Starting phenix.real_space_refine on Thu Jul 31 15:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zes_14692/07_2025/7zes_14692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zes_14692/07_2025/7zes_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_14692/07_2025/7zes_14692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zes_14692/07_2025/7zes_14692.map" model { file = "/net/cci-nas-00/data/ceres_data/7zes_14692/07_2025/7zes_14692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zes_14692/07_2025/7zes_14692.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.78, per 1000 atoms: 0.65 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.59 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: 4.65 Time building geometry restraints manager: 3.40 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=" 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 bond pdb=" N ARG B 124 " pdb=" CA ARG B 124 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.79e+00 bond pdb=" N ARG A 124 " pdb=" CA ARG A 124 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.65e+00 bond pdb=" C VAL A 597 " pdb=" N HIS A 598 " ideal model delta sigma weight residual 1.329 1.305 0.024 1.51e-02 4.39e+03 2.51e+00 bond pdb=" CD2 HIS A 598 " pdb=" NE2 HIS A 598 " ideal model delta sigma weight residual 1.374 1.357 0.017 1.10e-02 8.26e+03 2.31e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 17955 1.33 - 2.65: 612 2.65 - 3.98: 133 3.98 - 5.30: 21 5.30 - 6.63: 7 Bond angle restraints: 18728 Sorted by residual: 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 angle pdb=" C VAL B 731 " pdb=" CA VAL B 731 " pdb=" CB VAL B 731 " ideal model delta sigma weight residual 112.46 108.11 4.35 1.33e+00 5.65e-01 1.07e+01 angle pdb=" N ILE A 193 " pdb=" CA ILE A 193 " pdb=" C ILE A 193 " ideal model delta sigma weight residual 112.35 108.28 4.07 1.41e+00 5.03e-01 8.32e+00 angle pdb=" CA HIS A 598 " pdb=" CB HIS A 598 " pdb=" CG HIS A 598 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.28e+00 angle pdb=" CA MET A 830 " pdb=" CB MET A 830 " pdb=" CG MET A 830 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.14e+00 ... (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: 1205 0.031 - 0.062: 570 0.062 - 0.092: 169 0.092 - 0.123: 101 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' } 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: 2.550 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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= 0.263 Angle : 0.641 19.254 18734 Z= 0.340 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 347 HIS 0.010 0.001 HIS A 598 PHE 0.022 0.002 PHE A 218 TYR 0.013 0.001 TYR A 782 ARG 0.010 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.24773 ( 584) hydrogen bonds : angle 7.46007 ( 1656) metal coordination : bond 0.19382 ( 8) metal coordination : angle 11.05661 ( 6) covalent geometry : bond 0.00483 (13844) covalent geometry : angle 0.60937 (18728) *********************** 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 : 1.506 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: 0.2863 time to fit residues: 90.7227 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 : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 264 ASN A 580 GLN A 618 ASN A 821 HIS B 222 HIS B 264 ASN B 580 GLN B 618 ASN B 821 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123281 restraints weight = 14725.096| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.05 r_work: 0.3259 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13852 Z= 0.157 Angle : 0.550 6.246 18734 Z= 0.289 Chirality : 0.042 0.154 2058 Planarity : 0.005 0.059 2372 Dihedral : 7.841 56.507 1918 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.41 % Allowed : 5.95 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 640 sheet: 0.87 (0.33), residues: 244 loop : 0.06 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 413 HIS 0.008 0.001 HIS B 821 PHE 0.022 0.002 PHE B 295 TYR 0.021 0.001 TYR A 681 ARG 0.005 0.000 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 584) hydrogen bonds : angle 4.88309 ( 1656) metal coordination : bond 0.01135 ( 8) metal coordination : angle 3.52109 ( 6) covalent geometry : bond 0.00365 (13844) covalent geometry : angle 0.54597 (18728) *********************** 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 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 1.481 Fit side-chains REVERT: A 280 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8048 (ttpt) REVERT: A 288 GLN cc_start: 0.7957 (pm20) cc_final: 0.7733 (pm20) REVERT: B 258 LEU cc_start: 0.8329 (mt) cc_final: 0.8100 (mp) REVERT: B 280 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7630 (ptpt) REVERT: B 288 GLN cc_start: 0.7936 (pm20) cc_final: 0.7695 (pm20) REVERT: B 729 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7889 (mtt90) REVERT: B 787 GLN cc_start: 0.8075 (tt0) cc_final: 0.7822 (mt0) outliers start: 6 outliers final: 2 residues processed: 213 average time/residue: 0.3105 time to fit residues: 92.9203 Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 618 ASN A 821 HIS B 618 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 = 0.4001 r_free = 0.4001 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127764 restraints weight = 15082.968| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.07 r_work: 0.3332 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13852 Z= 0.182 Angle : 0.544 5.623 18734 Z= 0.284 Chirality : 0.043 0.171 2058 Planarity : 0.005 0.045 2372 Dihedral : 7.798 55.487 1918 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 7.92 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1638 helix: 1.45 (0.21), residues: 656 sheet: 0.68 (0.33), residues: 244 loop : -0.04 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 413 HIS 0.011 0.001 HIS A 821 PHE 0.026 0.002 PHE B 295 TYR 0.018 0.001 TYR B 201 ARG 0.005 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 584) hydrogen bonds : angle 4.53630 ( 1656) metal coordination : bond 0.00468 ( 8) metal coordination : angle 2.68032 ( 6) covalent geometry : bond 0.00444 (13844) covalent geometry : angle 0.54240 (18728) *********************** 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 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.420 Fit side-chains REVERT: A 195 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 280 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7915 (ttpt) REVERT: A 288 GLN cc_start: 0.8007 (pm20) cc_final: 0.7799 (pm20) REVERT: A 836 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.6103 (t) REVERT: B 280 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7617 (ptpt) REVERT: B 288 GLN cc_start: 0.7969 (pm20) cc_final: 0.7759 (pm20) REVERT: B 729 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7829 (mtt90) REVERT: B 786 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 787 GLN cc_start: 0.8143 (tt0) cc_final: 0.7908 (mt0) REVERT: B 789 MET cc_start: 0.7713 (mmm) cc_final: 0.7312 (mmm) REVERT: B 830 MET cc_start: 0.7326 (tpp) cc_final: 0.7109 (ttt) outliers start: 17 outliers final: 10 residues processed: 200 average time/residue: 0.3053 time to fit residues: 84.7486 Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 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 66 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 821 HIS B 580 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 = 0.3845 r_free = 0.3845 target = 0.159215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119168 restraints weight = 14865.498| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.93 r_work: 0.3303 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13852 Z= 0.195 Angle : 0.546 5.774 18734 Z= 0.284 Chirality : 0.043 0.157 2058 Planarity : 0.004 0.041 2372 Dihedral : 7.776 56.011 1918 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.62 % Allowed : 9.54 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1638 helix: 1.46 (0.21), residues: 658 sheet: 0.52 (0.34), residues: 244 loop : -0.16 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.006 0.001 HIS B 821 PHE 0.027 0.002 PHE B 295 TYR 0.014 0.001 TYR B 201 ARG 0.006 0.001 ARG A 778 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 584) hydrogen bonds : angle 4.46142 ( 1656) metal coordination : bond 0.00314 ( 8) metal coordination : angle 2.33995 ( 6) covalent geometry : bond 0.00480 (13844) covalent geometry : angle 0.54448 (18728) *********************** 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 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7815 (ttpt) REVERT: B 280 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7660 (ptpt) REVERT: B 729 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7768 (mtt90) REVERT: B 786 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 830 MET cc_start: 0.7383 (tpp) cc_final: 0.7122 (ttt) REVERT: B 836 VAL cc_start: 0.6434 (OUTLIER) cc_final: 0.6220 (t) outliers start: 24 outliers final: 15 residues processed: 207 average time/residue: 0.3108 time to fit residues: 89.5245 Evaluate side-chains 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 821 HIS 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 821 HIS Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 23 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3999 r_free = 0.3999 target = 0.167313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126496 restraints weight = 14891.372| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.05 r_work: 0.3357 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13852 Z= 0.178 Angle : 0.531 6.183 18734 Z= 0.276 Chirality : 0.042 0.152 2058 Planarity : 0.004 0.038 2372 Dihedral : 7.724 56.400 1918 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.83 % Allowed : 9.95 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 668 sheet: 0.40 (0.34), residues: 242 loop : -0.24 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.008 0.001 HIS B 821 PHE 0.029 0.002 PHE A 295 TYR 0.015 0.001 TYR A 309 ARG 0.006 0.000 ARG B 778 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 584) hydrogen bonds : angle 4.38754 ( 1656) metal coordination : bond 0.00291 ( 8) metal coordination : angle 2.24730 ( 6) covalent geometry : bond 0.00435 (13844) covalent geometry : angle 0.52914 (18728) *********************** 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 218 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7746 (mtm110) REVERT: A 280 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7832 (ttpt) REVERT: A 786 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7794 (tp30) REVERT: A 836 VAL cc_start: 0.6316 (OUTLIER) cc_final: 0.6066 (t) REVERT: B 280 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7649 (ptpt) REVERT: B 729 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7823 (mtt90) REVERT: B 830 MET cc_start: 0.7571 (tpp) cc_final: 0.7112 (ttt) REVERT: B 836 VAL cc_start: 0.6429 (OUTLIER) cc_final: 0.6227 (t) outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 0.2952 time to fit residues: 86.0289 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 313 CYS 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 821 HIS 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 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 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 157 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3859 r_free = 0.3859 target = 0.160396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120900 restraints weight = 14989.368| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.91 r_work: 0.3323 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2029 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= 0.142 Angle : 0.508 5.912 18734 Z= 0.265 Chirality : 0.041 0.134 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.626 55.949 1918 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.03 % Allowed : 10.42 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1638 helix: 1.55 (0.21), residues: 670 sheet: 0.39 (0.34), residues: 246 loop : -0.24 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.009 0.001 HIS B 821 PHE 0.029 0.001 PHE B 295 TYR 0.016 0.001 TYR B 201 ARG 0.008 0.000 ARG B 778 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 584) hydrogen bonds : angle 4.28242 ( 1656) metal coordination : bond 0.00432 ( 8) metal coordination : angle 2.23645 ( 6) covalent geometry : bond 0.00342 (13844) covalent geometry : angle 0.50700 (18728) *********************** 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 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7814 (mtm110) REVERT: A 280 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7790 (ttpt) REVERT: A 836 VAL cc_start: 0.6326 (OUTLIER) cc_final: 0.6074 (t) REVERT: B 569 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 729 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7845 (mtt90) REVERT: B 786 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7751 (tp30) REVERT: B 830 MET cc_start: 0.7568 (tpp) cc_final: 0.7228 (ttt) REVERT: B 836 VAL cc_start: 0.6407 (OUTLIER) cc_final: 0.6192 (t) outliers start: 30 outliers final: 21 residues processed: 206 average time/residue: 0.2906 time to fit residues: 84.8156 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 313 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 791 CYS 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 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 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 Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 158 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 HIS 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 = 0.4006 r_free = 0.4006 target = 0.168058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127310 restraints weight = 15012.436| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.04 r_work: 0.3408 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2072 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= 0.160 Angle : 0.523 8.779 18734 Z= 0.269 Chirality : 0.042 0.135 2058 Planarity : 0.004 0.036 2372 Dihedral : 7.603 56.276 1918 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.89 % Allowed : 11.16 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1638 helix: 1.54 (0.20), residues: 670 sheet: 0.32 (0.34), residues: 244 loop : -0.25 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.011 0.001 HIS B 821 PHE 0.029 0.001 PHE A 295 TYR 0.018 0.001 TYR A 309 ARG 0.007 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 584) hydrogen bonds : angle 4.28525 ( 1656) metal coordination : bond 0.00317 ( 8) metal coordination : angle 2.05729 ( 6) covalent geometry : bond 0.00391 (13844) covalent geometry : angle 0.52179 (18728) *********************** 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 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7716 (mtm110) REVERT: A 280 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7858 (ttpt) REVERT: A 482 GLU cc_start: 0.7621 (tp30) cc_final: 0.6902 (tm-30) REVERT: B 729 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7843 (mtt90) REVERT: B 830 MET cc_start: 0.7545 (tpp) cc_final: 0.7162 (ttt) outliers start: 28 outliers final: 22 residues processed: 204 average time/residue: 0.2832 time to fit residues: 82.4328 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 313 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 821 HIS 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 610 MET Chi-restraints excluded: chain B residue 612 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 Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 HIS 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 = 0.3867 r_free = 0.3867 target = 0.161114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121960 restraints weight = 14907.476| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.90 r_work: 0.3333 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13852 Z= 0.134 Angle : 0.515 6.500 18734 Z= 0.270 Chirality : 0.041 0.144 2058 Planarity : 0.004 0.036 2372 Dihedral : 7.525 55.913 1918 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.83 % Allowed : 11.57 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1638 helix: 1.64 (0.20), residues: 672 sheet: 0.29 (0.34), residues: 248 loop : -0.20 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.011 0.001 HIS A 821 PHE 0.021 0.001 PHE A 295 TYR 0.020 0.001 TYR B 629 ARG 0.008 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 584) hydrogen bonds : angle 4.24468 ( 1656) metal coordination : bond 0.00488 ( 8) metal coordination : angle 2.07055 ( 6) covalent geometry : bond 0.00320 (13844) covalent geometry : angle 0.51360 (18728) *********************** 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 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7660 (mtm110) REVERT: A 280 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7831 (ttpt) REVERT: A 482 GLU cc_start: 0.7612 (tp30) cc_final: 0.6913 (tm-30) REVERT: B 271 ARG cc_start: 0.9010 (mtp-110) cc_final: 0.8640 (ttm-80) REVERT: B 272 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7562 (mtm110) REVERT: B 482 GLU cc_start: 0.7721 (tp30) cc_final: 0.6961 (tm-30) REVERT: B 569 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8224 (mt) REVERT: B 729 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7794 (mtt90) REVERT: B 830 MET cc_start: 0.7496 (tpp) cc_final: 0.7199 (ttt) outliers start: 27 outliers final: 22 residues processed: 203 average time/residue: 0.3054 time to fit residues: 87.3902 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 301 ASN Chi-restraints excluded: chain A residue 313 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 791 CYS 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 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 HIS B 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129293 restraints weight = 14898.693| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.93 r_work: 0.3433 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13852 Z= 0.146 Angle : 0.526 7.483 18734 Z= 0.272 Chirality : 0.041 0.156 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.520 56.162 1918 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.76 % Allowed : 11.71 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1638 helix: 1.57 (0.20), residues: 680 sheet: 0.41 (0.34), residues: 244 loop : -0.26 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.010 0.001 HIS A 821 PHE 0.022 0.001 PHE A 295 TYR 0.022 0.001 TYR B 309 ARG 0.008 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 584) hydrogen bonds : angle 4.23908 ( 1656) metal coordination : bond 0.00365 ( 8) metal coordination : angle 2.00059 ( 6) covalent geometry : bond 0.00352 (13844) covalent geometry : angle 0.52456 (18728) *********************** 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 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7647 (mtm110) REVERT: A 280 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7792 (ttpt) REVERT: A 482 GLU cc_start: 0.7599 (tp30) cc_final: 0.6899 (tm-30) REVERT: B 271 ARG cc_start: 0.9015 (mtp-110) cc_final: 0.8616 (ttm-80) REVERT: B 272 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7550 (mtm110) REVERT: B 482 GLU cc_start: 0.7633 (tp30) cc_final: 0.6932 (tm-30) REVERT: B 569 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 729 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 830 MET cc_start: 0.7458 (tpp) cc_final: 0.7163 (ttt) outliers start: 26 outliers final: 21 residues processed: 201 average time/residue: 0.2969 time to fit residues: 84.3052 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 301 ASN Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 317 VAL 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 791 CYS 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 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN B 821 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121244 restraints weight = 14829.658| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.94 r_work: 0.3329 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13852 Z= 0.140 Angle : 0.520 6.992 18734 Z= 0.271 Chirality : 0.041 0.142 2058 Planarity : 0.004 0.040 2372 Dihedral : 7.489 56.230 1918 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.62 % Allowed : 11.84 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1638 helix: 1.62 (0.20), residues: 680 sheet: 0.28 (0.34), residues: 248 loop : -0.20 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.009 0.001 HIS B 821 PHE 0.028 0.001 PHE A 295 TYR 0.023 0.001 TYR A 309 ARG 0.009 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 584) hydrogen bonds : angle 4.22037 ( 1656) metal coordination : bond 0.00417 ( 8) metal coordination : angle 2.00983 ( 6) covalent geometry : bond 0.00335 (13844) covalent geometry : angle 0.51883 (18728) ********************** 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 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7665 (mtm110) REVERT: A 280 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7733 (ttpt) REVERT: A 482 GLU cc_start: 0.7642 (tp30) cc_final: 0.6885 (tm-30) REVERT: A 697 ILE cc_start: 0.8741 (mm) cc_final: 0.8514 (mt) REVERT: B 271 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8602 (ttm-80) REVERT: B 272 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7553 (mtm110) REVERT: B 482 GLU cc_start: 0.7621 (tp30) cc_final: 0.6838 (tm-30) REVERT: B 569 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 729 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7813 (mtt90) REVERT: B 830 MET cc_start: 0.7477 (tpp) cc_final: 0.7157 (ttt) outliers start: 24 outliers final: 19 residues processed: 200 average time/residue: 0.2943 time to fit residues: 83.6118 Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 313 CYS Chi-restraints excluded: chain A residue 317 VAL 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 791 CYS 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 748 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120330 restraints weight = 15043.139| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.96 r_work: 0.3298 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13852 Z= 0.202 Angle : 0.571 7.198 18734 Z= 0.294 Chirality : 0.043 0.157 2058 Planarity : 0.004 0.043 2372 Dihedral : 7.625 58.020 1918 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.62 % Allowed : 12.04 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 678 sheet: 0.26 (0.32), residues: 260 loop : -0.29 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS B 420 PHE 0.013 0.001 PHE A 223 TYR 0.023 0.001 TYR A 309 ARG 0.008 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 584) hydrogen bonds : angle 4.33766 ( 1656) metal coordination : bond 0.00426 ( 8) metal coordination : angle 1.84648 ( 6) covalent geometry : bond 0.00497 (13844) covalent geometry : angle 0.56973 (18728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7492.49 seconds wall clock time: 128 minutes 55.15 seconds (7735.15 seconds total)