Starting phenix.real_space_refine on Thu Feb 15 21:55:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_14692.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_14692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_14692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_14692.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zes_14692/02_2024/7zes_14692.pdb" } 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 Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.46, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.04 Conformation dependent library (CDL) restraints added in 2.4 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: 1.77 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: 4.75 Time building geometry restraints manager: 5.43 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: 99.84 - 106.69: 477 106.69 - 113.54: 7502 113.54 - 120.39: 5214 120.39 - 127.24: 5384 127.24 - 134.09: 151 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 2.520 nonbonded pdb=" NH2 ARG A 797 " pdb=" O LYS A 833 " model vdw 2.235 2.520 ... (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 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: 1.590 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: 7.510 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.760 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- 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 : 0.005 0.052 13844 Z= 0.316 Angle : 0.609 6.626 18728 Z= 0.336 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.664 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: 0.2925 time to fit residues: 92.2280 Evaluate side-chains 190 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13844 Z= 0.221 Angle : 0.527 5.473 18728 Z= 0.277 Chirality : 0.042 0.152 2058 Planarity : 0.004 0.060 2372 Dihedral : 7.721 56.712 1918 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.41 % Allowed : 5.55 % Favored : 94.05 % 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: 1.05 (0.21), residues: 1638 helix: 1.42 (0.20), residues: 640 sheet: 0.97 (0.33), residues: 252 loop : 0.05 (0.24), residues: 746 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 0.023 0.002 PHE A 295 TYR 0.024 0.001 TYR A 681 ARG 0.005 0.000 ARG B 271 *********************** 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 219 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 1.547 Fit side-chains REVERT: A 280 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8137 (ttpt) REVERT: A 288 GLN cc_start: 0.7782 (pm20) cc_final: 0.7476 (pm20) REVERT: B 280 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7629 (ptpt) REVERT: B 288 GLN cc_start: 0.7723 (pm20) cc_final: 0.7387 (pm20) REVERT: B 729 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7473 (mtt90) outliers start: 6 outliers final: 2 residues processed: 218 average time/residue: 0.3056 time to fit residues: 92.9473 Evaluate side-chains 190 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 82 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 147 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A 821 HIS B 618 ASN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13844 Z= 0.208 Angle : 0.494 5.266 18728 Z= 0.258 Chirality : 0.041 0.141 2058 Planarity : 0.004 0.043 2372 Dihedral : 7.573 57.517 1918 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.08 % Allowed : 7.78 % Favored : 91.14 % 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: 1.12 (0.21), residues: 1638 helix: 1.62 (0.21), residues: 656 sheet: 0.77 (0.34), residues: 242 loop : 0.02 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 413 HIS 0.011 0.001 HIS B 821 PHE 0.026 0.001 PHE B 295 TYR 0.018 0.001 TYR B 201 ARG 0.005 0.000 ARG A 271 *********************** 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 211 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.598 Fit side-chains REVERT: A 288 GLN cc_start: 0.7741 (pm20) cc_final: 0.7423 (pm20) REVERT: A 617 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7729 (ttp80) REVERT: A 836 VAL cc_start: 0.6334 (OUTLIER) cc_final: 0.6075 (t) REVERT: B 288 GLN cc_start: 0.7690 (pm20) cc_final: 0.7359 (pm20) REVERT: B 309 TYR cc_start: 0.8063 (t80) cc_final: 0.7858 (t80) REVERT: B 729 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7425 (mtt90) outliers start: 16 outliers final: 9 residues processed: 207 average time/residue: 0.3067 time to fit residues: 88.0810 Evaluate side-chains 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 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 702 LEU 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 147 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.192 Angle : 0.481 6.214 18728 Z= 0.252 Chirality : 0.041 0.146 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.503 58.334 1918 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.49 % Allowed : 9.13 % Favored : 89.38 % 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: 1.08 (0.21), residues: 1638 helix: 1.61 (0.21), residues: 670 sheet: 0.70 (0.34), residues: 242 loop : -0.04 (0.24), residues: 726 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 0.016 0.001 PHE A 223 TYR 0.017 0.001 TYR A 201 ARG 0.006 0.000 ARG B 778 *********************** 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 211 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.646 Fit side-chains REVERT: A 288 GLN cc_start: 0.7736 (pm20) cc_final: 0.7424 (pm20) REVERT: A 569 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8031 (mt) REVERT: B 288 GLN cc_start: 0.7702 (pm20) cc_final: 0.7370 (pm20) REVERT: B 729 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7426 (mtt90) outliers start: 22 outliers final: 13 residues processed: 200 average time/residue: 0.3233 time to fit residues: 91.3663 Evaluate side-chains 194 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 313 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 821 HIS B 787 GLN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.191 Angle : 0.474 5.319 18728 Z= 0.248 Chirality : 0.040 0.155 2058 Planarity : 0.004 0.035 2372 Dihedral : 7.458 59.282 1918 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.69 % Allowed : 9.61 % Favored : 88.70 % 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: 1.12 (0.21), residues: 1638 helix: 1.70 (0.20), residues: 670 sheet: 0.68 (0.34), residues: 242 loop : -0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.013 0.001 PHE A 223 TYR 0.015 0.001 TYR A 201 ARG 0.007 0.000 ARG A 778 *********************** 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 216 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.623 Fit side-chains REVERT: A 272 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7706 (mtm110) REVERT: A 569 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 836 VAL cc_start: 0.6299 (OUTLIER) cc_final: 0.6042 (t) REVERT: B 729 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7385 (mtt90) outliers start: 25 outliers final: 12 residues processed: 205 average time/residue: 0.2966 time to fit residues: 85.4359 Evaluate side-chains 194 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 836 VAL 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 533 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 787 GLN A 821 HIS B 658 ASN B 787 GLN B 821 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13844 Z= 0.156 Angle : 0.464 5.488 18728 Z= 0.242 Chirality : 0.040 0.136 2058 Planarity : 0.004 0.035 2372 Dihedral : 7.388 59.925 1918 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.83 % Allowed : 10.49 % Favored : 87.69 % 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: 1.26 (0.21), residues: 1638 helix: 1.90 (0.21), residues: 670 sheet: 0.68 (0.35), residues: 242 loop : -0.05 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.010 0.001 HIS B 821 PHE 0.020 0.001 PHE B 218 TYR 0.014 0.001 TYR A 201 ARG 0.008 0.000 ARG B 778 *********************** 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 218 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.577 Fit side-chains REVERT: A 272 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7567 (mtm110) REVERT: A 569 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 777 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 836 VAL cc_start: 0.6289 (OUTLIER) cc_final: 0.6031 (t) REVERT: B 729 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7392 (mtt90) REVERT: B 789 MET cc_start: 0.7382 (mmm) cc_final: 0.7046 (mmm) outliers start: 27 outliers final: 15 residues processed: 203 average time/residue: 0.2834 time to fit residues: 81.5323 Evaluate side-chains 201 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 697 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 777 LEU 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 533 MET 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 787 GLN Chi-restraints excluded: chain B residue 821 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS A 787 GLN A 821 HIS B 787 GLN B 821 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.175 Angle : 0.469 5.676 18728 Z= 0.243 Chirality : 0.040 0.135 2058 Planarity : 0.004 0.035 2372 Dihedral : 7.351 59.130 1918 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.76 % Allowed : 10.69 % 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: 1.29 (0.21), residues: 1638 helix: 1.93 (0.20), residues: 670 sheet: 0.66 (0.35), residues: 242 loop : -0.03 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.012 0.001 HIS A 821 PHE 0.015 0.001 PHE A 223 TYR 0.017 0.001 TYR A 309 ARG 0.007 0.000 ARG A 271 *********************** 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 219 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.576 Fit side-chains REVERT: A 272 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7538 (mtm110) REVERT: A 569 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 271 ARG cc_start: 0.9031 (mtp-110) cc_final: 0.8642 (ttm-80) REVERT: B 272 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7456 (mtm110) REVERT: B 729 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7413 (mtt90) REVERT: B 789 MET cc_start: 0.7442 (mmm) cc_final: 0.7108 (mmm) outliers start: 26 outliers final: 16 residues processed: 204 average time/residue: 0.2958 time to fit residues: 85.1736 Evaluate side-chains 201 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 280 LYS 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 748 ILE Chi-restraints excluded: chain A residue 774 GLN 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 533 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS A 821 HIS B 217 GLN B 580 GLN B 658 ASN B 787 GLN B 821 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.201 Angle : 0.495 7.136 18728 Z= 0.256 Chirality : 0.041 0.139 2058 Planarity : 0.004 0.034 2372 Dihedral : 7.348 57.154 1918 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.83 % Allowed : 11.30 % Favored : 86.87 % 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: 1.24 (0.21), residues: 1638 helix: 1.89 (0.20), residues: 670 sheet: 0.64 (0.35), residues: 242 loop : -0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.008 0.001 HIS A 821 PHE 0.015 0.001 PHE B 223 TYR 0.015 0.001 TYR A 309 ARG 0.009 0.000 ARG A 271 *********************** 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 213 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.662 Fit side-chains REVERT: A 272 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7498 (mtm110) REVERT: A 482 GLU cc_start: 0.7002 (tp30) cc_final: 0.6706 (tm-30) REVERT: A 569 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8056 (mt) REVERT: B 271 ARG cc_start: 0.9005 (mtp-110) cc_final: 0.8595 (ttm-80) REVERT: B 272 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7442 (mtm110) REVERT: B 482 GLU cc_start: 0.7007 (tp30) cc_final: 0.6711 (tm-30) REVERT: B 729 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7434 (mtt90) REVERT: B 789 MET cc_start: 0.7379 (mmm) cc_final: 0.6776 (mmm) outliers start: 27 outliers final: 21 residues processed: 198 average time/residue: 0.3090 time to fit residues: 86.3364 Evaluate side-chains 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 280 LYS 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 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 280 LYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 658 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS A 821 HIS B 787 GLN B 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13844 Z= 0.212 Angle : 0.505 9.346 18728 Z= 0.260 Chirality : 0.041 0.138 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.338 56.290 1918 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.56 % Allowed : 11.43 % Favored : 87.01 % 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: 1.23 (0.21), residues: 1638 helix: 1.89 (0.20), residues: 670 sheet: 0.61 (0.35), residues: 242 loop : -0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.013 0.001 HIS B 821 PHE 0.014 0.001 PHE B 223 TYR 0.021 0.001 TYR B 309 ARG 0.008 0.000 ARG A 271 *********************** 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 212 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7739 (mtm110) cc_final: 0.7512 (mtm110) REVERT: A 569 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8047 (mt) REVERT: B 271 ARG cc_start: 0.8955 (mtp-110) cc_final: 0.8608 (ttm-80) REVERT: B 272 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7429 (mtm110) REVERT: B 482 GLU cc_start: 0.6985 (tp30) cc_final: 0.6740 (tm-30) REVERT: B 729 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7408 (mtt90) outliers start: 23 outliers final: 21 residues processed: 198 average time/residue: 0.3136 time to fit residues: 87.9095 Evaluate side-chains 205 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 280 LYS 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 612 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN 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 405 LEU Chi-restraints excluded: chain B residue 533 MET 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 787 GLN Chi-restraints excluded: chain B residue 791 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 chunk 108 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS B 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13844 Z= 0.303 Angle : 0.555 10.855 18728 Z= 0.286 Chirality : 0.043 0.147 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.470 54.354 1918 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.76 % Allowed : 11.43 % Favored : 86.81 % 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: 0.99 (0.21), residues: 1638 helix: 1.69 (0.20), residues: 668 sheet: 0.48 (0.34), residues: 242 loop : -0.20 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 769 HIS 0.004 0.001 HIS A 420 PHE 0.014 0.002 PHE B 223 TYR 0.021 0.001 TYR B 309 ARG 0.008 0.000 ARG A 271 ********************** 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 208 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8566 (ttm-80) REVERT: A 272 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7516 (mtm110) REVERT: B 271 ARG cc_start: 0.8966 (mtp-110) cc_final: 0.8606 (ttm-80) REVERT: B 272 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7459 (mtm110) REVERT: B 482 GLU cc_start: 0.7018 (tp30) cc_final: 0.6712 (tm-30) REVERT: B 729 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7411 (mtt90) outliers start: 26 outliers final: 22 residues processed: 197 average time/residue: 0.2936 time to fit residues: 81.7384 Evaluate side-chains 200 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 280 LYS 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 612 ILE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 GLN 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 405 LEU Chi-restraints excluded: chain B residue 533 MET 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 787 GLN Chi-restraints excluded: chain B residue 791 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 HIS B 821 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130340 restraints weight = 14865.745| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13844 Z= 0.212 Angle : 0.509 10.920 18728 Z= 0.263 Chirality : 0.041 0.135 2058 Planarity : 0.004 0.037 2372 Dihedral : 7.394 54.073 1918 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.42 % Allowed : 11.57 % Favored : 87.01 % 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: 1.08 (0.21), residues: 1638 helix: 1.76 (0.21), residues: 672 sheet: 0.50 (0.35), residues: 242 loop : -0.13 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.007 0.001 HIS B 821 PHE 0.023 0.001 PHE A 218 TYR 0.018 0.001 TYR B 309 ARG 0.008 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.02 seconds wall clock time: 56 minutes 41.12 seconds (3401.12 seconds total)