Starting phenix.real_space_refine on Thu Sep 18 05:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erf_19914/09_2025/9erf_19914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erf_19914/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9erf_19914/09_2025/9erf_19914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erf_19914/09_2025/9erf_19914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9erf_19914/09_2025/9erf_19914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erf_19914/09_2025/9erf_19914.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 52 5.49 5 Mg 3 5.21 5 S 86 5.16 5 C 9007 2.51 5 N 2530 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14459 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "T" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1038 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 22, 'rna3p_pyr': 16} Link IDs: {'rna2p': 10, 'rna3p': 37} Chain breaks: 1 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 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: 3.43, per 1000 atoms: 0.24 Number of scatterers: 14459 At special positions: 0 Unit cell: (95.237, 131.587, 147.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 3 24.99 S 86 16.00 P 52 15.00 Mg 3 11.99 O 2776 8.00 N 2530 7.00 C 9007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 581.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 18 sheets defined 45.9% alpha, 19.1% beta 19 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.649A pdb=" N SER A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.629A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 266 through 281 removed outlier: 3.568A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 398 removed outlier: 5.809A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 482 through 501 Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.619A pdb=" N GLY A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.539A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 763' Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.932A pdb=" N MET A 844 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.582A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.580A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 398 removed outlier: 5.799A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 482 through 501 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.620A pdb=" N GLY B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 Processing helix chain 'B' and resid 587 through 592 removed outlier: 4.162A pdb=" N LYS B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.981A pdb=" N ARG B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.551A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.643A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 816 through 831 removed outlier: 4.169A pdb=" N GLU B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 3.861A pdb=" N MET B 844 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 removed outlier: 4.032A pdb=" N VAL B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.320A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.512A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.512A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.594A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.469A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.658A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.145A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 810 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 868 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 812 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.353A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.527A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.527A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.558A pdb=" N ALA B 323 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.377A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.267A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.055A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 810 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE B 868 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 812 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.60 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 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: 4.160 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.20), residues: 1638 helix: 1.37 (0.20), residues: 660 sheet: 0.21 (0.29), residues: 284 loop : 0.38 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 689 TYR 0.015 0.001 TYR B 740 PHE 0.015 0.001 PHE A 223 TRP 0.007 0.001 TRP B 332 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00443 (14871) covalent geometry : angle 0.61889 (20333) hydrogen bonds : bond 0.12332 ( 662) hydrogen bonds : angle 5.44621 ( 1831) metal coordination : bond 0.01567 ( 8) metal coordination : angle 2.62633 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.572 Fit side-chains REVERT: B 395 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: B 613 MET cc_start: 0.8293 (mtm) cc_final: 0.8069 (mtt) outliers start: 11 outliers final: 5 residues processed: 198 average time/residue: 0.8728 time to fit residues: 184.6782 Evaluate side-chains 181 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 888 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.164609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126395 restraints weight = 15628.913| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.06 r_work: 0.3116 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14879 Z= 0.201 Angle : 0.587 5.480 20339 Z= 0.312 Chirality : 0.044 0.207 2278 Planarity : 0.005 0.073 2414 Dihedral : 14.613 171.225 2649 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 11.03 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1638 helix: 1.48 (0.20), residues: 656 sheet: 0.17 (0.31), residues: 250 loop : 0.22 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 647 TYR 0.017 0.002 TYR B 234 PHE 0.014 0.002 PHE A 223 TRP 0.012 0.002 TRP B 332 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00476 (14871) covalent geometry : angle 0.58573 (20333) hydrogen bonds : bond 0.04977 ( 662) hydrogen bonds : angle 4.56518 ( 1831) metal coordination : bond 0.00732 ( 8) metal coordination : angle 2.13074 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.557 Fit side-chains REVERT: A 99 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: A 847 ASP cc_start: 0.8157 (t0) cc_final: 0.7835 (t70) REVERT: B 291 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7249 (pmt170) REVERT: B 482 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: B 513 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8507 (ttmt) REVERT: B 658 ASN cc_start: 0.6493 (m-40) cc_final: 0.6237 (p0) outliers start: 30 outliers final: 14 residues processed: 197 average time/residue: 0.8425 time to fit residues: 177.9671 Evaluate side-chains 186 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 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 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.167174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128886 restraints weight = 15727.415| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.08 r_work: 0.3153 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14879 Z= 0.116 Angle : 0.495 5.658 20339 Z= 0.263 Chirality : 0.041 0.199 2278 Planarity : 0.004 0.046 2414 Dihedral : 14.416 174.141 2640 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.69 % Allowed : 12.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1638 helix: 1.80 (0.20), residues: 656 sheet: 0.14 (0.31), residues: 254 loop : 0.36 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 729 TYR 0.013 0.001 TYR B 234 PHE 0.012 0.001 PHE B 223 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00258 (14871) covalent geometry : angle 0.49356 (20333) hydrogen bonds : bond 0.03982 ( 662) hydrogen bonds : angle 4.26647 ( 1831) metal coordination : bond 0.01148 ( 8) metal coordination : angle 2.38798 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.644 Fit side-chains REVERT: A 99 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: A 200 GLU cc_start: 0.8068 (tt0) cc_final: 0.7684 (tp30) REVERT: A 847 ASP cc_start: 0.8132 (t0) cc_final: 0.7817 (t70) REVERT: B 124 ARG cc_start: 0.8211 (tpt90) cc_final: 0.7971 (tpt90) REVERT: B 200 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 291 ARG cc_start: 0.7712 (ptt-90) cc_final: 0.7164 (pmt170) REVERT: B 482 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: B 513 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8500 (ttmt) REVERT: B 618 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6604 (m-40) outliers start: 25 outliers final: 8 residues processed: 199 average time/residue: 0.7938 time to fit residues: 169.2441 Evaluate side-chains 188 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN 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 150 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.0270 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129328 restraints weight = 15778.992| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.11 r_work: 0.3156 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14879 Z= 0.115 Angle : 0.489 5.660 20339 Z= 0.257 Chirality : 0.040 0.198 2278 Planarity : 0.004 0.050 2414 Dihedral : 14.305 172.428 2637 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 12.18 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1638 helix: 1.95 (0.20), residues: 656 sheet: 0.04 (0.31), residues: 258 loop : 0.49 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 689 TYR 0.012 0.001 TYR A 582 PHE 0.012 0.001 PHE B 223 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00259 (14871) covalent geometry : angle 0.48742 (20333) hydrogen bonds : bond 0.03785 ( 662) hydrogen bonds : angle 4.14240 ( 1831) metal coordination : bond 0.01065 ( 8) metal coordination : angle 2.07125 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.596 Fit side-chains REVERT: A 99 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 200 GLU cc_start: 0.8044 (tt0) cc_final: 0.7657 (tp30) REVERT: A 262 LYS cc_start: 0.7323 (ptpp) cc_final: 0.6751 (mtmt) REVERT: A 419 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 479 GLN cc_start: 0.8153 (tp40) cc_final: 0.7766 (mm-40) REVERT: A 847 ASP cc_start: 0.8091 (t0) cc_final: 0.7807 (t70) REVERT: B 41 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: B 124 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (tpt90) REVERT: B 200 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: B 513 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8476 (ttmt) REVERT: B 618 ASN cc_start: 0.7033 (OUTLIER) cc_final: 0.6578 (m-40) REVERT: B 637 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7654 (tmt-80) REVERT: B 688 THR cc_start: 0.8381 (p) cc_final: 0.8154 (m) outliers start: 32 outliers final: 9 residues processed: 202 average time/residue: 0.7841 time to fit residues: 170.1388 Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 634 GLN A 742 GLN A 771 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128202 restraints weight = 15630.028| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.10 r_work: 0.3126 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14879 Z= 0.128 Angle : 0.493 5.948 20339 Z= 0.259 Chirality : 0.041 0.200 2278 Planarity : 0.004 0.056 2414 Dihedral : 14.281 172.758 2637 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 13.06 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.21), residues: 1638 helix: 2.00 (0.20), residues: 656 sheet: 0.02 (0.31), residues: 258 loop : 0.47 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 689 TYR 0.012 0.001 TYR A 582 PHE 0.012 0.001 PHE B 223 TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00295 (14871) covalent geometry : angle 0.49202 (20333) hydrogen bonds : bond 0.03893 ( 662) hydrogen bonds : angle 4.12065 ( 1831) metal coordination : bond 0.00878 ( 8) metal coordination : angle 1.93340 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.472 Fit side-chains REVERT: A 99 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: A 200 GLU cc_start: 0.8095 (tt0) cc_final: 0.7752 (tp30) REVERT: A 262 LYS cc_start: 0.7321 (ptpp) cc_final: 0.6816 (mtmt) REVERT: A 419 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 479 GLN cc_start: 0.8124 (tp40) cc_final: 0.7739 (mm-40) REVERT: A 847 ASP cc_start: 0.8074 (t0) cc_final: 0.7796 (t70) REVERT: B 41 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: B 124 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (tpt90) REVERT: B 200 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: B 291 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7066 (pmt170) REVERT: B 513 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8496 (ttpt) REVERT: B 613 MET cc_start: 0.8217 (mtm) cc_final: 0.8012 (mtt) REVERT: B 618 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6663 (m-40) REVERT: B 637 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7820 (tmt-80) outliers start: 33 outliers final: 14 residues processed: 204 average time/residue: 0.8228 time to fit residues: 180.1696 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 387 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 41 GLN Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 200 GLU 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 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 742 GLN A 771 GLN B 428 ASN B 432 GLN B 746 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125181 restraints weight = 15663.756| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.18 r_work: 0.3068 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14879 Z= 0.205 Angle : 0.562 6.438 20339 Z= 0.295 Chirality : 0.043 0.199 2278 Planarity : 0.005 0.073 2414 Dihedral : 14.335 173.124 2637 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.37 % Allowed : 13.67 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.20), residues: 1638 helix: 1.75 (0.20), residues: 656 sheet: -0.09 (0.31), residues: 254 loop : 0.28 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 689 TYR 0.016 0.002 TYR A 582 PHE 0.014 0.002 PHE B 223 TRP 0.011 0.002 TRP B 332 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00489 (14871) covalent geometry : angle 0.56159 (20333) hydrogen bonds : bond 0.04668 ( 662) hydrogen bonds : angle 4.29681 ( 1831) metal coordination : bond 0.00670 ( 8) metal coordination : angle 1.76714 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.522 Fit side-chains REVERT: A 99 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: A 196 LYS cc_start: 0.7911 (mttt) cc_final: 0.7684 (mtpp) REVERT: A 200 GLU cc_start: 0.8132 (tt0) cc_final: 0.7766 (tp30) REVERT: A 262 LYS cc_start: 0.7409 (ptpp) cc_final: 0.6997 (mtmt) REVERT: A 847 ASP cc_start: 0.8093 (t0) cc_final: 0.7808 (t70) REVERT: B 291 ARG cc_start: 0.7654 (ptt-90) cc_final: 0.7245 (pmm-80) REVERT: B 482 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: B 513 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8476 (ttpt) REVERT: B 618 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6610 (m-40) REVERT: B 637 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7850 (tmt-80) outliers start: 35 outliers final: 18 residues processed: 201 average time/residue: 0.8186 time to fit residues: 176.5809 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 : 0.556 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 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 612 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 0.4980 chunk 139 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 742 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127368 restraints weight = 15515.667| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.98 r_work: 0.3156 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14879 Z= 0.119 Angle : 0.492 6.870 20339 Z= 0.259 Chirality : 0.040 0.198 2278 Planarity : 0.004 0.051 2414 Dihedral : 14.286 172.038 2637 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.62 % Allowed : 14.48 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.21), residues: 1638 helix: 1.92 (0.20), residues: 658 sheet: -0.20 (0.31), residues: 262 loop : 0.43 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 590 TYR 0.012 0.001 TYR B 234 PHE 0.011 0.001 PHE B 223 TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00271 (14871) covalent geometry : angle 0.49098 (20333) hydrogen bonds : bond 0.03797 ( 662) hydrogen bonds : angle 4.14581 ( 1831) metal coordination : bond 0.00881 ( 8) metal coordination : angle 2.14698 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.546 Fit side-chains REVERT: A 99 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: A 196 LYS cc_start: 0.7909 (mttt) cc_final: 0.7692 (mtpp) REVERT: A 200 GLU cc_start: 0.8073 (tt0) cc_final: 0.7715 (tp30) REVERT: A 262 LYS cc_start: 0.7339 (ptpp) cc_final: 0.6873 (mtmt) REVERT: A 479 GLN cc_start: 0.8049 (tp40) cc_final: 0.7663 (mm-40) REVERT: A 847 ASP cc_start: 0.8077 (t0) cc_final: 0.7814 (t70) REVERT: B 200 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: B 291 ARG cc_start: 0.7591 (ptt-90) cc_final: 0.7181 (pmm-80) REVERT: B 513 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8463 (ttpt) REVERT: B 618 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6603 (m110) REVERT: B 637 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7735 (tmt-80) outliers start: 24 outliers final: 13 residues processed: 197 average time/residue: 0.8284 time to fit residues: 174.8080 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 79 optimal weight: 0.0770 chunk 143 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 771 GLN B 428 ASN B 432 GLN B 771 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125500 restraints weight = 15503.922| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.00 r_work: 0.3088 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14879 Z= 0.213 Angle : 0.567 7.240 20339 Z= 0.297 Chirality : 0.043 0.199 2278 Planarity : 0.005 0.072 2414 Dihedral : 14.333 172.889 2637 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.23 % Allowed : 13.87 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.20), residues: 1638 helix: 1.74 (0.20), residues: 656 sheet: -0.28 (0.31), residues: 258 loop : 0.25 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 690 TYR 0.016 0.002 TYR A 582 PHE 0.014 0.002 PHE B 223 TRP 0.010 0.002 TRP B 332 HIS 0.006 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00509 (14871) covalent geometry : angle 0.56668 (20333) hydrogen bonds : bond 0.04654 ( 662) hydrogen bonds : angle 4.28421 ( 1831) metal coordination : bond 0.00689 ( 8) metal coordination : angle 1.68687 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.517 Fit side-chains REVERT: A 99 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: A 196 LYS cc_start: 0.7998 (mttt) cc_final: 0.7760 (mtpp) REVERT: A 200 GLU cc_start: 0.8130 (tt0) cc_final: 0.7772 (tp30) REVERT: A 262 LYS cc_start: 0.7401 (ptpp) cc_final: 0.7007 (mtmt) REVERT: A 828 LYS cc_start: 0.7775 (tttt) cc_final: 0.7414 (mtmm) REVERT: A 847 ASP cc_start: 0.8104 (t0) cc_final: 0.7828 (t70) REVERT: B 124 ARG cc_start: 0.8169 (tpt90) cc_final: 0.7837 (tpt90) REVERT: B 291 ARG cc_start: 0.7606 (ptt-90) cc_final: 0.7222 (pmm-80) REVERT: B 513 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8454 (ttpt) REVERT: B 618 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6616 (m-40) REVERT: B 637 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7777 (tmt-80) outliers start: 33 outliers final: 18 residues processed: 194 average time/residue: 0.8307 time to fit residues: 173.1457 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 791 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 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 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 290 GLN B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127602 restraints weight = 15648.690| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.98 r_work: 0.3111 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14879 Z= 0.156 Angle : 0.525 7.555 20339 Z= 0.276 Chirality : 0.042 0.198 2278 Planarity : 0.004 0.064 2414 Dihedral : 14.316 172.371 2637 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.62 % Allowed : 14.61 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.21), residues: 1638 helix: 1.74 (0.20), residues: 658 sheet: -0.18 (0.31), residues: 256 loop : 0.27 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 590 TYR 0.013 0.001 TYR B 234 PHE 0.013 0.001 PHE A 620 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00367 (14871) covalent geometry : angle 0.52366 (20333) hydrogen bonds : bond 0.04193 ( 662) hydrogen bonds : angle 4.21745 ( 1831) metal coordination : bond 0.00768 ( 8) metal coordination : angle 1.90316 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.616 Fit side-chains REVERT: A 99 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: A 196 LYS cc_start: 0.8011 (mttt) cc_final: 0.7784 (mtpp) REVERT: A 200 GLU cc_start: 0.8113 (tt0) cc_final: 0.7760 (tp30) REVERT: A 262 LYS cc_start: 0.7326 (ptpp) cc_final: 0.6935 (mtmt) REVERT: A 828 LYS cc_start: 0.7780 (tttt) cc_final: 0.7422 (mtmm) REVERT: A 847 ASP cc_start: 0.8095 (t0) cc_final: 0.7822 (t70) REVERT: B 124 ARG cc_start: 0.8180 (tpt90) cc_final: 0.7821 (tpt90) REVERT: B 291 ARG cc_start: 0.7589 (ptt-90) cc_final: 0.7174 (pmm-80) REVERT: B 513 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8464 (ttpt) REVERT: B 618 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6574 (m110) REVERT: B 637 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7758 (tmt-80) outliers start: 24 outliers final: 18 residues processed: 189 average time/residue: 0.7907 time to fit residues: 161.0980 Evaluate side-chains 196 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 252 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126156 restraints weight = 15488.404| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.01 r_work: 0.3120 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14879 Z= 0.233 Angle : 0.582 7.812 20339 Z= 0.305 Chirality : 0.044 0.199 2278 Planarity : 0.005 0.075 2414 Dihedral : 14.365 172.940 2637 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 14.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1638 helix: 1.56 (0.20), residues: 656 sheet: -0.26 (0.31), residues: 252 loop : 0.13 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 590 TYR 0.017 0.002 TYR B 740 PHE 0.015 0.002 PHE A 620 TRP 0.011 0.002 TRP B 332 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00558 (14871) covalent geometry : angle 0.58107 (20333) hydrogen bonds : bond 0.04821 ( 662) hydrogen bonds : angle 4.33454 ( 1831) metal coordination : bond 0.00618 ( 8) metal coordination : angle 1.69195 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.575 Fit side-chains REVERT: A 99 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: A 196 LYS cc_start: 0.8065 (mttt) cc_final: 0.7797 (mtpp) REVERT: A 200 GLU cc_start: 0.8146 (tt0) cc_final: 0.7791 (tp30) REVERT: A 262 LYS cc_start: 0.7355 (ptpp) cc_final: 0.6947 (mtmt) REVERT: A 828 LYS cc_start: 0.7778 (tttt) cc_final: 0.7415 (mtmm) REVERT: A 847 ASP cc_start: 0.8094 (t0) cc_final: 0.7822 (t70) REVERT: B 124 ARG cc_start: 0.8175 (tpt90) cc_final: 0.7810 (tpt90) REVERT: B 482 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: B 513 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8459 (ttpt) REVERT: B 618 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.7014 (t0) REVERT: B 637 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7817 (tmt-80) outliers start: 24 outliers final: 17 residues processed: 188 average time/residue: 0.8302 time to fit residues: 167.4290 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 252 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 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 719 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 771 GLN B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127591 restraints weight = 15602.942| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.93 r_work: 0.3123 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14879 Z= 0.119 Angle : 0.506 7.677 20339 Z= 0.265 Chirality : 0.041 0.197 2278 Planarity : 0.004 0.048 2414 Dihedral : 14.310 172.084 2637 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.42 % Allowed : 15.02 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.21), residues: 1638 helix: 1.78 (0.20), residues: 658 sheet: -0.24 (0.31), residues: 256 loop : 0.31 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 643 TYR 0.018 0.001 TYR B 740 PHE 0.014 0.001 PHE A 620 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00275 (14871) covalent geometry : angle 0.50454 (20333) hydrogen bonds : bond 0.03834 ( 662) hydrogen bonds : angle 4.16565 ( 1831) metal coordination : bond 0.00857 ( 8) metal coordination : angle 2.14562 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6687.44 seconds wall clock time: 114 minutes 18.48 seconds (6858.48 seconds total)