Starting phenix.real_space_refine on Fri Jul 3 12:54:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7v_29825/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7v_29825/07_2026/8g7v_29825.map" } 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-dev-6108/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: {'RNA': 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: {'RNA': 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: 3.15, per 1000 atoms: 0.22 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: 1.11 Conformation dependent library (CDL) restraints added in 631.8 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: 1.63 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: 2.43 Time building geometry restraints manager: 1.48 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: 19344 2.59 - 5.18: 305 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: 8152 26.36 - 52.72: 384 52.72 - 79.08: 48 79.08 - 105.44: 12 105.44 - 131.80: 2 Dihedral angle restraints: 8598 sinusoidal: 3832 harmonic: 4766 Sorted by residual: dihedral pdb=" C4' GTP X 1 " pdb=" C5' GTP X 1 " pdb=" O5' GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 260.87 129.08 131.80 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O3B GTP X 1 " pdb=" O3A GTP X 1 " pdb=" PB GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 291.08 166.30 124.78 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" CA SER A 855 " pdb=" C SER A 855 " pdb=" N PHE A 856 " pdb=" CA PHE A 856 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1928 0.078 - 0.156: 268 0.156 - 0.234: 19 0.234 - 0.312: 1 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=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 875 " pdb=" CA ILE A 875 " pdb=" CG1 ILE A 875 " pdb=" CG2 ILE A 875 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.560 Find NCS groups from input model: 0.200 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- 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 : 0.897 33.534 19701 Z= 0.461 Chirality : 0.053 0.390 2217 Planarity : 0.007 0.151 2330 Dihedral : 15.271 131.797 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 0.00719 / 0.33 (14407) covalent geometry : angle 0.84908 / 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 : 0.519 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: 0.1360 time to fit residues: 39.6977 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 : 0.534 ------------------------------------------------------------------------------- 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 305 GLN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098089 restraints weight = 36713.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096409 restraints weight = 35523.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097576 restraints weight = 33463.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097821 restraints weight = 23507.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098035 restraints weight = 22248.302| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14416 Z= 0.185 Angle : 0.631 13.171 19701 Z= 0.323 Chirality : 0.042 0.231 2217 Planarity : 0.005 0.102 2330 Dihedral : 8.256 101.095 2285 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.22 % Allowed : 13.81 % Favored : 83.97 % 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: -0.31 (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 0.023 0.002 PHE A 853 TRP 0.026 0.001 TRP B 379 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (14407) covalent geometry : angle 0.62893 / 0.32 (19691) SS BOND : bond 0.00399 / 0.21 ( 2) SS BOND : angle 0.48691 / 0.34 ( 4) hydrogen bonds : bond 0.04267 / 2.74 ( 536) hydrogen bonds : angle 4.95271 / 3.35 ( 1501) metal coordination : bond 0.00943 / 0.45 ( 6) metal coordination : angle 2.91270 / 1.76 ( 6) Misc. bond : bond 0.00015 / 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 181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8944 (mmm) cc_final: 0.8550 (mtp) REVERT: A 387 MET cc_start: 0.8849 (mmm) cc_final: 0.8623 (mmp) REVERT: A 573 ASN cc_start: 0.8361 (t0) cc_final: 0.8135 (t0) REVERT: A 828 GLU cc_start: 0.7386 (mp0) cc_final: 0.7055 (mp0) REVERT: B 337 ASP cc_start: 0.8037 (m-30) cc_final: 0.7788 (m-30) REVERT: B 379 TRP cc_start: 0.6815 (t-100) cc_final: 0.6498 (t-100) REVERT: C 300 ILE cc_start: 0.9249 (mm) cc_final: 0.8809 (mt) REVERT: C 419 ASN cc_start: 0.8873 (p0) cc_final: 0.8413 (p0) REVERT: C 598 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8144 (mp0) REVERT: C 624 LEU cc_start: 0.8710 (tt) cc_final: 0.8423 (mp) outliers start: 32 outliers final: 23 residues processed: 175 average time/residue: 0.1178 time to fit residues: 31.0933 Evaluate side-chains 151 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 412 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: 4.9990 chunk 15 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.8084 ------------------------------------------------------------------------------- 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** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097213 restraints weight = 36714.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097313 restraints weight = 36098.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098432 restraints weight = 29326.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098149 restraints weight = 20492.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098450 restraints weight = 19742.220| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14416 Z= 0.197 Angle : 0.620 14.317 19701 Z= 0.313 Chirality : 0.043 0.245 2217 Planarity : 0.005 0.094 2330 Dihedral : 7.724 89.021 2283 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.19 % Allowed : 15.13 % Favored : 81.68 % 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: -2.15 (0.20), residues: 1595 helix: 0.32 (0.21), residues: 586 sheet: -2.27 (0.32), residues: 247 loop : -2.60 (0.20), residues: 762 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 0.028 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 0.00444 / 0.20 (14407) covalent geometry : angle 0.61859 / 0.31 (19691) SS BOND : bond 0.00145 / 0.08 ( 2) SS BOND : angle 0.29153 / 0.19 ( 4) hydrogen bonds : bond 0.04204 / 2.70 ( 536) hydrogen bonds : angle 4.79668 / 3.26 ( 1501) metal coordination : bond 0.00934 / 0.45 ( 6) metal coordination : angle 2.78836 / 1.71 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 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 187 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8917 (mmm) cc_final: 0.8554 (mtp) REVERT: A 434 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9020 (tt) REVERT: A 573 ASN cc_start: 0.8325 (t0) cc_final: 0.8073 (t0) REVERT: A 828 GLU cc_start: 0.7427 (mp0) cc_final: 0.7109 (mp0) REVERT: B 337 ASP cc_start: 0.8008 (m-30) cc_final: 0.7747 (m-30) REVERT: C 300 ILE cc_start: 0.9193 (mm) cc_final: 0.8769 (mt) REVERT: C 419 ASN cc_start: 0.8788 (p0) cc_final: 0.8301 (p0) REVERT: C 598 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8009 (mt-10) REVERT: C 716 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7107 (tm-30) outliers start: 46 outliers final: 34 residues processed: 179 average time/residue: 0.1090 time to fit residues: 29.9229 Evaluate side-chains 157 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 0.7980 chunk 141 optimal weight: 0.1980 chunk 71 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 147 optimal weight: 50.0000 chunk 1 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 GLN A 794 GLN B 420 HIS B 423 ASN D 324 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097177 restraints weight = 36599.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097282 restraints weight = 26367.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098143 restraints weight = 19177.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.098749 restraints weight = 16483.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098583 restraints weight = 15806.354| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2197 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= 0.096 Angle : 0.531 10.293 19701 Z= 0.269 Chirality : 0.040 0.255 2217 Planarity : 0.004 0.078 2330 Dihedral : 7.007 91.190 2282 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.85 % Allowed : 16.72 % Favored : 80.43 % 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: -1.61 (0.21), residues: 1595 helix: 0.88 (0.22), residues: 586 sheet: -1.95 (0.33), residues: 247 loop : -2.40 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.014 0.001 TYR C 313 PHE 0.032 0.001 PHE C 471 TRP 0.022 0.001 TRP B 315 HIS 0.002 0.000 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (14407) covalent geometry : angle 0.52953 / 0.27 (19691) SS BOND : bond 0.00230 / 0.12 ( 2) SS BOND : angle 0.36742 / 0.24 ( 4) hydrogen bonds : bond 0.03291 / 2.16 ( 536) hydrogen bonds : angle 4.33754 / 2.93 ( 1501) metal coordination : bond 0.00393 / 0.18 ( 6) metal coordination : angle 2.29817 / 1.28 ( 6) Misc. bond : bond 0.00004 / 0.00 ( 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 189 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8940 (mmm) cc_final: 0.8705 (mmm) REVERT: A 387 MET cc_start: 0.8886 (mmp) cc_final: 0.8651 (mmp) REVERT: A 434 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9105 (tt) REVERT: A 525 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7178 (tmm) REVERT: A 573 ASN cc_start: 0.8434 (t0) cc_final: 0.8225 (t0) REVERT: A 828 GLU cc_start: 0.7364 (mp0) cc_final: 0.7060 (mp0) REVERT: B 277 ASP cc_start: 0.8064 (p0) cc_final: 0.7730 (p0) REVERT: B 337 ASP cc_start: 0.8125 (m-30) cc_final: 0.7843 (m-30) REVERT: C 385 MET cc_start: 0.8570 (mmm) cc_final: 0.8261 (mmp) REVERT: C 412 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (t) REVERT: C 419 ASN cc_start: 0.8822 (p0) cc_final: 0.8411 (p0) REVERT: C 598 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8213 (mt-10) REVERT: C 624 LEU cc_start: 0.8608 (tt) cc_final: 0.8309 (mp) REVERT: C 716 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7103 (tm-30) outliers start: 41 outliers final: 33 residues processed: 180 average time/residue: 0.1048 time to fit residues: 29.4709 Evaluate side-chains 165 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 434 LEU 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 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 412 VAL Chi-restraints excluded: chain C residue 471 PHE 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 826 ILE Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 151 optimal weight: 40.0000 chunk 122 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS C 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.122321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099349 restraints weight = 36655.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099952 restraints weight = 33261.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101066 restraints weight = 24774.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100545 restraints weight = 19927.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100858 restraints weight = 18883.313| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2362 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= 0.135 Angle : 0.562 11.553 19701 Z= 0.282 Chirality : 0.041 0.248 2217 Planarity : 0.004 0.075 2330 Dihedral : 6.975 90.703 2281 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.33 % Allowed : 17.83 % Favored : 78.83 % 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: -1.39 (0.21), residues: 1595 helix: 1.06 (0.22), residues: 586 sheet: -1.85 (0.34), residues: 239 loop : -2.27 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 824 TYR 0.020 0.001 TYR C 313 PHE 0.037 0.001 PHE C 471 TRP 0.020 0.001 TRP B 315 HIS 0.003 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (14407) covalent geometry : angle 0.56076 / 0.28 (19691) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 0.20303 / 0.13 ( 4) hydrogen bonds : bond 0.03548 / 2.30 ( 536) hydrogen bonds : angle 4.32754 / 2.94 ( 1501) metal coordination : bond 0.00730 / 0.35 ( 6) metal coordination : angle 1.84797 / 1.22 ( 6) Misc. bond : bond 0.00017 / 0.01 ( 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 184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8901 (mmm) cc_final: 0.8678 (mmm) REVERT: A 525 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7139 (tmm) REVERT: A 573 ASN cc_start: 0.8326 (t0) cc_final: 0.8106 (t0) REVERT: A 828 GLU cc_start: 0.7351 (mp0) cc_final: 0.7047 (mp0) REVERT: B 337 ASP cc_start: 0.8020 (m-30) cc_final: 0.7737 (m-30) REVERT: C 419 ASN cc_start: 0.8742 (p0) cc_final: 0.8368 (p0) REVERT: C 479 MET cc_start: 0.8951 (mmm) cc_final: 0.8685 (mmt) REVERT: C 598 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8068 (mt-10) outliers start: 48 outliers final: 38 residues processed: 173 average time/residue: 0.1002 time to fit residues: 27.4614 Evaluate side-chains 167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 582 ILE 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 412 VAL Chi-restraints excluded: chain C residue 471 PHE 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 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: 0.9990 chunk 97 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.122377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098571 restraints weight = 36233.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099861 restraints weight = 31117.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100393 restraints weight = 21959.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100555 restraints weight = 17686.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100642 restraints weight = 16801.736| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2539 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= 0.113 Angle : 0.538 10.794 19701 Z= 0.270 Chirality : 0.041 0.247 2217 Planarity : 0.004 0.069 2330 Dihedral : 6.768 90.759 2281 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.79 % 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 (0.21), residues: 1595 helix: 1.16 (0.22), residues: 592 sheet: -1.60 (0.36), residues: 232 loop : -2.16 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 559 TYR 0.017 0.001 TYR C 313 PHE 0.027 0.001 PHE C 471 TRP 0.022 0.001 TRP B 315 HIS 0.002 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14407) covalent geometry : angle 0.53713 / 0.27 (19691) SS BOND : bond 0.00113 / 0.06 ( 2) SS BOND : angle 0.19824 / 0.14 ( 4) hydrogen bonds : bond 0.03345 / 2.21 ( 536) hydrogen bonds : angle 4.18838 / 2.84 ( 1501) metal coordination : bond 0.00559 / 0.27 ( 6) metal coordination : angle 1.84914 / 1.18 ( 6) Misc. bond : bond 0.00014 / 0.01 ( 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 182 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8661 (mtt) cc_final: 0.8401 (mtt) REVERT: A 525 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7187 (tmm) REVERT: A 828 GLU cc_start: 0.7318 (mp0) cc_final: 0.7030 (mp0) REVERT: B 337 ASP cc_start: 0.8070 (m-30) cc_final: 0.7782 (m-30) REVERT: B 414 PHE cc_start: 0.8110 (m-80) cc_final: 0.7901 (m-80) REVERT: C 385 MET cc_start: 0.8575 (mmm) cc_final: 0.8322 (mmp) REVERT: C 419 ASN cc_start: 0.8706 (p0) cc_final: 0.8362 (p0) REVERT: C 598 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 624 LEU cc_start: 0.8765 (mp) cc_final: 0.8219 (tt) outliers start: 45 outliers final: 38 residues processed: 174 average time/residue: 0.1070 time to fit residues: 29.1798 Evaluate side-chains 167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU 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 412 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 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: 9.9990 chunk 135 optimal weight: 10.0000 chunk 156 optimal weight: 0.0040 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 overall best weight: 2.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094419 restraints weight = 36671.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096154 restraints weight = 25624.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096511 restraints weight = 20650.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097302 restraints weight = 16037.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097454 restraints weight = 14061.923| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2620 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= 0.139 Angle : 0.570 11.881 19701 Z= 0.283 Chirality : 0.041 0.246 2217 Planarity : 0.004 0.070 2330 Dihedral : 6.812 89.659 2281 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.47 % Allowed : 19.15 % Favored : 77.38 % 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: 1.18 (0.22), residues: 592 sheet: -1.69 (0.35), residues: 249 loop : -2.13 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 559 TYR 0.018 0.001 TYR C 313 PHE 0.015 0.001 PHE A 853 TRP 0.022 0.001 TRP B 315 HIS 0.003 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14407) covalent geometry : angle 0.56914 / 0.28 (19691) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.17268 / 0.11 ( 4) hydrogen bonds : bond 0.03534 / 2.31 ( 536) hydrogen bonds : angle 4.20516 / 2.86 ( 1501) metal coordination : bond 0.00702 / 0.34 ( 6) metal coordination : angle 2.04383 / 1.30 ( 6) Misc. bond : bond 0.00015 / 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 184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8704 (mtt) cc_final: 0.8470 (mtt) REVERT: A 525 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: A 828 GLU cc_start: 0.7394 (mp0) cc_final: 0.7093 (mp0) REVERT: B 316 GLU cc_start: 0.4290 (tp30) cc_final: 0.3826 (tp30) REVERT: B 414 PHE cc_start: 0.8322 (m-80) cc_final: 0.8078 (m-80) REVERT: C 247 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: C 385 MET cc_start: 0.8568 (mmm) cc_final: 0.8285 (mmp) REVERT: C 419 ASN cc_start: 0.8713 (p0) cc_final: 0.8396 (p0) REVERT: C 598 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8293 (mt-10) REVERT: C 624 LEU cc_start: 0.8761 (mp) cc_final: 0.8305 (tt) outliers start: 50 outliers final: 42 residues processed: 173 average time/residue: 0.0998 time to fit residues: 26.8663 Evaluate side-chains 169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 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 247 GLN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 425 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 70 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 GLN B 321 ASN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099403 restraints weight = 36037.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099708 restraints weight = 30588.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100431 restraints weight = 23854.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100684 restraints weight = 18405.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100810 restraints weight = 16683.063| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2794 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= 0.102 Angle : 0.536 9.978 19701 Z= 0.267 Chirality : 0.041 0.239 2217 Planarity : 0.004 0.065 2330 Dihedral : 6.486 91.191 2281 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.12 % Allowed : 19.92 % Favored : 76.96 % 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: -1.01 (0.22), residues: 1595 helix: 1.31 (0.22), residues: 592 sheet: -1.56 (0.35), residues: 249 loop : -2.05 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 342 TYR 0.017 0.001 TYR C 313 PHE 0.014 0.001 PHE A 471 TRP 0.022 0.001 TRP B 315 HIS 0.002 0.000 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14407) covalent geometry : angle 0.53597 / 0.27 (19691) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.21602 / 0.15 ( 4) hydrogen bonds : bond 0.03155 / 2.08 ( 536) hydrogen bonds : angle 4.04639 / 2.75 ( 1501) metal coordination : bond 0.00527 / 0.25 ( 6) metal coordination : angle 1.46378 / 0.97 ( 6) Misc. bond : bond 0.00004 / 0.00 ( 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 184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8674 (mtt) cc_final: 0.8449 (mtt) REVERT: A 828 GLU cc_start: 0.7352 (mp0) cc_final: 0.7070 (mp0) REVERT: B 316 GLU cc_start: 0.4648 (tp30) cc_final: 0.4292 (tp30) REVERT: B 417 TYR cc_start: 0.8201 (t80) cc_final: 0.7885 (t80) REVERT: C 385 MET cc_start: 0.8531 (mmm) cc_final: 0.8267 (mmp) REVERT: C 419 ASN cc_start: 0.8657 (p0) cc_final: 0.8349 (p0) REVERT: C 598 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 624 LEU cc_start: 0.8842 (mp) cc_final: 0.8348 (tt) outliers start: 45 outliers final: 35 residues processed: 175 average time/residue: 0.0948 time to fit residues: 25.9765 Evaluate side-chains 164 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 441 THR Chi-restraints excluded: chain A residue 489 ILE 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 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 383 GLU 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 412 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 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 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: 10.0000 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096278 restraints weight = 36456.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095776 restraints weight = 30978.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096838 restraints weight = 27449.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096896 restraints weight = 19896.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.097004 restraints weight = 19368.852| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14416 Z= 0.203 Angle : 0.633 13.798 19701 Z= 0.313 Chirality : 0.043 0.237 2217 Planarity : 0.004 0.071 2330 Dihedral : 6.926 88.937 2281 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.19 % Allowed : 19.85 % Favored : 76.96 % 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: -1.17 (0.22), residues: 1595 helix: 1.20 (0.21), residues: 592 sheet: -1.82 (0.33), residues: 267 loop : -2.07 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 342 TYR 0.017 0.002 TYR B 400 PHE 0.018 0.001 PHE A 853 TRP 0.020 0.001 TRP C 646 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (14407) covalent geometry : angle 0.63192 / 0.31 (19691) SS BOND : bond 0.00174 / 0.09 ( 2) SS BOND : angle 0.12892 / 0.08 ( 4) hydrogen bonds : bond 0.03964 / 2.56 ( 536) hydrogen bonds : angle 4.34420 / 2.95 ( 1501) metal coordination : bond 0.01024 / 0.50 ( 6) metal coordination : angle 2.03316 / 1.52 ( 6) Misc. bond : bond 0.00019 / 0.01 ( 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 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 VAL cc_start: 0.9321 (t) cc_final: 0.9099 (t) REVERT: A 525 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7176 (tmm) REVERT: A 755 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7736 (pmm) REVERT: A 828 GLU cc_start: 0.7401 (mp0) cc_final: 0.7081 (mp0) REVERT: B 316 GLU cc_start: 0.4871 (tp30) cc_final: 0.4324 (tp30) REVERT: B 417 TYR cc_start: 0.8256 (t80) cc_final: 0.7892 (t80) REVERT: C 247 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: C 385 MET cc_start: 0.8599 (mmm) cc_final: 0.8334 (mmp) REVERT: C 419 ASN cc_start: 0.8689 (p0) cc_final: 0.8370 (p0) REVERT: C 598 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8168 (mt-10) REVERT: C 624 LEU cc_start: 0.8892 (mp) cc_final: 0.8362 (tt) outliers start: 46 outliers final: 39 residues processed: 164 average time/residue: 0.0941 time to fit residues: 24.1504 Evaluate side-chains 168 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 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 383 GLU 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 425 ASP 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 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 70 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN C 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.100926 restraints weight = 36190.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100912 restraints weight = 29749.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101627 restraints weight = 26310.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101981 restraints weight = 18592.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102126 restraints weight = 16982.575| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2977 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= 0.094 Angle : 0.547 9.794 19701 Z= 0.274 Chirality : 0.041 0.230 2217 Planarity : 0.004 0.065 2330 Dihedral : 6.306 91.209 2281 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.64 % Allowed : 20.68 % Favored : 76.68 % 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: -0.84 (0.22), residues: 1595 helix: 1.51 (0.22), residues: 589 sheet: -1.64 (0.35), residues: 246 loop : -1.92 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 342 TYR 0.026 0.001 TYR B 400 PHE 0.017 0.001 PHE A 471 TRP 0.024 0.001 TRP C 646 HIS 0.002 0.000 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (14407) covalent geometry : angle 0.54634 / 0.27 (19691) SS BOND : bond 0.00170 / 0.09 ( 2) SS BOND : angle 0.29476 / 0.21 ( 4) hydrogen bonds : bond 0.03104 / 2.06 ( 536) hydrogen bonds : angle 4.01135 / 2.71 ( 1501) metal coordination : bond 0.00317 / 0.15 ( 6) metal coordination : angle 1.67720 / 1.00 ( 6) Misc. bond : bond 0.00004 / 0.00 ( 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 177 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7243 (tmm) REVERT: A 755 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7716 (pmm) REVERT: A 828 GLU cc_start: 0.7346 (mp0) cc_final: 0.7061 (mp0) REVERT: A 923 MET cc_start: 0.5732 (mmm) cc_final: 0.5506 (mmm) REVERT: B 417 TYR cc_start: 0.8170 (t80) cc_final: 0.7805 (t80) REVERT: C 385 MET cc_start: 0.8542 (mmm) cc_final: 0.8266 (mmp) REVERT: C 419 ASN cc_start: 0.8634 (p0) cc_final: 0.8335 (p0) REVERT: C 598 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8207 (mt-10) REVERT: C 624 LEU cc_start: 0.8848 (mp) cc_final: 0.8386 (tt) outliers start: 38 outliers final: 36 residues processed: 168 average time/residue: 0.0956 time to fit residues: 24.7771 Evaluate side-chains 168 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 525 MET 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 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 383 GLU 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 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 331 SER 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: 8.9990 chunk 57 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099448 restraints weight = 36070.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099744 restraints weight = 31159.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100439 restraints weight = 25048.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100961 restraints weight = 18369.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100974 restraints weight = 18048.198| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14416 Z= 0.113 Angle : 0.571 10.191 19701 Z= 0.282 Chirality : 0.041 0.234 2217 Planarity : 0.004 0.067 2330 Dihedral : 6.283 90.909 2281 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.71 % Allowed : 20.68 % Favored : 76.61 % 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: -0.82 (0.22), residues: 1595 helix: 1.55 (0.21), residues: 589 sheet: -1.50 (0.35), residues: 258 loop : -1.97 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 342 TYR 0.036 0.001 TYR C 313 PHE 0.011 0.001 PHE A 853 TRP 0.023 0.001 TRP C 646 HIS 0.003 0.001 HIS C 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14407) covalent geometry : angle 0.57018 / 0.28 (19691) SS BOND : bond 0.00106 / 0.06 ( 2) SS BOND : angle 0.40479 / 0.24 ( 4) hydrogen bonds : bond 0.03222 / 2.12 ( 536) hydrogen bonds : angle 4.01078 / 2.72 ( 1501) metal coordination : bond 0.00572 / 0.27 ( 6) metal coordination : angle 1.79599 / 1.17 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.77 seconds wall clock time: 35 minutes 56.47 seconds (2156.47 seconds total)