Starting phenix.real_space_refine on Sat Sep 12 03:55:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zes_14692/09_2026/7zes_14692.cif" } resolution = 3.1 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= 0.002 sd= 0.106 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 86 5.16 5 C 8604 2.51 5 N 2356 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 71.891 74.522 73.975 1.00 67.29 S ATOM 2310 SG CYS A 321 71.507 75.478 77.639 1.00 45.08 S ATOM 2316 SG CYS A 322 71.129 71.926 76.538 1.00 41.17 S ATOM 8698 SG CYS B 287 38.684 34.161 74.110 1.00 65.53 S ATOM 8975 SG CYS B 321 39.255 33.258 77.786 1.00 45.53 S ATOM 8981 SG CYS B 322 39.705 36.860 76.573 1.00 42.58 S Time building chain proxies: 3.09, per 1000 atoms: 0.23 Number of scatterers: 13538 At special positions: 0 Unit cell: (111.922, 109.83, 126.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 86 16.00 P 10 15.00 Mg 2 11.99 O 2478 8.00 N 2356 7.00 C 8604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 595.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 45.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.591A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.558A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix removed outlier: 3.689A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.500A pdb=" N ARG A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 481 through 501 removed outlier: 4.355A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER A 540 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 563 through 586 removed outlier: 3.543A pdb=" N GLU A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 removed outlier: 3.883A pdb=" N ARG A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.612A pdb=" N ARG A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.577A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.602A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 removed outlier: 4.154A pdb=" N LEU A 761 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.633A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 825 " --> pdb=" O HIS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.589A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.557A pdb=" N PHE B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix removed outlier: 3.691A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 481 through 501 removed outlier: 4.321A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 499 " --> pdb=" O LYS B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER B 540 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.542A pdb=" N GLU B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 590 removed outlier: 3.881A pdb=" N ARG B 590 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 587 through 590' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.616A pdb=" N ARG B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.605A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 4.155A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 removed outlier: 3.624A pdb=" N TYR B 824 " --> pdb=" O GLU B 820 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 825 " --> pdb=" O HIS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.196A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.567A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.528A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.329A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.151A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.184A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.557A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS B 304 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.543A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.317A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.168A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 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: 1.20 - 1.32: 2276 1.32 - 1.44: 3601 1.44 - 1.57: 7827 1.57 - 1.69: 18 1.69 - 1.81: 122 Bond restraints: 13844 Sorted by residual: bond pdb=" C3' DG D 4 " pdb=" C2' DG D 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG E 4 " pdb=" C2' DG E 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC E 3 " pdb=" C2' DC E 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DC D 3 " pdb=" C2' DC D 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 bond pdb=" C HIS A 598 " pdb=" O HIS A 598 " ideal model delta sigma weight residual 1.232 1.199 0.033 1.20e-02 6.94e+03 7.48e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 17927 1.33 - 2.65: 638 2.65 - 3.98: 135 3.98 - 5.30: 21 5.30 - 6.63: 7 Bond angle restraints: 18728 Sorted by residual: angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" O4 DT D 7 " pdb=" C4 DT D 7 " pdb=" C5 DT D 7 " ideal model delta sigma weight residual 124.90 122.34 2.56 7.00e-01 2.04e+00 1.34e+01 angle pdb=" O4 DT E 7 " pdb=" C4 DT E 7 " pdb=" C5 DT E 7 " ideal model delta sigma weight residual 124.90 122.36 2.54 7.00e-01 2.04e+00 1.32e+01 angle pdb=" C VAL A 731 " pdb=" CA VAL A 731 " pdb=" CB VAL A 731 " ideal model delta sigma weight residual 112.46 108.09 4.37 1.33e+00 5.65e-01 1.08e+01 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7623 17.48 - 34.95: 606 34.95 - 52.42: 149 52.42 - 69.90: 25 69.90 - 87.37: 13 Dihedral angle restraints: 8416 sinusoidal: 3584 harmonic: 4832 Sorted by residual: dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU B 11 " pdb=" C GLU B 11 " pdb=" N PRO B 12 " pdb=" CA PRO B 12 " ideal model delta harmonic sigma weight residual 180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1193 0.031 - 0.062: 572 0.062 - 0.092: 177 0.092 - 0.123: 103 0.123 - 0.154: 13 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CG LEU A 569 " pdb=" CB LEU A 569 " pdb=" CD1 LEU A 569 " pdb=" CD2 LEU A 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CG LEU B 569 " pdb=" CB LEU B 569 " pdb=" CD1 LEU B 569 " pdb=" CD2 LEU B 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 248 " pdb=" N ILE B 248 " pdb=" C ILE B 248 " pdb=" CB ILE B 248 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2055 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 878 " 0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 879 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 879 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 879 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 878 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO B 879 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 879 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 879 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 598 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C HIS A 598 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 598 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 599 " 0.010 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 79 2.55 - 3.14: 10265 3.14 - 3.73: 20108 3.73 - 4.31: 29834 4.31 - 4.90: 50395 Nonbonded interactions: 110681 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MG MG A1002 " model vdw 1.966 2.170 nonbonded pdb=" OE2 GLU B 214 " pdb="MG MG B1002 " model vdw 1.969 2.170 nonbonded pdb=" OE2 GLU A 209 " pdb="MG MG A1002 " model vdw 2.184 2.170 nonbonded pdb=" NH2 ARG B 797 " pdb=" O LYS B 833 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG A 797 " pdb=" O LYS A 833 " model vdw 2.235 3.120 ... (remaining 110676 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.460 Find NCS groups from input model: 0.120 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.500 13852 Z= 0.280 Angle : 0.646 19.254 18734 Z= 0.353 Chirality : 0.043 0.154 2058 Planarity : 0.005 0.093 2372 Dihedral : 13.688 87.374 5292 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.35 (0.21), residues: 1638 helix: 0.35 (0.20), residues: 622 sheet: 1.00 (0.32), residues: 268 loop : -0.01 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 271 TYR 0.013 0.001 TYR A 782 PHE 0.022 0.002 PHE A 218 TRP 0.006 0.001 TRP B 347 HIS 0.010 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (13844) covalent geometry : angle 0.61467 / 0.35 (18728) hydrogen bonds : bond 0.24773 / 16.71 ( 584) hydrogen bonds : angle 7.46007 / 5.19 ( 1656) metal coordination : bond 0.19382 / 10.30 ( 8) metal coordination : angle 11.05661 / 5.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.597 Fit side-chains REVERT: A 280 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8132 (ttpt) REVERT: A 479 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 729 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7434 (mtt90) REVERT: B 729 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7464 (mtt90) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1355 time to fit residues: 43.6097 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS A 580 GLN A 618 ASN A 821 HIS B 222 HIS B 580 GLN B 618 ASN B 821 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121598 restraints weight = 14828.014| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.92 r_work: 0.3263 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13852 Z= 0.151 Angle : 0.570 7.373 18734 Z= 0.305 Chirality : 0.043 0.154 2058 Planarity : 0.005 0.056 2372 Dihedral : 7.799 58.344 1918 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.34 % Allowed : 6.16 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.04 (0.21), residues: 1638 helix: 1.44 (0.20), residues: 636 sheet: 0.89 (0.33), residues: 244 loop : 0.08 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 82 TYR 0.025 0.001 TYR A 681 PHE 0.022 0.002 PHE A 295 TRP 0.005 0.001 TRP B 413 HIS 0.007 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13844) covalent geometry : angle 0.56546 / 0.30 (18728) hydrogen bonds : bond 0.05896 / 4.01 ( 584) hydrogen bonds : angle 5.09322 / 3.48 ( 1656) metal coordination : bond 0.01764 / 1.11 ( 8) metal coordination : angle 4.03292 / 2.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 0.583 Fit side-chains REVERT: A 280 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7984 (ttpt) REVERT: A 288 GLN cc_start: 0.7925 (pm20) cc_final: 0.7713 (pm20) REVERT: B 280 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7491 (ptpt) REVERT: B 288 GLN cc_start: 0.7891 (pm20) cc_final: 0.7686 (pm20) REVERT: B 729 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7810 (mtt90) REVERT: B 787 GLN cc_start: 0.8073 (tt0) cc_final: 0.7811 (mt0) outliers start: 5 outliers final: 3 residues processed: 206 average time/residue: 0.1422 time to fit residues: 41.2953 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 618 ASN A 821 HIS B 580 GLN B 618 ASN B 821 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127754 restraints weight = 14942.163| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.06 r_work: 0.3367 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13852 Z= 0.189 Angle : 0.559 6.181 18734 Z= 0.297 Chirality : 0.043 0.155 2058 Planarity : 0.004 0.042 2372 Dihedral : 7.768 57.672 1918 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.08 % Allowed : 8.46 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1638 helix: 1.54 (0.20), residues: 640 sheet: 0.69 (0.33), residues: 244 loop : -0.08 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 271 TYR 0.018 0.001 TYR B 201 PHE 0.023 0.002 PHE B 295 TRP 0.007 0.001 TRP B 413 HIS 0.011 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (13844) covalent geometry : angle 0.55711 / 0.30 (18728) hydrogen bonds : bond 0.05167 / 3.51 ( 584) hydrogen bonds : angle 4.72063 / 3.25 ( 1656) metal coordination : bond 0.00792 / 0.50 ( 8) metal coordination : angle 2.90177 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.605 Fit side-chains REVERT: A 195 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8080 (mm-40) REVERT: A 256 GLU cc_start: 0.8070 (pt0) cc_final: 0.7844 (pt0) REVERT: A 280 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8019 (ttpt) REVERT: A 836 VAL cc_start: 0.6301 (OUTLIER) cc_final: 0.6049 (t) REVERT: A 881 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7829 (p) REVERT: B 195 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8086 (mm-40) REVERT: B 256 GLU cc_start: 0.8057 (pt0) cc_final: 0.7845 (pt0) REVERT: B 280 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7656 (ptpt) REVERT: B 729 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7838 (mtt90) REVERT: B 787 GLN cc_start: 0.8046 (tt0) cc_final: 0.7739 (mt0) outliers start: 16 outliers final: 11 residues processed: 204 average time/residue: 0.1428 time to fit residues: 41.1216 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 HIS A 658 ASN A 821 HIS B 658 ASN B 821 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.160728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120853 restraints weight = 14899.255| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.93 r_work: 0.3320 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13852 Z= 0.164 Angle : 0.533 5.308 18734 Z= 0.283 Chirality : 0.042 0.147 2058 Planarity : 0.004 0.036 2372 Dihedral : 7.743 58.819 1918 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 9.81 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1638 helix: 1.44 (0.20), residues: 656 sheet: 0.60 (0.33), residues: 244 loop : -0.09 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 82 TYR 0.023 0.001 TYR B 822 PHE 0.026 0.002 PHE B 295 TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (13844) covalent geometry : angle 0.53142 / 0.28 (18728) hydrogen bonds : bond 0.04553 / 3.12 ( 584) hydrogen bonds : angle 4.57221 / 3.17 ( 1656) metal coordination : bond 0.00711 / 0.43 ( 8) metal coordination : angle 2.38180 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 195 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7946 (mm-40) REVERT: A 256 GLU cc_start: 0.8055 (pt0) cc_final: 0.7838 (pt0) REVERT: A 280 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7962 (ttpt) REVERT: A 617 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8249 (ttp80) REVERT: A 836 VAL cc_start: 0.6289 (OUTLIER) cc_final: 0.6040 (t) REVERT: B 280 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7546 (ptpt) REVERT: B 729 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7787 (mtt90) REVERT: B 787 GLN cc_start: 0.8122 (tt0) cc_final: 0.7915 (mt0) outliers start: 26 outliers final: 13 residues processed: 200 average time/residue: 0.1476 time to fit residues: 41.2354 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 776 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 821 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129448 restraints weight = 14926.387| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.03 r_work: 0.3432 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13852 Z= 0.123 Angle : 0.490 5.239 18734 Z= 0.259 Chirality : 0.041 0.146 2058 Planarity : 0.004 0.034 2372 Dihedral : 7.661 59.755 1918 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.10 % Allowed : 9.40 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.04 (0.21), residues: 1638 helix: 1.63 (0.21), residues: 658 sheet: 0.49 (0.34), residues: 242 loop : -0.01 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.018 0.001 TYR A 201 PHE 0.018 0.001 PHE A 295 TRP 0.008 0.001 TRP A 413 HIS 0.007 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13844) covalent geometry : angle 0.48835 / 0.26 (18728) hydrogen bonds : bond 0.04014 / 2.73 ( 584) hydrogen bonds : angle 4.42345 / 3.06 ( 1656) metal coordination : bond 0.00927 / 0.56 ( 8) metal coordination : angle 2.31093 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.518 Fit side-chains REVERT: A 280 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7918 (ttpt) REVERT: A 569 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 617 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8124 (ttp80) REVERT: A 836 VAL cc_start: 0.6238 (OUTLIER) cc_final: 0.5998 (t) REVERT: B 280 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7689 (ptpt) REVERT: B 729 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7858 (mtt90) REVERT: B 787 GLN cc_start: 0.8151 (tt0) cc_final: 0.7908 (mt0) REVERT: B 789 MET cc_start: 0.7400 (mmm) cc_final: 0.7192 (mmm) outliers start: 31 outliers final: 12 residues processed: 203 average time/residue: 0.1504 time to fit residues: 42.3355 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 774 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN A 787 GLN B 821 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120904 restraints weight = 14876.022| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.93 r_work: 0.3325 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13852 Z= 0.157 Angle : 0.517 5.768 18734 Z= 0.271 Chirality : 0.042 0.140 2058 Planarity : 0.004 0.035 2372 Dihedral : 7.669 59.576 1918 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 9.47 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.98 (0.21), residues: 1638 helix: 1.64 (0.21), residues: 656 sheet: 0.49 (0.34), residues: 244 loop : -0.12 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.016 0.001 TYR B 309 PHE 0.028 0.002 PHE B 218 TRP 0.007 0.001 TRP A 413 HIS 0.007 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (13844) covalent geometry : angle 0.51555 / 0.27 (18728) hydrogen bonds : bond 0.04137 / 2.82 ( 584) hydrogen bonds : angle 4.35933 / 3.03 ( 1656) metal coordination : bond 0.00545 / 0.33 ( 8) metal coordination : angle 2.16160 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.565 Fit side-chains REVERT: A 280 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7875 (ttpt) REVERT: A 836 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6055 (t) REVERT: B 280 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7605 (ptpt) REVERT: B 729 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7763 (mtt90) REVERT: B 787 GLN cc_start: 0.8158 (tt0) cc_final: 0.7925 (mt0) outliers start: 28 outliers final: 17 residues processed: 197 average time/residue: 0.1425 time to fit residues: 39.7159 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 821 HIS B 821 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128960 restraints weight = 14844.843| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.02 r_work: 0.3430 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13852 Z= 0.128 Angle : 0.500 6.264 18734 Z= 0.263 Chirality : 0.041 0.187 2058 Planarity : 0.004 0.035 2372 Dihedral : 7.622 59.551 1918 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 9.88 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.96 (0.21), residues: 1638 helix: 1.61 (0.21), residues: 672 sheet: 0.42 (0.34), residues: 242 loop : -0.13 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 271 TYR 0.018 0.001 TYR A 309 PHE 0.032 0.001 PHE B 295 TRP 0.008 0.001 TRP A 413 HIS 0.012 0.001 HIS A 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13844) covalent geometry : angle 0.49835 / 0.26 (18728) hydrogen bonds : bond 0.03881 / 2.65 ( 584) hydrogen bonds : angle 4.29547 / 2.99 ( 1656) metal coordination : bond 0.00712 / 0.43 ( 8) metal coordination : angle 2.10897 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.604 Fit side-chains REVERT: A 272 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7756 (mtm110) REVERT: A 280 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7872 (ttpt) REVERT: A 569 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 786 GLU cc_start: 0.7942 (tp30) cc_final: 0.7734 (mm-30) REVERT: B 729 ARG cc_start: 0.8252 (mtt90) cc_final: 0.7794 (mtt90) outliers start: 31 outliers final: 20 residues processed: 209 average time/residue: 0.1440 time to fit residues: 42.5260 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 821 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 821 HIS B 821 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119874 restraints weight = 14846.831| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.94 r_work: 0.3309 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13852 Z= 0.191 Angle : 0.540 7.041 18734 Z= 0.284 Chirality : 0.043 0.151 2058 Planarity : 0.005 0.049 2372 Dihedral : 7.670 59.898 1918 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.89 % Allowed : 11.03 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.88 (0.21), residues: 1638 helix: 1.60 (0.21), residues: 660 sheet: 0.37 (0.34), residues: 242 loop : -0.21 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 271 TYR 0.015 0.001 TYR B 629 PHE 0.032 0.002 PHE A 295 TRP 0.006 0.001 TRP A 413 HIS 0.012 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (13844) covalent geometry : angle 0.53892 / 0.28 (18728) hydrogen bonds : bond 0.04182 / 2.85 ( 584) hydrogen bonds : angle 4.33436 / 3.01 ( 1656) metal coordination : bond 0.00290 / 0.16 ( 8) metal coordination : angle 2.06716 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.573 Fit side-chains REVERT: A 272 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7800 (mtm110) REVERT: A 280 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7730 (ttpt) REVERT: B 729 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7714 (mtt90) outliers start: 28 outliers final: 21 residues processed: 195 average time/residue: 0.1397 time to fit residues: 38.7689 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 821 HIS B 787 GLN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.171097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134173 restraints weight = 14646.887| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.82 r_work: 0.3447 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13852 Z= 0.139 Angle : 0.521 11.923 18734 Z= 0.274 Chirality : 0.042 0.135 2058 Planarity : 0.004 0.047 2372 Dihedral : 7.646 59.885 1918 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.62 % Allowed : 11.64 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.95 (0.21), residues: 1638 helix: 1.68 (0.21), residues: 660 sheet: 0.35 (0.34), residues: 242 loop : -0.16 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 271 TYR 0.014 0.001 TYR B 629 PHE 0.016 0.001 PHE A 223 TRP 0.008 0.001 TRP A 413 HIS 0.021 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (13844) covalent geometry : angle 0.52017 / 0.27 (18728) hydrogen bonds : bond 0.03930 / 2.68 ( 584) hydrogen bonds : angle 4.30385 / 2.99 ( 1656) metal coordination : bond 0.00554 / 0.33 ( 8) metal coordination : angle 1.98079 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.622 Fit side-chains REVERT: A 272 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7788 (mtm110) REVERT: A 280 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7794 (ttpt) REVERT: A 569 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8262 (mt) REVERT: B 729 ARG cc_start: 0.8320 (mtt90) cc_final: 0.7906 (mtt90) outliers start: 24 outliers final: 20 residues processed: 192 average time/residue: 0.1420 time to fit residues: 38.9125 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 787 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN B 787 GLN B 821 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127216 restraints weight = 15033.064| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.97 r_work: 0.3416 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13852 Z= 0.137 Angle : 0.511 7.069 18734 Z= 0.268 Chirality : 0.041 0.135 2058 Planarity : 0.004 0.046 2372 Dihedral : 7.612 59.801 1918 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.56 % Allowed : 11.77 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.00 (0.21), residues: 1638 helix: 1.74 (0.20), residues: 660 sheet: 0.34 (0.34), residues: 242 loop : -0.14 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 271 TYR 0.022 0.001 TYR B 629 PHE 0.015 0.001 PHE A 223 TRP 0.008 0.001 TRP A 413 HIS 0.011 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13844) covalent geometry : angle 0.50944 / 0.27 (18728) hydrogen bonds : bond 0.03849 / 2.63 ( 584) hydrogen bonds : angle 4.27385 / 2.97 ( 1656) metal coordination : bond 0.00572 / 0.34 ( 8) metal coordination : angle 1.98371 / 1.37 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.557 Fit side-chains REVERT: A 272 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7693 (mtm110) REVERT: A 280 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7780 (ttpt) REVERT: A 569 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 271 ARG cc_start: 0.8969 (mtp-110) cc_final: 0.8685 (ttm-80) REVERT: B 729 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7924 (mtt90) outliers start: 23 outliers final: 21 residues processed: 193 average time/residue: 0.1387 time to fit residues: 38.3201 Evaluate side-chains 201 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 3 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 GLN A 821 HIS B 787 GLN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121390 restraints weight = 14954.545| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3328 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13852 Z= 0.154 Angle : 0.525 7.244 18734 Z= 0.277 Chirality : 0.042 0.135 2058 Planarity : 0.004 0.046 2372 Dihedral : 7.602 59.630 1918 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.69 % Allowed : 12.04 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1638 helix: 1.71 (0.20), residues: 660 sheet: 0.38 (0.34), residues: 244 loop : -0.18 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 271 TYR 0.024 0.001 TYR B 309 PHE 0.014 0.001 PHE A 223 TRP 0.007 0.001 TRP A 413 HIS 0.019 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (13844) covalent geometry : angle 0.52395 / 0.28 (18728) hydrogen bonds : bond 0.03901 / 2.66 ( 584) hydrogen bonds : angle 4.27582 / 2.97 ( 1656) metal coordination : bond 0.00448 / 0.26 ( 8) metal coordination : angle 1.95730 / 1.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3897.48 seconds wall clock time: 67 minutes 27.01 seconds (4047.01 seconds total)