Starting phenix.real_space_refine on Fri May 16 11:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erf_19914/05_2025/9erf_19914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erf_19914/05_2025/9erf_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_19914/05_2025/9erf_19914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erf_19914/05_2025/9erf_19914.map" model { file = "/net/cci-nas-00/data/ceres_data/9erf_19914/05_2025/9erf_19914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erf_19914/05_2025/9erf_19914.cif" } resolution = 2.64 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= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 9.54, per 1000 atoms: 0.66 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: 4.08 Conformation dependent library (CDL) restraints added in 2.0 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 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: 5.38 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: 5.86 Time building geometry restraints manager: 4.65 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 2.320 nonbonded pdb=" OE2 GLU A 214 " pdb="MN MN A1002 " model vdw 2.029 2.320 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 2.320 nonbonded pdb=" O PHE B 215 " pdb="MN MN B1002 " model vdw 2.115 2.320 ... (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 899 or resid 1001 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: 6.400 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.100 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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= 0.245 Angle : 0.620 10.332 20339 Z= 0.360 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 (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: 1.03 (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 TRP 0.007 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 PHE 0.015 0.001 PHE A 223 TYR 0.015 0.001 TYR B 740 ARG 0.013 0.001 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.12332 ( 662) hydrogen bonds : angle 5.44621 ( 1831) metal coordination : bond 0.01567 ( 8) metal coordination : angle 2.62633 ( 6) covalent geometry : bond 0.00443 (14871) covalent geometry : angle 0.61889 (20333) *********************** 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 : 1.519 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: 1.7900 time to fit residues: 380.5922 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 : 1.493 ------------------------------------------------------------------------------- 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 141 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 479 GLN A 618 ASN A 638 ASN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127185 restraints weight = 15582.137| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.10 r_work: 0.3095 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14879 Z= 0.180 Angle : 0.566 5.403 20339 Z= 0.302 Chirality : 0.044 0.206 2278 Planarity : 0.005 0.067 2414 Dihedral : 14.597 171.334 2649 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.83 % Allowed : 10.89 % Favored : 87.28 % 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: 1.07 (0.20), residues: 1638 helix: 1.55 (0.20), residues: 656 sheet: 0.19 (0.31), residues: 250 loop : 0.27 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.005 0.001 HIS B 420 PHE 0.014 0.002 PHE A 223 TYR 0.016 0.002 TYR B 234 ARG 0.005 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 662) hydrogen bonds : angle 4.54061 ( 1831) metal coordination : bond 0.00853 ( 8) metal coordination : angle 2.25227 ( 6) covalent geometry : bond 0.00422 (14871) covalent geometry : angle 0.56522 (20333) *********************** 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 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 1.613 Fit side-chains REVERT: A 99 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: A 847 ASP cc_start: 0.8125 (t0) cc_final: 0.7827 (t70) REVERT: B 291 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.7204 (pmt170) REVERT: B 482 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: B 513 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8500 (ttmt) REVERT: B 637 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7620 (tmt-80) REVERT: B 658 ASN cc_start: 0.6560 (m-40) cc_final: 0.6279 (p0) outliers start: 27 outliers final: 12 residues processed: 194 average time/residue: 1.7038 time to fit residues: 355.1220 Evaluate side-chains 182 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN 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 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 482 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 138 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 0.0030 chunk 150 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 618 ASN 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 = 0.3868 r_free = 0.3868 target = 0.165904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127783 restraints weight = 15622.368| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.11 r_work: 0.3132 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14879 Z= 0.143 Angle : 0.522 5.646 20339 Z= 0.277 Chirality : 0.042 0.201 2278 Planarity : 0.004 0.062 2414 Dihedral : 14.441 174.071 2639 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.83 % Allowed : 12.11 % Favored : 86.06 % 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: 1.18 (0.20), residues: 1638 helix: 1.70 (0.20), residues: 656 sheet: 0.14 (0.31), residues: 254 loop : 0.30 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.015 0.001 TYR B 234 ARG 0.008 0.000 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 662) hydrogen bonds : angle 4.35280 ( 1831) metal coordination : bond 0.01016 ( 8) metal coordination : angle 2.18460 ( 6) covalent geometry : bond 0.00330 (14871) covalent geometry : angle 0.52091 (20333) *********************** 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 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.484 Fit side-chains REVERT: A 99 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: A 200 GLU cc_start: 0.8071 (tt0) cc_final: 0.7729 (tp30) REVERT: A 847 ASP cc_start: 0.8148 (t0) cc_final: 0.7848 (t70) REVERT: B 200 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: B 291 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7192 (pmt170) REVERT: B 482 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: B 513 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: B 618 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6651 (m-40) REVERT: B 637 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7692 (tmt-80) outliers start: 27 outliers final: 13 residues processed: 193 average time/residue: 1.7173 time to fit residues: 356.4844 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN 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 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 482 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 618 ASN A 634 GLN A 742 GLN A 771 GLN B 771 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126107 restraints weight = 15540.094| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.04 r_work: 0.3084 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14879 Z= 0.186 Angle : 0.551 5.676 20339 Z= 0.291 Chirality : 0.043 0.200 2278 Planarity : 0.005 0.071 2414 Dihedral : 14.413 173.907 2639 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 12.11 % Favored : 85.45 % 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: 1.07 (0.20), residues: 1638 helix: 1.65 (0.20), residues: 656 sheet: -0.07 (0.31), residues: 254 loop : 0.26 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 PHE 0.013 0.001 PHE B 223 TYR 0.015 0.001 TYR B 234 ARG 0.009 0.001 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 662) hydrogen bonds : angle 4.33398 ( 1831) metal coordination : bond 0.00734 ( 8) metal coordination : angle 1.88097 ( 6) covalent geometry : bond 0.00442 (14871) covalent geometry : angle 0.55028 (20333) *********************** 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 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.627 Fit side-chains REVERT: A 99 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: A 200 GLU cc_start: 0.8088 (tt0) cc_final: 0.7704 (tp30) REVERT: A 262 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6979 (mtmt) REVERT: A 847 ASP cc_start: 0.8148 (t0) cc_final: 0.7840 (t70) REVERT: B 482 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: B 513 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8496 (ttmt) REVERT: B 618 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6588 (m-40) REVERT: B 637 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7686 (tmt-80) outliers start: 36 outliers final: 18 residues processed: 201 average time/residue: 1.6856 time to fit residues: 364.3816 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 LYS 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 13 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 252 ASP 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 482 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 742 GLN A 771 GLN B 432 GLN B 771 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125340 restraints weight = 15571.111| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.02 r_work: 0.3084 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1413 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= 0.162 Angle : 0.523 6.221 20339 Z= 0.276 Chirality : 0.042 0.199 2278 Planarity : 0.004 0.064 2414 Dihedral : 14.363 173.164 2639 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % 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: 1.13 (0.20), residues: 1638 helix: 1.74 (0.20), residues: 656 sheet: -0.08 (0.31), residues: 258 loop : 0.28 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 PHE 0.013 0.001 PHE B 223 TYR 0.015 0.001 TYR B 234 ARG 0.007 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 662) hydrogen bonds : angle 4.27170 ( 1831) metal coordination : bond 0.00903 ( 8) metal coordination : angle 2.08914 ( 6) covalent geometry : bond 0.00382 (14871) covalent geometry : angle 0.52201 (20333) *********************** 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 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 1.458 Fit side-chains REVERT: A 99 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: A 200 GLU cc_start: 0.8131 (tt0) cc_final: 0.7748 (tp30) REVERT: A 262 LYS cc_start: 0.7382 (ptpp) cc_final: 0.6993 (mtmt) REVERT: A 847 ASP cc_start: 0.8120 (t0) cc_final: 0.7827 (t70) REVERT: B 124 ARG cc_start: 0.8185 (tpt90) cc_final: 0.7785 (tpt90) REVERT: B 200 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: B 291 ARG cc_start: 0.7630 (ptt-90) cc_final: 0.7064 (pmt170) REVERT: B 482 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: B 513 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8448 (ttmt) REVERT: B 618 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6611 (m-40) outliers start: 35 outliers final: 20 residues processed: 200 average time/residue: 1.6876 time to fit residues: 363.3588 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN 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 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 71 VAL 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 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 482 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 742 GLN A 771 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 = 0.3854 r_free = 0.3854 target = 0.164950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125360 restraints weight = 15636.635| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.95 r_work: 0.3091 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14879 Z= 0.150 Angle : 0.518 6.569 20339 Z= 0.272 Chirality : 0.041 0.199 2278 Planarity : 0.005 0.060 2414 Dihedral : 14.340 172.806 2639 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.10 % Allowed : 13.40 % Favored : 84.51 % 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: 1.19 (0.21), residues: 1638 helix: 1.80 (0.20), residues: 656 sheet: 0.00 (0.31), residues: 252 loop : 0.26 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.014 0.001 TYR B 234 ARG 0.012 0.001 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 662) hydrogen bonds : angle 4.23837 ( 1831) metal coordination : bond 0.00942 ( 8) metal coordination : angle 2.01731 ( 6) covalent geometry : bond 0.00350 (14871) covalent geometry : angle 0.51655 (20333) *********************** 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 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.698 Fit side-chains REVERT: A 99 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: A 196 LYS cc_start: 0.7912 (mttt) cc_final: 0.7677 (mtpp) REVERT: A 200 GLU cc_start: 0.8131 (tt0) cc_final: 0.7769 (tp30) REVERT: A 262 LYS cc_start: 0.7389 (ptpp) cc_final: 0.6999 (mtmt) REVERT: A 847 ASP cc_start: 0.8128 (t0) cc_final: 0.7851 (t70) REVERT: A 858 SER cc_start: 0.9094 (m) cc_final: 0.8887 (m) REVERT: B 200 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: B 513 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8475 (ttpt) REVERT: B 618 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6640 (m-40) REVERT: B 688 THR cc_start: 0.8465 (p) cc_final: 0.8199 (m) REVERT: B 825 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6496 (mt-10) outliers start: 31 outliers final: 19 residues processed: 199 average time/residue: 1.6188 time to fit residues: 347.6005 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN 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 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 71 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 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 161 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 618 ASN A 742 GLN A 771 GLN B 432 GLN B 771 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126606 restraints weight = 15546.467| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.07 r_work: 0.3124 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14879 Z= 0.144 Angle : 0.510 7.014 20339 Z= 0.268 Chirality : 0.041 0.198 2278 Planarity : 0.004 0.058 2414 Dihedral : 14.322 172.537 2639 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.30 % Allowed : 13.46 % 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 (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: 1.86 (0.20), residues: 656 sheet: -0.01 (0.31), residues: 252 loop : 0.28 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR B 234 ARG 0.012 0.001 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 662) hydrogen bonds : angle 4.19944 ( 1831) metal coordination : bond 0.00823 ( 8) metal coordination : angle 2.01784 ( 6) covalent geometry : bond 0.00337 (14871) covalent geometry : angle 0.50873 (20333) *********************** 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 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.718 Fit side-chains REVERT: A 99 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 196 LYS cc_start: 0.7946 (mttt) cc_final: 0.7700 (mtpp) REVERT: A 200 GLU cc_start: 0.8132 (tt0) cc_final: 0.7751 (tp30) REVERT: A 262 LYS cc_start: 0.7347 (ptpp) cc_final: 0.6987 (mtmt) REVERT: A 847 ASP cc_start: 0.8068 (t0) cc_final: 0.7797 (t70) REVERT: A 858 SER cc_start: 0.9067 (m) cc_final: 0.8849 (m) REVERT: B 200 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: B 291 ARG cc_start: 0.7595 (ptt-90) cc_final: 0.7183 (pmm-80) REVERT: B 482 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 513 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: B 618 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6606 (m-40) REVERT: B 688 THR cc_start: 0.8423 (p) cc_final: 0.8192 (m) outliers start: 34 outliers final: 19 residues processed: 198 average time/residue: 1.6204 time to fit residues: 346.9807 Evaluate side-chains 197 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 229 ARG 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 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 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 482 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 32 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 0.0670 chunk 102 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 618 ASN A 742 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 = 0.3869 r_free = 0.3869 target = 0.166248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127031 restraints weight = 15581.048| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.99 r_work: 0.3139 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14879 Z= 0.131 Angle : 0.502 6.383 20339 Z= 0.264 Chirality : 0.041 0.198 2278 Planarity : 0.004 0.053 2414 Dihedral : 14.308 172.277 2639 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.69 % Allowed : 14.28 % Favored : 84.03 % 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: 1.87 (0.20), residues: 658 sheet: -0.16 (0.31), residues: 256 loop : 0.33 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR B 234 ARG 0.011 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 662) hydrogen bonds : angle 4.16496 ( 1831) metal coordination : bond 0.00823 ( 8) metal coordination : angle 1.86668 ( 6) covalent geometry : bond 0.00303 (14871) covalent geometry : angle 0.50056 (20333) *********************** 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 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 2.044 Fit side-chains REVERT: A 99 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: A 196 LYS cc_start: 0.7982 (mttt) cc_final: 0.7751 (mtpp) REVERT: A 200 GLU cc_start: 0.8082 (tt0) cc_final: 0.7722 (tp30) REVERT: A 229 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7589 (ttt-90) REVERT: A 262 LYS cc_start: 0.7341 (ptpp) cc_final: 0.7024 (mtmt) REVERT: A 479 GLN cc_start: 0.8129 (tp40) cc_final: 0.7761 (mm-40) REVERT: A 847 ASP cc_start: 0.8087 (t0) cc_final: 0.7828 (t70) REVERT: A 858 SER cc_start: 0.9076 (m) cc_final: 0.8868 (m) REVERT: B 200 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: B 482 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: B 513 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8441 (ttmt) REVERT: B 618 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6647 (m-40) REVERT: B 688 THR cc_start: 0.8432 (p) cc_final: 0.8180 (m) outliers start: 25 outliers final: 14 residues processed: 191 average time/residue: 1.6591 time to fit residues: 341.3076 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 229 ARG 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 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 482 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 618 ASN A 771 GLN B 290 GLN B 432 GLN B 746 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126326 restraints weight = 15513.013| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.92 r_work: 0.3105 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1670 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= 0.170 Angle : 0.532 7.732 20339 Z= 0.279 Chirality : 0.042 0.198 2278 Planarity : 0.005 0.062 2414 Dihedral : 14.321 172.549 2637 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.89 % Allowed : 14.28 % Favored : 83.83 % 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: 1.11 (0.21), residues: 1638 helix: 1.77 (0.20), residues: 658 sheet: -0.20 (0.31), residues: 252 loop : 0.25 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.018 0.001 TYR B 740 ARG 0.009 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 662) hydrogen bonds : angle 4.22036 ( 1831) metal coordination : bond 0.00775 ( 8) metal coordination : angle 1.73242 ( 6) covalent geometry : bond 0.00401 (14871) covalent geometry : angle 0.53103 (20333) *********************** 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 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.871 Fit side-chains REVERT: A 99 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: A 196 LYS cc_start: 0.8021 (mttt) cc_final: 0.7792 (mtpp) REVERT: A 200 GLU cc_start: 0.8120 (tt0) cc_final: 0.7766 (tp30) REVERT: A 262 LYS cc_start: 0.7379 (ptpp) cc_final: 0.7058 (mtmt) REVERT: A 828 LYS cc_start: 0.7779 (tttt) cc_final: 0.7429 (mtmm) REVERT: A 847 ASP cc_start: 0.8108 (t0) cc_final: 0.7843 (t70) REVERT: A 858 SER cc_start: 0.9106 (m) cc_final: 0.8899 (m) REVERT: B 200 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: B 482 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: B 513 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8468 (ttpt) REVERT: B 618 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6644 (m-40) REVERT: B 688 THR cc_start: 0.8426 (p) cc_final: 0.8185 (m) outliers start: 28 outliers final: 18 residues processed: 195 average time/residue: 1.6836 time to fit residues: 355.0444 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 397 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 200 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 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 150 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 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 = 0.3856 r_free = 0.3856 target = 0.164967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126717 restraints weight = 15589.014| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.99 r_work: 0.3094 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14879 Z= 0.174 Angle : 0.541 7.484 20339 Z= 0.284 Chirality : 0.042 0.198 2278 Planarity : 0.005 0.062 2414 Dihedral : 14.332 172.534 2637 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.76 % Allowed : 14.75 % 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 (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: 1.70 (0.20), residues: 658 sheet: -0.21 (0.31), residues: 252 loop : 0.23 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS A 420 PHE 0.012 0.001 PHE B 223 TYR 0.018 0.001 TYR B 629 ARG 0.014 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 662) hydrogen bonds : angle 4.24335 ( 1831) metal coordination : bond 0.00650 ( 8) metal coordination : angle 1.73065 ( 6) covalent geometry : bond 0.00414 (14871) covalent geometry : angle 0.53979 (20333) ********************** 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 201 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.688 Fit side-chains REVERT: A 99 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: A 196 LYS cc_start: 0.8057 (mttt) cc_final: 0.7831 (mtpp) REVERT: A 200 GLU cc_start: 0.8100 (tt0) cc_final: 0.7733 (tp30) REVERT: A 262 LYS cc_start: 0.7388 (ptpp) cc_final: 0.7057 (mtmt) REVERT: A 828 LYS cc_start: 0.7777 (tttt) cc_final: 0.7401 (mtmm) REVERT: A 847 ASP cc_start: 0.8085 (t0) cc_final: 0.7819 (t70) REVERT: A 858 SER cc_start: 0.9093 (m) cc_final: 0.8877 (m) REVERT: B 482 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: B 513 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: B 618 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.7004 (t0) REVERT: B 688 THR cc_start: 0.8456 (p) cc_final: 0.8159 (m) outliers start: 26 outliers final: 20 residues processed: 191 average time/residue: 1.6148 time to fit residues: 332.8268 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 488 THR 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 241 THR Chi-restraints excluded: chain B residue 252 ASP 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 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 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 395 GLN A 618 ASN 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 = 0.3867 r_free = 0.3867 target = 0.166066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127749 restraints weight = 15665.245| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.01 r_work: 0.3122 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14879 Z= 0.137 Angle : 0.509 7.346 20339 Z= 0.267 Chirality : 0.041 0.197 2278 Planarity : 0.004 0.055 2414 Dihedral : 14.305 172.160 2637 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.76 % Allowed : 14.68 % 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 (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: 1.17 (0.21), residues: 1638 helix: 1.80 (0.20), residues: 658 sheet: -0.17 (0.31), residues: 256 loop : 0.32 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 PHE 0.011 0.001 PHE B 223 TYR 0.017 0.001 TYR B 740 ARG 0.009 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 662) hydrogen bonds : angle 4.15971 ( 1831) metal coordination : bond 0.00845 ( 8) metal coordination : angle 1.87559 ( 6) covalent geometry : bond 0.00320 (14871) covalent geometry : angle 0.50760 (20333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13191.44 seconds wall clock time: 227 minutes 39.86 seconds (13659.86 seconds total)