Starting phenix.real_space_refine on Fri Jul 3 13:33:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.map" model { file = "/net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erf_19914/07_2026/9erf_19914.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.089 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: 8 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 52 5.49 5 Mg 3 5.21 5 S 86 5.16 5 C 9007 2.51 5 N 2530 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14459 Number of models: 1 Model: "" Number of chains: 7 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: "T" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1038 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 22, 'rna3p_pyr': 16} Link IDs: {'rna2p': 10, 'rna3p': 37} Chain breaks: 1 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 74.655 55.921 71.035 1.00 50.44 S ATOM 2310 SG CYS A 321 74.308 54.164 67.659 1.00 41.58 S ATOM 2316 SG CYS A 322 71.867 56.853 68.688 1.00 40.63 S ATOM 8698 SG CYS B 287 23.276 69.151 70.509 1.00 56.23 S ATOM 8975 SG CYS B 321 23.476 69.809 66.765 1.00 41.42 S ATOM 8981 SG CYS B 322 25.955 67.477 68.431 1.00 43.03 S Time building chain proxies: 2.96, per 1000 atoms: 0.20 Number of scatterers: 14459 At special positions: 0 Unit cell: (95.237, 131.587, 147.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 3 24.99 S 86 16.00 P 52 15.00 Mg 3 11.99 O 2776 8.00 N 2530 7.00 C 9007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 626.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " 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: 71 helices and 18 sheets defined 45.9% alpha, 19.1% beta 19 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.649A pdb=" N SER A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.629A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (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 Processing helix chain 'A' and resid 266 through 281 removed outlier: 3.568A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 398 removed outlier: 5.809A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) 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 482 through 501 Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.619A pdb=" N GLY A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' 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 642 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 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.539A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 763' 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 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 840 through 844 removed outlier: 3.932A pdb=" N MET A 844 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.582A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (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 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.580A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 398 removed outlier: 5.799A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) 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 482 through 501 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.620A pdb=" N GLY B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 Processing helix chain 'B' and resid 587 through 592 removed outlier: 4.162A pdb=" N LYS B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) 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 642 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 removed outlier: 3.981A pdb=" N ARG B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.551A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.643A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (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 816 through 831 removed outlier: 4.169A pdb=" N GLU B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.861A pdb=" N MET B 844 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 removed outlier: 4.032A pdb=" N VAL B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.320A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.287A 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: 6.512A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.512A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.594A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.469A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.658A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.145A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 810 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 868 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 812 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.353A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.527A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.527A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.558A pdb=" N ALA B 323 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.377A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.267A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.055A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 810 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE B 868 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 812 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2222 1.30 - 1.43: 4157 1.43 - 1.56: 8267 1.56 - 1.69: 103 1.69 - 1.82: 122 Bond restraints: 14871 Sorted by residual: bond pdb=" CA ASP B 252 " pdb=" C ASP B 252 " ideal model delta sigma weight residual 1.524 1.401 0.122 1.29e-02 6.01e+03 8.98e+01 bond pdb=" CA GLN B 217 " pdb=" C GLN B 217 " ideal model delta sigma weight residual 1.526 1.461 0.065 1.08e-02 8.57e+03 3.59e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.30e-02 5.92e+03 2.39e+01 bond pdb=" C VAL A 250 " pdb=" O VAL A 250 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.04e-02 9.25e+03 1.96e+01 bond pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.40e-02 5.10e+03 1.84e+01 ... (remaining 14866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 20018 2.07 - 4.13: 285 4.13 - 6.20: 25 6.20 - 8.27: 2 8.27 - 10.33: 3 Bond angle restraints: 20333 Sorted by residual: angle pdb=" N LYS A 253 " pdb=" CA LYS A 253 " pdb=" C LYS A 253 " ideal model delta sigma weight residual 113.97 104.67 9.30 1.28e+00 6.10e-01 5.28e+01 angle pdb=" C ASP B 252 " pdb=" CA ASP B 252 " pdb=" CB ASP B 252 " ideal model delta sigma weight residual 110.85 100.52 10.33 1.70e+00 3.46e-01 3.69e+01 angle pdb=" C ASP A 252 " pdb=" CA ASP A 252 " pdb=" CB ASP A 252 " ideal model delta sigma weight residual 110.56 119.74 -9.18 1.69e+00 3.50e-01 2.95e+01 angle pdb=" CA ASP A 252 " pdb=" CB ASP A 252 " pdb=" CG ASP A 252 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.91e+01 angle pdb=" CA PRO A 695 " pdb=" N PRO A 695 " pdb=" CD PRO A 695 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 ... (remaining 20328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 8759 33.95 - 67.90: 339 67.90 - 101.85: 33 101.85 - 135.80: 2 135.80 - 169.75: 2 Dihedral angle restraints: 9135 sinusoidal: 4303 harmonic: 4832 Sorted by residual: dihedral pdb=" C4' G T 7 " pdb=" C3' G T 7 " pdb=" C2' G T 7 " pdb=" C1' G T 7 " ideal model delta sinusoidal sigma weight residual -35.00 33.26 -68.26 1 8.00e+00 1.56e-02 9.45e+01 dihedral pdb=" C5' G T 7 " pdb=" C4' G T 7 " pdb=" C3' G T 7 " pdb=" O3' G T 7 " ideal model delta sinusoidal sigma weight residual 147.00 81.02 65.98 1 8.00e+00 1.56e-02 8.89e+01 dihedral pdb=" O4' G T 7 " pdb=" C4' G T 7 " pdb=" C3' G T 7 " pdb=" C2' G T 7 " ideal model delta sinusoidal sigma weight residual 24.00 -34.80 58.80 1 8.00e+00 1.56e-02 7.23e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2106 0.084 - 0.168: 167 0.168 - 0.251: 3 0.251 - 0.335: 1 0.335 - 0.419: 1 Chirality restraints: 2278 Sorted by residual: chirality pdb=" CA ASP A 252 " pdb=" N ASP A 252 " pdb=" C ASP A 252 " pdb=" CB ASP A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C3' G T 7 " pdb=" C4' G T 7 " pdb=" O3' G T 7 " pdb=" C2' G T 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ARG B 729 " pdb=" N ARG B 729 " pdb=" C ARG B 729 " pdb=" CB ARG B 729 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2275 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 18 " -0.042 2.00e-02 2.50e+03 1.81e-02 9.79e+00 pdb=" N9 G T 18 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G T 18 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G T 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G T 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G T 18 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G T 18 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G T 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G T 18 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 248 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ILE A 248 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 248 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 694 " -0.044 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 695 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 695 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 695 " -0.036 5.00e-02 4.00e+02 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 58 2.52 - 3.12: 10571 3.12 - 3.71: 22803 3.71 - 4.31: 34148 4.31 - 4.90: 55312 Nonbonded interactions: 122892 Sorted by model distance: nonbonded pdb=" OP1 U U 66 " pdb="MN MN B1002 " model vdw 1.928 3.060 nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 2.029 3.060 nonbonded pdb=" O2' U T 46 " pdb=" OP2 C T 47 " model vdw 2.073 3.040 nonbonded pdb=" OE2 GLU B 214 " pdb="MN MN B1002 " model vdw 2.091 3.060 nonbonded pdb=" O PHE B 215 " pdb="MN MN B1002 " model vdw 2.115 3.060 ... (remaining 122887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 7 through 1002) } 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: 5.600 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.004 0.122 14879 Z= 0.252 Angle : 0.620 10.332 20339 Z= 0.377 Chirality : 0.043 0.419 2278 Planarity : 0.005 0.065 2414 Dihedral : 16.897 169.749 6011 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.74 % Allowed : 10.49 % Favored : 88.77 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1638 helix: 1.37 (0.20), residues: 660 sheet: 0.21 (0.29), residues: 284 loop : 0.38 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 689 TYR 0.015 0.001 TYR B 740 PHE 0.015 0.001 PHE A 223 TRP 0.007 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.25 (14871) covalent geometry : angle 0.61890 / 0.38 (20333) hydrogen bonds : bond 0.12332 / 8.16 ( 662) hydrogen bonds : angle 5.44621 / 3.94 ( 1831) metal coordination : bond 0.01567 / 0.97 ( 8) metal coordination : angle 2.62633 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.503 Fit side-chains REVERT: B 395 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: B 613 MET cc_start: 0.8293 (mtm) cc_final: 0.8069 (mtt) outliers start: 11 outliers final: 5 residues processed: 198 average time/residue: 0.8327 time to fit residues: 176.7259 Evaluate side-chains 181 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 888 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN A 395 GLN A 479 GLN A 638 ASN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126290 restraints weight = 15616.677| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.99 r_work: 0.3090 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14879 Z= 0.204 Angle : 0.594 8.299 20339 Z= 0.321 Chirality : 0.045 0.212 2278 Planarity : 0.005 0.076 2414 Dihedral : 14.908 173.320 2649 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.96 % Allowed : 10.96 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1638 helix: 1.44 (0.20), residues: 658 sheet: 0.24 (0.31), residues: 252 loop : 0.25 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 689 TYR 0.017 0.002 TYR B 234 PHE 0.015 0.002 PHE B 223 TRP 0.010 0.002 TRP B 332 HIS 0.006 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (14871) covalent geometry : angle 0.59231 / 0.32 (20333) hydrogen bonds : bond 0.05127 / 3.42 ( 662) hydrogen bonds : angle 4.64635 / 3.36 ( 1831) metal coordination : bond 0.01150 / 0.71 ( 8) metal coordination : angle 2.45028 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.542 Fit side-chains REVERT: B 291 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7230 (pmt170) REVERT: B 513 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8507 (ttmt) REVERT: B 637 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7718 (tmt-80) REVERT: B 658 ASN cc_start: 0.6554 (m-40) cc_final: 0.6281 (p0) outliers start: 29 outliers final: 14 residues processed: 195 average time/residue: 0.7983 time to fit residues: 167.6166 Evaluate side-chains 185 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 479 GLN A 618 ASN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128058 restraints weight = 15658.405| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.07 r_work: 0.3104 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14879 Z= 0.145 Angle : 0.522 5.702 20339 Z= 0.282 Chirality : 0.042 0.202 2278 Planarity : 0.004 0.060 2414 Dihedral : 14.544 174.149 2641 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 12.38 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1638 helix: 1.63 (0.20), residues: 656 sheet: 0.07 (0.31), residues: 254 loop : 0.28 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 729 TYR 0.014 0.001 TYR B 234 PHE 0.013 0.001 PHE B 223 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (14871) covalent geometry : angle 0.52070 / 0.28 (20333) hydrogen bonds : bond 0.04523 / 3.01 ( 662) hydrogen bonds : angle 4.43314 / 3.20 ( 1831) metal coordination : bond 0.01131 / 0.69 ( 8) metal coordination : angle 2.31964 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.561 Fit side-chains REVERT: A 200 GLU cc_start: 0.8072 (tt0) cc_final: 0.7731 (tp30) REVERT: A 847 ASP cc_start: 0.8142 (t0) cc_final: 0.7854 (t70) REVERT: B 291 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7211 (pmt170) REVERT: B 513 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8514 (ttmt) REVERT: B 637 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7657 (tmt-80) REVERT: B 658 ASN cc_start: 0.6537 (m-40) cc_final: 0.6294 (p0) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 0.8246 time to fit residues: 168.5328 Evaluate side-chains 185 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 637 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 0.0060 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 618 ASN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.166587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128037 restraints weight = 15743.489| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.09 r_work: 0.3122 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14879 Z= 0.125 Angle : 0.499 5.982 20339 Z= 0.267 Chirality : 0.041 0.202 2278 Planarity : 0.004 0.052 2414 Dihedral : 14.454 173.545 2639 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.69 % Allowed : 12.45 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1638 helix: 1.79 (0.20), residues: 656 sheet: 0.10 (0.31), residues: 254 loop : 0.34 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 590 TYR 0.012 0.001 TYR B 234 PHE 0.012 0.001 PHE B 223 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14871) covalent geometry : angle 0.49756 / 0.27 (20333) hydrogen bonds : bond 0.04122 / 2.73 ( 662) hydrogen bonds : angle 4.24280 / 3.06 ( 1831) metal coordination : bond 0.01085 / 0.66 ( 8) metal coordination : angle 2.19502 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.539 Fit side-chains REVERT: A 200 GLU cc_start: 0.8036 (tt0) cc_final: 0.7693 (tp30) REVERT: A 847 ASP cc_start: 0.8122 (t0) cc_final: 0.7825 (t70) REVERT: A 858 SER cc_start: 0.9061 (m) cc_final: 0.8861 (m) REVERT: B 200 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 291 ARG cc_start: 0.7724 (ptt-90) cc_final: 0.7201 (pmt170) REVERT: B 513 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8499 (ttmt) REVERT: B 618 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6619 (m-40) REVERT: B 637 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7680 (tmt-80) outliers start: 25 outliers final: 12 residues processed: 198 average time/residue: 0.8033 time to fit residues: 171.4249 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 161 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 17 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 618 ASN A 771 GLN B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127527 restraints weight = 15578.545| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.96 r_work: 0.3125 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14879 Z= 0.108 Angle : 0.476 5.681 20339 Z= 0.255 Chirality : 0.040 0.199 2278 Planarity : 0.004 0.044 2414 Dihedral : 14.368 173.009 2637 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.76 % Allowed : 12.38 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.21), residues: 1638 helix: 1.86 (0.20), residues: 668 sheet: 0.00 (0.31), residues: 258 loop : 0.50 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 689 TYR 0.011 0.001 TYR A 582 PHE 0.012 0.001 PHE B 223 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14871) covalent geometry : angle 0.47416 / 0.25 (20333) hydrogen bonds : bond 0.03784 / 2.50 ( 662) hydrogen bonds : angle 4.13294 / 2.97 ( 1831) metal coordination : bond 0.01201 / 0.74 ( 8) metal coordination : angle 2.20547 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.596 Fit side-chains REVERT: A 200 GLU cc_start: 0.8084 (tt0) cc_final: 0.7714 (tp30) REVERT: A 479 GLN cc_start: 0.8166 (tp40) cc_final: 0.7744 (mm-40) REVERT: A 847 ASP cc_start: 0.8130 (t0) cc_final: 0.7838 (t70) REVERT: B 41 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: B 200 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: B 513 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8473 (ttmt) REVERT: B 618 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6614 (m-40) REVERT: B 637 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7761 (tmt-80) REVERT: B 825 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6322 (mt-10) outliers start: 26 outliers final: 10 residues processed: 205 average time/residue: 0.7985 time to fit residues: 176.3687 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 634 GLN A 742 GLN A 771 GLN B 395 GLN B 428 ASN B 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124385 restraints weight = 15611.983| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.94 r_work: 0.3085 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14879 Z= 0.236 Angle : 0.577 6.641 20339 Z= 0.306 Chirality : 0.045 0.201 2278 Planarity : 0.005 0.079 2414 Dihedral : 14.408 173.958 2637 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.37 % Allowed : 12.86 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1638 helix: 1.72 (0.20), residues: 656 sheet: -0.07 (0.31), residues: 254 loop : 0.24 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 689 TYR 0.018 0.002 TYR A 582 PHE 0.014 0.002 PHE B 223 TRP 0.010 0.002 TRP B 332 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (14871) covalent geometry : angle 0.57656 / 0.31 (20333) hydrogen bonds : bond 0.04870 / 3.24 ( 662) hydrogen bonds : angle 4.31511 / 3.10 ( 1831) metal coordination : bond 0.00469 / 0.28 ( 8) metal coordination : angle 1.68052 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.600 Fit side-chains REVERT: A 200 GLU cc_start: 0.8123 (tt0) cc_final: 0.7765 (tp30) REVERT: A 262 LYS cc_start: 0.7223 (ptpp) cc_final: 0.6842 (mtmt) REVERT: A 847 ASP cc_start: 0.8140 (t0) cc_final: 0.7848 (t70) REVERT: B 482 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: B 513 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8465 (ttmt) REVERT: B 618 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6608 (m-40) REVERT: B 637 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7742 (tmt-80) REVERT: B 825 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6391 (mt-10) outliers start: 35 outliers final: 19 residues processed: 199 average time/residue: 0.8003 time to fit residues: 171.6960 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN A 395 GLN A 742 GLN A 771 GLN B 395 GLN B 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127154 restraints weight = 15485.006| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.08 r_work: 0.3136 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14879 Z= 0.154 Angle : 0.518 6.980 20339 Z= 0.276 Chirality : 0.042 0.199 2278 Planarity : 0.004 0.062 2414 Dihedral : 14.375 173.174 2637 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 14.21 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1638 helix: 1.77 (0.20), residues: 656 sheet: -0.11 (0.31), residues: 258 loop : 0.30 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 689 TYR 0.013 0.001 TYR B 234 PHE 0.013 0.001 PHE B 223 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (14871) covalent geometry : angle 0.51663 / 0.28 (20333) hydrogen bonds : bond 0.04304 / 2.86 ( 662) hydrogen bonds : angle 4.24096 / 3.04 ( 1831) metal coordination : bond 0.00879 / 0.53 ( 8) metal coordination : angle 1.92111 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.545 Fit side-chains REVERT: A 200 GLU cc_start: 0.8112 (tt0) cc_final: 0.7744 (tp30) REVERT: A 262 LYS cc_start: 0.7216 (ptpp) cc_final: 0.6856 (mtmt) REVERT: A 847 ASP cc_start: 0.8106 (t0) cc_final: 0.7807 (t70) REVERT: B 200 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 291 ARG cc_start: 0.7706 (ptt-90) cc_final: 0.7494 (ptt-90) REVERT: B 513 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8446 (ttmt) REVERT: B 618 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6640 (m-40) REVERT: B 825 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6359 (mt-10) outliers start: 24 outliers final: 14 residues processed: 189 average time/residue: 0.8021 time to fit residues: 163.2973 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.0000 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN A 395 GLN A 771 GLN B 395 GLN B 428 ASN B 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128711 restraints weight = 15523.469| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.02 r_work: 0.3175 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14879 Z= 0.103 Angle : 0.478 7.319 20339 Z= 0.255 Chirality : 0.040 0.197 2278 Planarity : 0.004 0.050 2414 Dihedral : 14.327 172.133 2637 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.56 % Allowed : 14.21 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1638 helix: 1.96 (0.21), residues: 656 sheet: -0.20 (0.31), residues: 262 loop : 0.47 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 689 TYR 0.010 0.001 TYR B 234 PHE 0.012 0.001 PHE B 223 TRP 0.008 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14871) covalent geometry : angle 0.47653 / 0.25 (20333) hydrogen bonds : bond 0.03663 / 2.42 ( 662) hydrogen bonds : angle 4.11227 / 2.95 ( 1831) metal coordination : bond 0.01200 / 0.74 ( 8) metal coordination : angle 2.29892 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.492 Fit side-chains REVERT: A 200 GLU cc_start: 0.8043 (tt0) cc_final: 0.7650 (tp30) REVERT: A 262 LYS cc_start: 0.7142 (ptpp) cc_final: 0.6684 (mttt) REVERT: A 479 GLN cc_start: 0.8127 (tp40) cc_final: 0.7717 (mm-40) REVERT: A 847 ASP cc_start: 0.8066 (t0) cc_final: 0.7782 (t70) REVERT: B 41 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 200 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 291 ARG cc_start: 0.7631 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: B 513 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8382 (ttmt) REVERT: B 618 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6532 (m110) REVERT: B 825 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6323 (mt-10) outliers start: 23 outliers final: 11 residues processed: 189 average time/residue: 0.7514 time to fit residues: 153.1971 Evaluate side-chains 185 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 742 GLN A 771 GLN B 395 GLN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127482 restraints weight = 15705.871| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.20 r_work: 0.3087 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14879 Z= 0.156 Angle : 0.519 7.568 20339 Z= 0.276 Chirality : 0.042 0.200 2278 Planarity : 0.005 0.064 2414 Dihedral : 14.322 172.685 2637 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.29 % Allowed : 15.09 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1638 helix: 1.89 (0.20), residues: 656 sheet: -0.17 (0.31), residues: 262 loop : 0.38 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 689 TYR 0.014 0.001 TYR A 582 PHE 0.012 0.001 PHE B 223 TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14871) covalent geometry : angle 0.51768 / 0.28 (20333) hydrogen bonds : bond 0.04140 / 2.75 ( 662) hydrogen bonds : angle 4.15552 / 2.98 ( 1831) metal coordination : bond 0.00786 / 0.48 ( 8) metal coordination : angle 1.85716 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.703 Fit side-chains REVERT: A 196 LYS cc_start: 0.7933 (mttt) cc_final: 0.7684 (mtpp) REVERT: A 200 GLU cc_start: 0.8122 (tt0) cc_final: 0.7747 (tp30) REVERT: A 229 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7557 (ttt-90) REVERT: A 262 LYS cc_start: 0.7211 (ptpp) cc_final: 0.6793 (mttt) REVERT: A 479 GLN cc_start: 0.8137 (tp40) cc_final: 0.7716 (mm-40) REVERT: A 847 ASP cc_start: 0.8153 (t0) cc_final: 0.7871 (t70) REVERT: B 291 ARG cc_start: 0.7702 (ptt-90) cc_final: 0.7464 (ptt-90) REVERT: B 513 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8477 (ttmt) REVERT: B 618 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6624 (m-40) outliers start: 19 outliers final: 12 residues processed: 188 average time/residue: 0.7755 time to fit residues: 157.0570 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 0.0770 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 166 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 742 GLN A 771 GLN B 395 GLN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127280 restraints weight = 15473.452| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.86 r_work: 0.3129 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14879 Z= 0.223 Angle : 0.577 7.917 20339 Z= 0.306 Chirality : 0.045 0.200 2278 Planarity : 0.005 0.071 2414 Dihedral : 14.365 173.205 2637 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.15 % Allowed : 15.29 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1638 helix: 1.68 (0.20), residues: 656 sheet: -0.18 (0.31), residues: 254 loop : 0.18 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 689 TYR 0.019 0.002 TYR A 582 PHE 0.014 0.002 PHE B 223 TRP 0.010 0.002 TRP B 332 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (14871) covalent geometry : angle 0.57648 / 0.31 (20333) hydrogen bonds : bond 0.04812 / 3.21 ( 662) hydrogen bonds : angle 4.33260 / 3.11 ( 1831) metal coordination : bond 0.00613 / 0.36 ( 8) metal coordination : angle 1.62087 / 0.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.525 Fit side-chains REVERT: A 196 LYS cc_start: 0.7993 (mttt) cc_final: 0.7774 (mtpp) REVERT: A 200 GLU cc_start: 0.8113 (tt0) cc_final: 0.7778 (tp30) REVERT: A 229 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (ttt-90) REVERT: A 262 LYS cc_start: 0.7273 (ptpp) cc_final: 0.7005 (mtmt) REVERT: A 828 LYS cc_start: 0.7813 (tttt) cc_final: 0.7466 (mtmm) REVERT: A 847 ASP cc_start: 0.8130 (t0) cc_final: 0.7849 (t70) REVERT: B 513 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8488 (ttpt) REVERT: B 618 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.7040 (t0) REVERT: B 825 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6391 (mt-10) outliers start: 17 outliers final: 12 residues processed: 187 average time/residue: 0.7366 time to fit residues: 148.7482 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN A 395 GLN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126714 restraints weight = 15635.437| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.15 r_work: 0.3090 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14879 Z= 0.186 Angle : 0.546 7.868 20339 Z= 0.291 Chirality : 0.043 0.198 2278 Planarity : 0.005 0.067 2414 Dihedral : 14.360 172.697 2637 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.42 % Allowed : 15.09 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1638 helix: 1.69 (0.20), residues: 656 sheet: -0.36 (0.31), residues: 256 loop : 0.21 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 689 TYR 0.015 0.001 TYR A 582 PHE 0.013 0.001 PHE B 223 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (14871) covalent geometry : angle 0.54481 / 0.29 (20333) hydrogen bonds : bond 0.04474 / 2.98 ( 662) hydrogen bonds : angle 4.27402 / 3.07 ( 1831) metal coordination : bond 0.00697 / 0.42 ( 8) metal coordination : angle 1.82691 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6396.70 seconds wall clock time: 109 minutes 41.99 seconds (6581.99 seconds total)