coordination : angle 1.59970 / 0.95 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 828 GLU cc_start: 0.7362 (mp0) cc_final: 0.7073 (mp0) REVERT: B 257 TRP cc_start: 0.5762 (m100) cc_final: 0.5553 (m100) REVERT: B 316 GLU cc_start: 0.4622 (tp30) cc_final: 0.4175 (tp30) REVERT: B 337 ASP cc_start: 0.8052 (m-30) cc_final: 0.7745 (m-30) REVERT: C 385 MET cc_start: 0.8553 (mmm) cc_final: 0.8312 (mmp) REVERT: C 598 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 716 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6896 (tm-30) outliers start: 47 outliers final: 35 residues processed: 181 average time/residue: 0.0796 time to fit residues: 22.8277 Evaluate side-chains 160 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN A 794 GLN B 301 GLN B 420 HIS C 619 GLN C 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096831 restraints weight = 36595.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096943 restraints weight = 34455.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097498 restraints weight = 31195.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097597 restraints weight = 21275.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097755 restraints weight = 20335.565| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14416 Z= 0.206 Angle : 0.682 13.516 19701 Z= 0.325 Chirality : 0.047 0.253 2217 Planarity : 0.004 0.075 2330 Dihedral : 8.979 88.348 2281 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.47 % Allowed : 20.61 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1595 helix: 1.09 (0.22), residues: 587 sheet: -1.82 (0.34), residues: 259 loop : -2.11 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 824 TYR 0.015 0.001 TYR B 417 PHE 0.030 0.002 PHE C 471 TRP 0.022 0.001 TRP B 315 HIS 0.005 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (14407) covalent geometry : angle 0.68091 / 0.33 (19691) SS BOND : bond 0.00189 / 0.10 ( 2) SS BOND : angle 0.22677 / 0.13 ( 4) hydrogen bonds : bond 0.03950 / 2.55 ( 536) hydrogen bonds : angle 4.40704 / 3.00 ( 1501) metal coordination : bond 0.01010 / 0.50 ( 6) metal coordination : angle 2.02532 / 1.40 ( 6) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8776 (mmm) cc_final: 0.8356 (mtp) REVERT: A 828 GLU cc_start: 0.7431 (mp0) cc_final: 0.7097 (mp0) REVERT: B 257 TRP cc_start: 0.5966 (m100) cc_final: 0.5765 (m100) REVERT: B 316 GLU cc_start: 0.4945 (tp30) cc_final: 0.4417 (tp30) REVERT: B 337 ASP cc_start: 0.8146 (m-30) cc_final: 0.7852 (m-30) REVERT: C 247 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 385 MET cc_start: 0.8571 (mmm) cc_final: 0.8296 (mmp) REVERT: C 598 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8153 (mt-10) REVERT: C 716 GLU cc_start: 0.7647 (tm-30) cc_final: 0.6912 (tm-30) outliers start: 50 outliers final: 44 residues processed: 164 average time/residue: 0.0843 time to fit residues: 21.8165 Evaluate side-chains 167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 75 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 HIS C 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.121447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098043 restraints weight = 36736.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098778 restraints weight = 35274.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099574 restraints weight = 27823.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099464 restraints weight = 21094.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099673 restraints weight = 20457.661| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14416 Z= 0.150 Angle : 0.641 12.169 19701 Z= 0.308 Chirality : 0.046 0.252 2217 Planarity : 0.004 0.074 2330 Dihedral : 8.873 89.374 2281 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.12 % Allowed : 21.51 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1595 helix: 1.17 (0.21), residues: 587 sheet: -1.69 (0.35), residues: 253 loop : -2.09 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.028 0.001 TYR B 400 PHE 0.029 0.001 PHE C 471 TRP 0.023 0.001 TRP B 315 HIS 0.003 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14407) covalent geometry : angle 0.63996 / 0.31 (19691) SS BOND : bond 0.00211 / 0.11 ( 2) SS BOND : angle 0.30460 / 0.19 ( 4) hydrogen bonds : bond 0.03591 / 2.33 ( 536) hydrogen bonds : angle 4.27125 / 2.91 ( 1501) metal coordination : bond 0.00729 / 0.35 ( 6) metal coordination : angle 1.97537 / 1.21 ( 6) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8830 (mmm) cc_final: 0.8416 (mtp) REVERT: A 828 GLU cc_start: 0.7463 (mp0) cc_final: 0.7139 (mp0) REVERT: B 316 GLU cc_start: 0.4825 (tp30) cc_final: 0.4395 (tp30) REVERT: B 417 TYR cc_start: 0.8241 (t80) cc_final: 0.7882 (t80) REVERT: C 385 MET cc_start: 0.8604 (mmm) cc_final: 0.8326 (mmp) REVERT: C 598 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8148 (mt-10) REVERT: C 716 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6889 (tm-30) outliers start: 45 outliers final: 40 residues processed: 164 average time/residue: 0.0828 time to fit residues: 21.7901 Evaluate side-chains 162 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 109 optimal weight: 0.0060 chunk 136 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099198 restraints weight = 36212.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098980 restraints weight = 31113.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099941 restraints weight = 25191.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100190 restraints weight = 18812.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100312 restraints weight = 17373.936| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14416 Z= 0.107 Angle : 0.602 12.356 19701 Z= 0.290 Chirality : 0.044 0.240 2217 Planarity : 0.004 0.069 2330 Dihedral : 8.685 91.724 2281 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.85 % Allowed : 21.58 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1595 helix: 1.43 (0.22), residues: 581 sheet: -1.48 (0.35), residues: 269 loop : -1.96 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 342 TYR 0.021 0.001 TYR B 400 PHE 0.029 0.001 PHE C 471 TRP 0.025 0.001 TRP B 315 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14407) covalent geometry : angle 0.60149 / 0.29 (19691) SS BOND : bond 0.00190 / 0.10 ( 2) SS BOND : angle 0.31516 / 0.22 ( 4) hydrogen bonds : bond 0.03231 / 2.15 ( 536) hydrogen bonds : angle 4.17135 / 2.83 ( 1501) metal coordination : bond 0.00468 / 0.22 ( 6) metal coordination : angle 1.98355 / 1.15 ( 6) Misc. bond : bond 0.00013 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7141 (tmm) REVERT: A 755 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7782 (pmm) REVERT: A 828 GLU cc_start: 0.7409 (mp0) cc_final: 0.7092 (mp0) REVERT: B 257 TRP cc_start: 0.5602 (m100) cc_final: 0.5334 (m100) REVERT: B 312 LYS cc_start: 0.6778 (mmtm) cc_final: 0.6185 (mmtm) REVERT: B 417 TYR cc_start: 0.8164 (t80) cc_final: 0.7743 (t80) REVERT: C 385 MET cc_start: 0.8562 (mmm) cc_final: 0.8277 (mmp) REVERT: C 419 ASN cc_start: 0.8579 (p0) cc_final: 0.8276 (p0) REVERT: C 598 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 716 GLU cc_start: 0.7726 (tm-30) cc_final: 0.6920 (tm-30) REVERT: C 896 ASP cc_start: 0.7628 (m-30) cc_final: 0.7370 (m-30) outliers start: 41 outliers final: 36 residues processed: 164 average time/residue: 0.0910 time to fit residues: 23.4455 Evaluate side-chains 169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 151 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097053 restraints weight = 36193.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097038 restraints weight = 29583.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097725 restraints weight = 23712.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097972 restraints weight = 19422.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098043 restraints weight = 17216.021| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14416 Z= 0.157 Angle : 0.644 12.745 19701 Z= 0.307 Chirality : 0.046 0.273 2217 Planarity : 0.004 0.070 2330 Dihedral : 8.730 89.843 2281 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.12 % Allowed : 21.24 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1595 helix: 1.38 (0.22), residues: 583 sheet: -1.55 (0.35), residues: 261 loop : -2.00 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 559 TYR 0.025 0.001 TYR B 400 PHE 0.025 0.001 PHE C 471 TRP 0.022 0.001 TRP C 646 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (14407) covalent geometry : angle 0.64332 / 0.31 (19691) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.31382 / 0.19 ( 4) hydrogen bonds : bond 0.03568 / 2.35 ( 536) hydrogen bonds : angle 4.26923 / 2.90 ( 1501) metal coordination : bond 0.00777 / 0.38 ( 6) metal coordination : angle 1.89464 / 1.19 ( 6) Misc. bond : bond 0.00032 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.76 seconds wall clock time: 30 minutes 2.81 seconds (1802.81 seconds total)