Starting phenix.real_space_refine on Fri Jul 3 13:45:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmw_51456/07_2026/9gmw_51456.cif" } resolution = 3.0 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= 0.061 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 56 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 9043 2.51 5 N 2541 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14541 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "T" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1202 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 26, 'rna3p_pyr': 21} Link IDs: {'rna2p': 9, 'rna3p': 46} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 73.938 71.936 73.983 1.00 81.26 S ATOM 2310 SG CYS A 321 73.603 73.272 77.563 1.00 62.21 S ATOM 2316 SG CYS A 322 71.140 70.720 76.248 1.00 68.49 S ATOM 8698 SG CYS B 287 22.807 59.043 73.155 1.00 83.06 S ATOM 8975 SG CYS B 321 22.939 57.708 76.760 1.00 69.10 S ATOM 8981 SG CYS B 322 25.305 60.422 75.628 1.00 77.61 S Time building chain proxies: 2.91, per 1000 atoms: 0.20 Number of scatterers: 14541 At special positions: 0 Unit cell: (95.964, 130.133, 146.127, 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 56 15.00 Mg 4 11.99 O 2806 8.00 N 2541 7.00 C 9043 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: 1.22 Conformation dependent library (CDL) restraints added in 579.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 45.2% alpha, 18.9% beta 23 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.591A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 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 144 through 157 Processing helix chain 'A' and resid 189 through 195 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 280 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 384 through 397 removed outlier: 5.517A pdb=" N LYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.216A 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 481 through 501 removed outlier: 4.469A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.606A 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 592 removed outlier: 3.762A pdb=" N ASN A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) 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 655 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 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.628A pdb=" N GLN A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix 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 removed outlier: 3.644A pdb=" N ALA A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.095A 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 removed outlier: 3.631A pdb=" N LEU A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) 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 144 through 156 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.629A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix removed outlier: 3.581A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) 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: 3.906A 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: 5.769A pdb=" N LYS B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.206A 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 481 through 501 removed outlier: 4.292A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.556A pdb=" N TYR B 539 " --> pdb=" O PRO B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 Processing helix chain 'B' and resid 587 through 590 removed outlier: 3.767A pdb=" N ARG B 590 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 587 through 590' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.503A pdb=" N ASP B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.689A 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 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.880A pdb=" N GLN B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 831 removed outlier: 3.909A pdb=" N GLU B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 824 " --> pdb=" O GLU B 820 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 829 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 removed outlier: 4.149A pdb=" N VAL B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 4.318A 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: 6.350A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.346A 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: 6.443A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.443A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.235A 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 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: 6.395A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.369A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 595 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU A 702 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL A 597 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.116A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.252A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.333A 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 135 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.425A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.331A 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: 6.425A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.796A 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: 3.533A 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: 6.405A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.323A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.685A 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: 6.171A 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: 6.096A pdb=" N THR B 776 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 895 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B 778 " --> pdb=" O ILE B 895 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 810 " --> pdb=" O PHE B 866 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 868 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 812 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2269 1.32 - 1.44: 4263 1.44 - 1.57: 8197 1.57 - 1.69: 108 1.69 - 1.82: 122 Bond restraints: 14959 Sorted by residual: bond pdb=" CA ARG B 637 " pdb=" C ARG B 637 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.27e-02 6.20e+03 2.36e+01 bond pdb=" C SER A 586 " pdb=" N ARG A 587 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.38e-02 5.25e+03 1.22e+01 bond pdb=" C MET B 63 " pdb=" O MET B 63 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" CA ARG A 124 " pdb=" C ARG A 124 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.66e+00 bond pdb=" N ARG A 587 " pdb=" CA ARG A 587 " ideal model delta sigma weight residual 1.457 1.415 0.042 1.35e-02 5.49e+03 9.56e+00 ... (remaining 14954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20161 2.16 - 4.32: 275 4.32 - 6.47: 26 6.47 - 8.63: 3 8.63 - 10.79: 2 Bond angle restraints: 20467 Sorted by residual: angle pdb=" N ASP A 336 " pdb=" CA ASP A 336 " pdb=" C ASP A 336 " ideal model delta sigma weight residual 108.67 97.88 10.79 1.67e+00 3.59e-01 4.17e+01 angle pdb=" N SER A 586 " pdb=" CA SER A 586 " pdb=" C SER A 586 " ideal model delta sigma weight residual 112.54 118.40 -5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" N SER A 588 " pdb=" CA SER A 588 " pdb=" C SER A 588 " ideal model delta sigma weight residual 113.01 107.28 5.73 1.20e+00 6.94e-01 2.28e+01 angle pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" CB LEU B 125 " ideal model delta sigma weight residual 111.08 104.17 6.91 1.71e+00 3.42e-01 1.63e+01 angle pdb=" C1' G T 10 " pdb=" N9 G T 10 " pdb=" C4 G T 10 " ideal model delta sigma weight residual 126.50 131.69 -5.19 1.30e+00 5.92e-01 1.60e+01 ... (remaining 20462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 8160 18.01 - 36.03: 677 36.03 - 54.04: 231 54.04 - 72.06: 107 72.06 - 90.07: 27 Dihedral angle restraints: 9202 sinusoidal: 4370 harmonic: 4832 Sorted by residual: dihedral pdb=" CA CYS B 646 " pdb=" C CYS B 646 " pdb=" N ARG B 647 " pdb=" CA ARG B 647 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 158.41 73.59 1 1.70e+01 3.46e-03 2.38e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1938 0.051 - 0.101: 259 0.101 - 0.152: 96 0.152 - 0.202: 2 0.202 - 0.253: 3 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA ILE A 756 " pdb=" N ILE A 756 " pdb=" C ILE A 756 " pdb=" CB ILE A 756 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO B 123 " pdb=" N PRO B 123 " pdb=" C PRO B 123 " pdb=" CB PRO B 123 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 690 " -0.210 9.50e-02 1.11e+02 9.48e-02 7.17e+00 pdb=" NE ARG B 690 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 690 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 690 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 690 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G T 6 " -0.031 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G T 6 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G T 6 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G T 6 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G T 6 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G T 6 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G T 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G T 6 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G T 6 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 231 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO B 232 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " -0.026 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 66 2.48 - 3.08: 9953 3.08 - 3.69: 22144 3.69 - 4.29: 34284 4.29 - 4.90: 56250 Nonbonded interactions: 122697 Sorted by model distance: nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.874 2.170 nonbonded pdb=" OP2 U T 60 " pdb="MG MG T 101 " model vdw 1.914 2.170 nonbonded pdb=" OD2 ASP A 252 " pdb="MN MN A1002 " model vdw 1.999 3.060 nonbonded pdb=" OE1 GLU B 209 " pdb="MN MN B1003 " model vdw 2.001 3.060 nonbonded pdb=" N7 G T 15 " pdb="MG MG T 102 " model vdw 2.058 2.250 ... (remaining 122692 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.200 Find NCS groups from input model: 0.220 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 0.062 14967 Z= 0.207 Angle : 0.629 10.788 20473 Z= 0.387 Chirality : 0.042 0.253 2298 Planarity : 0.004 0.095 2418 Dihedral : 16.814 90.074 6078 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.34 % Allowed : 13.80 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1638 helix: 1.01 (0.21), residues: 652 sheet: 0.48 (0.30), residues: 287 loop : 0.20 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 690 TYR 0.026 0.001 TYR B 681 PHE 0.022 0.001 PHE B 435 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.21 (14959) covalent geometry : angle 0.62781 / 0.39 (20467) hydrogen bonds : bond 0.13175 / 8.73 ( 639) hydrogen bonds : angle 5.53927 / 3.79 ( 1747) metal coordination : bond 0.00852 / 0.43 ( 8) metal coordination : angle 2.24949 / 1.19 ( 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 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7659 (ttp80) REVERT: A 228 LYS cc_start: 0.8472 (tttt) cc_final: 0.7840 (mmtp) REVERT: B 788 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7142 (mp) outliers start: 5 outliers final: 3 residues processed: 205 average time/residue: 0.6363 time to fit residues: 141.1173 Evaluate side-chains 180 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 638 ASN A 663 GLN A 880 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114160 restraints weight = 17782.788| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.93 r_work: 0.3112 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14967 Z= 0.163 Angle : 0.565 6.662 20473 Z= 0.298 Chirality : 0.042 0.214 2298 Planarity : 0.004 0.041 2418 Dihedral : 14.474 87.509 2711 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 14.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1638 helix: 1.22 (0.21), residues: 653 sheet: 0.31 (0.30), residues: 278 loop : 0.25 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 690 TYR 0.033 0.002 TYR B 681 PHE 0.013 0.001 PHE B 434 TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14959) covalent geometry : angle 0.56266 / 0.30 (20467) hydrogen bonds : bond 0.05085 / 3.37 ( 639) hydrogen bonds : angle 4.64235 / 3.18 ( 1747) metal coordination : bond 0.00802 / 0.40 ( 8) metal coordination : angle 2.77604 / 1.38 ( 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 218 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.536 Fit side-chains REVERT: A 68 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: A 124 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7813 (ttp80) REVERT: A 221 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7446 (mmtm) REVERT: A 228 LYS cc_start: 0.8743 (tttt) cc_final: 0.8212 (mppt) REVERT: A 657 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 44 GLU cc_start: 0.8146 (tp30) cc_final: 0.7729 (tt0) REVERT: B 590 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7547 (ttt-90) REVERT: B 610 MET cc_start: 0.8871 (mtm) cc_final: 0.8623 (mtp) REVERT: B 617 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8137 (tpp80) REVERT: B 649 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 744 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 789 MET cc_start: 0.7294 (mmm) cc_final: 0.6110 (tpp) REVERT: B 830 MET cc_start: 0.6257 (tpp) cc_final: 0.6011 (ttt) outliers start: 26 outliers final: 7 residues processed: 204 average time/residue: 0.6072 time to fit residues: 134.0031 Evaluate side-chains 175 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 88 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112128 restraints weight = 18008.887| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.86 r_work: 0.3102 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14967 Z= 0.229 Angle : 0.597 9.107 20473 Z= 0.311 Chirality : 0.045 0.315 2298 Planarity : 0.005 0.075 2418 Dihedral : 14.377 84.928 2704 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.04 % Allowed : 13.46 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1638 helix: 1.03 (0.20), residues: 655 sheet: 0.29 (0.30), residues: 278 loop : 0.12 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 617 TYR 0.028 0.002 TYR B 681 PHE 0.016 0.002 PHE A 295 TRP 0.013 0.002 TRP B 332 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (14959) covalent geometry : angle 0.59616 / 0.31 (20467) hydrogen bonds : bond 0.05059 / 3.36 ( 639) hydrogen bonds : angle 4.60565 / 3.16 ( 1747) metal coordination : bond 0.01066 / 0.69 ( 8) metal coordination : angle 2.12657 / 1.11 ( 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 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8011 (mttt) REVERT: A 68 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 124 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7828 (ttp80) REVERT: A 134 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8359 (ptt180) REVERT: A 221 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7429 (mmtm) REVERT: A 228 LYS cc_start: 0.8736 (tttt) cc_final: 0.8178 (mppt) REVERT: A 229 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6948 (ttp-170) REVERT: A 657 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: A 735 ASP cc_start: 0.8268 (t0) cc_final: 0.8000 (m-30) REVERT: B 583 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: B 590 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7510 (ttt-90) REVERT: B 617 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8086 (tpp80) REVERT: B 649 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 744 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7804 (mp0) outliers start: 45 outliers final: 12 residues processed: 204 average time/residue: 0.6386 time to fit residues: 141.2536 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 432 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 167 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 107 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 746 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112154 restraints weight = 17965.092| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.92 r_work: 0.3097 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14967 Z= 0.193 Angle : 0.569 9.977 20473 Z= 0.296 Chirality : 0.043 0.294 2298 Planarity : 0.004 0.042 2418 Dihedral : 14.396 83.299 2704 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.91 % Allowed : 14.34 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1638 helix: 1.10 (0.21), residues: 655 sheet: 0.28 (0.30), residues: 278 loop : 0.17 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 617 TYR 0.026 0.002 TYR B 681 PHE 0.011 0.001 PHE B 434 TRP 0.011 0.002 TRP B 332 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (14959) covalent geometry : angle 0.56761 / 0.30 (20467) hydrogen bonds : bond 0.04682 / 3.10 ( 639) hydrogen bonds : angle 4.54488 / 3.12 ( 1747) metal coordination : bond 0.00719 / 0.46 ( 8) metal coordination : angle 1.96064 / 0.96 ( 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 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.403 Fit side-chains REVERT: A 66 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7989 (mttt) REVERT: A 68 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 124 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7835 (ttp80) REVERT: A 146 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: A 221 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7446 (mmtm) REVERT: A 228 LYS cc_start: 0.8767 (tttt) cc_final: 0.8143 (mppt) REVERT: A 229 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6957 (ttp-170) REVERT: A 657 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 780 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6310 (mttm) REVERT: B 134 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: B 583 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: B 590 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7532 (ttt-90) REVERT: B 617 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8064 (tpp80) REVERT: B 649 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 744 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 830 MET cc_start: 0.6294 (tpp) cc_final: 0.5856 (ttt) outliers start: 43 outliers final: 17 residues processed: 203 average time/residue: 0.5884 time to fit residues: 129.0622 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 432 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 112 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 35 GLN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113052 restraints weight = 17873.411| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.89 r_work: 0.3104 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14967 Z= 0.158 Angle : 0.548 11.914 20473 Z= 0.286 Chirality : 0.042 0.167 2298 Planarity : 0.004 0.063 2418 Dihedral : 14.403 81.987 2704 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.98 % Allowed : 15.16 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1638 helix: 1.21 (0.21), residues: 654 sheet: 0.32 (0.30), residues: 281 loop : 0.24 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 617 TYR 0.028 0.001 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (14959) covalent geometry : angle 0.54757 / 0.29 (20467) hydrogen bonds : bond 0.04422 / 2.92 ( 639) hydrogen bonds : angle 4.47794 / 3.08 ( 1747) metal coordination : bond 0.00559 / 0.31 ( 8) metal coordination : angle 1.87082 / 0.89 ( 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: 44 poor density : 175 time to evaluate : 0.407 Fit side-chains REVERT: A 68 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 134 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8341 (ptt180) REVERT: A 146 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8024 (mtp180) REVERT: A 221 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7445 (mmtm) REVERT: A 228 LYS cc_start: 0.8761 (tttt) cc_final: 0.8155 (mppt) REVERT: A 229 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6893 (ttp-170) REVERT: A 533 MET cc_start: 0.7932 (ttm) cc_final: 0.7318 (ttt) REVERT: A 657 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 134 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8447 (ptt180) REVERT: B 340 CYS cc_start: 0.8846 (m) cc_final: 0.8631 (p) REVERT: B 583 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: B 590 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7522 (ttt-90) REVERT: B 617 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8046 (tpp80) REVERT: B 649 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 744 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: B 830 MET cc_start: 0.6152 (tpp) cc_final: 0.5780 (ttt) outliers start: 44 outliers final: 18 residues processed: 204 average time/residue: 0.6135 time to fit residues: 135.2362 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111516 restraints weight = 17867.244| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.90 r_work: 0.3086 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14967 Z= 0.224 Angle : 0.578 8.737 20473 Z= 0.301 Chirality : 0.043 0.163 2298 Planarity : 0.005 0.058 2418 Dihedral : 14.422 79.942 2704 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.79 % Allowed : 15.43 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1638 helix: 1.08 (0.21), residues: 648 sheet: 0.19 (0.31), residues: 271 loop : 0.09 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 690 TYR 0.031 0.002 TYR B 681 PHE 0.011 0.001 PHE B 434 TRP 0.013 0.002 TRP B 332 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (14959) covalent geometry : angle 0.57736 / 0.30 (20467) hydrogen bonds : bond 0.04743 / 3.16 ( 639) hydrogen bonds : angle 4.54470 / 3.13 ( 1747) metal coordination : bond 0.01089 / 0.71 ( 8) metal coordination : angle 1.84759 / 0.98 ( 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 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.520 Fit side-chains REVERT: A 66 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: A 68 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 134 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8315 (ptt180) REVERT: A 146 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: A 221 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7514 (mmtm) REVERT: A 228 LYS cc_start: 0.8771 (tttt) cc_final: 0.8153 (mppt) REVERT: A 229 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6934 (ttp-170) REVERT: A 657 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: A 735 ASP cc_start: 0.8284 (t0) cc_final: 0.8006 (m-30) REVERT: A 745 MET cc_start: 0.8174 (mmm) cc_final: 0.7905 (mtp) REVERT: A 780 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6306 (mttm) REVERT: B 144 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 453 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: B 583 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 590 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7555 (ttt-90) REVERT: B 617 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8081 (tpp80) REVERT: B 649 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 744 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: B 830 MET cc_start: 0.6182 (tpp) cc_final: 0.5785 (ttt) outliers start: 56 outliers final: 23 residues processed: 204 average time/residue: 0.6203 time to fit residues: 137.3075 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113089 restraints weight = 17778.515| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.90 r_work: 0.3114 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14967 Z= 0.143 Angle : 0.537 11.742 20473 Z= 0.279 Chirality : 0.041 0.306 2298 Planarity : 0.004 0.047 2418 Dihedral : 14.413 78.939 2704 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.30 % Allowed : 16.91 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1638 helix: 1.19 (0.21), residues: 656 sheet: 0.19 (0.31), residues: 274 loop : 0.21 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.025 0.001 TYR B 681 PHE 0.009 0.001 PHE A 585 TRP 0.014 0.001 TRP A 699 HIS 0.004 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (14959) covalent geometry : angle 0.53626 / 0.28 (20467) hydrogen bonds : bond 0.04254 / 2.81 ( 639) hydrogen bonds : angle 4.44669 / 3.06 ( 1747) metal coordination : bond 0.00538 / 0.28 ( 8) metal coordination : angle 1.85268 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.548 Fit side-chains REVERT: A 66 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8034 (mttt) REVERT: A 68 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: A 146 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (mtp180) REVERT: A 221 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7484 (mmtm) REVERT: A 228 LYS cc_start: 0.8773 (tttt) cc_final: 0.8154 (mppt) REVERT: A 229 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6885 (ttp-170) REVERT: A 657 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: A 745 MET cc_start: 0.8135 (mmm) cc_final: 0.7866 (mtp) REVERT: A 789 MET cc_start: 0.6058 (ttm) cc_final: 0.5547 (ttm) REVERT: B 453 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: B 583 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: B 590 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7550 (ttt-90) REVERT: B 617 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8019 (tpp80) REVERT: B 649 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 744 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: B 830 MET cc_start: 0.6089 (tpp) cc_final: 0.5709 (ttt) outliers start: 34 outliers final: 13 residues processed: 187 average time/residue: 0.6273 time to fit residues: 127.1954 Evaluate side-chains 176 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 148 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 35 GLN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111856 restraints weight = 17802.374| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.90 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14967 Z= 0.208 Angle : 0.568 10.879 20473 Z= 0.294 Chirality : 0.043 0.213 2298 Planarity : 0.004 0.060 2418 Dihedral : 14.406 76.635 2704 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.11 % Allowed : 16.58 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1638 helix: 1.11 (0.21), residues: 650 sheet: 0.09 (0.31), residues: 264 loop : 0.12 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 690 TYR 0.026 0.002 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.012 0.002 TRP B 332 HIS 0.004 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (14959) covalent geometry : angle 0.56712 / 0.29 (20467) hydrogen bonds : bond 0.04614 / 3.07 ( 639) hydrogen bonds : angle 4.51390 / 3.10 ( 1747) metal coordination : bond 0.00915 / 0.60 ( 8) metal coordination : angle 1.78218 / 0.99 ( 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 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.384 Fit side-chains REVERT: A 66 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: A 68 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: A 146 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: A 221 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7501 (mmtm) REVERT: A 228 LYS cc_start: 0.8789 (tttt) cc_final: 0.8156 (mppt) REVERT: A 229 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6920 (ttp-170) REVERT: A 657 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 735 ASP cc_start: 0.8282 (t0) cc_final: 0.7990 (m-30) REVERT: A 745 MET cc_start: 0.8147 (mmm) cc_final: 0.7893 (mtp) REVERT: B 144 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8273 (p0) REVERT: B 583 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: B 590 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7582 (ttt-90) REVERT: B 617 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8010 (tpp80) REVERT: B 649 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 744 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 830 MET cc_start: 0.6157 (tpp) cc_final: 0.5760 (ttt) outliers start: 46 outliers final: 22 residues processed: 188 average time/residue: 0.6321 time to fit residues: 128.6580 Evaluate side-chains 183 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 134 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 35 GLN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114430 restraints weight = 17805.855| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.90 r_work: 0.3117 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14967 Z= 0.119 Angle : 0.539 12.368 20473 Z= 0.280 Chirality : 0.041 0.195 2298 Planarity : 0.004 0.039 2418 Dihedral : 14.395 76.363 2704 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.17 % Allowed : 17.66 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1638 helix: 1.29 (0.21), residues: 649 sheet: 0.14 (0.31), residues: 263 loop : 0.25 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 690 TYR 0.026 0.001 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.016 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14959) covalent geometry : angle 0.53846 / 0.28 (20467) hydrogen bonds : bond 0.04116 / 2.71 ( 639) hydrogen bonds : angle 4.45023 / 3.07 ( 1747) metal coordination : bond 0.00721 / 0.37 ( 8) metal coordination : angle 1.78715 / 0.87 ( 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 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.386 Fit side-chains REVERT: A 66 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: A 146 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: A 192 LEU cc_start: 0.8657 (mt) cc_final: 0.8410 (mp) REVERT: A 221 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7493 (mmtm) REVERT: A 228 LYS cc_start: 0.8786 (tttt) cc_final: 0.8151 (mppt) REVERT: A 229 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6880 (ttp-170) REVERT: A 657 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 44 GLU cc_start: 0.8027 (tp30) cc_final: 0.7674 (tt0) REVERT: B 583 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: B 590 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7565 (ttt-90) REVERT: B 617 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7989 (tpp80) REVERT: B 649 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 744 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 830 MET cc_start: 0.6184 (tpp) cc_final: 0.5657 (ttt) outliers start: 32 outliers final: 13 residues processed: 181 average time/residue: 0.6343 time to fit residues: 124.9158 Evaluate side-chains 174 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 634 GLN A 880 ASN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110653 restraints weight = 18060.377| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.91 r_work: 0.3071 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14967 Z= 0.280 Angle : 0.633 13.490 20473 Z= 0.326 Chirality : 0.046 0.211 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.419 74.125 2704 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 18.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1638 helix: 0.94 (0.20), residues: 650 sheet: 0.07 (0.31), residues: 272 loop : 0.02 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 617 TYR 0.032 0.002 TYR B 681 PHE 0.011 0.002 PHE A 896 TRP 0.016 0.002 TRP A 699 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.28 (14959) covalent geometry : angle 0.63243 / 0.33 (20467) hydrogen bonds : bond 0.05014 / 3.35 ( 639) hydrogen bonds : angle 4.66620 / 3.22 ( 1747) metal coordination : bond 0.01600 / 1.03 ( 8) metal coordination : angle 1.82704 / 1.11 ( 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 183 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.473 Fit side-chains REVERT: A 66 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8103 (mttt) REVERT: A 146 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: A 221 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7507 (mmtm) REVERT: A 228 LYS cc_start: 0.8796 (tttt) cc_final: 0.8147 (mppt) REVERT: A 229 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.7009 (ttp-170) REVERT: A 657 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: A 735 ASP cc_start: 0.8314 (t0) cc_final: 0.8016 (m-30) REVERT: B 583 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: B 590 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7581 (ttt-90) REVERT: B 617 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8031 (tpp80) REVERT: B 649 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 744 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: B 786 GLU cc_start: 0.8096 (mp0) cc_final: 0.7696 (mm-30) REVERT: B 830 MET cc_start: 0.6325 (tpp) cc_final: 0.5770 (ttt) outliers start: 31 outliers final: 16 residues processed: 171 average time/residue: 0.6567 time to fit residues: 121.5921 Evaluate side-chains 173 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114243 restraints weight = 17673.119| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.88 r_work: 0.3123 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14967 Z= 0.129 Angle : 0.562 16.703 20473 Z= 0.288 Chirality : 0.041 0.191 2298 Planarity : 0.004 0.042 2418 Dihedral : 14.392 73.640 2704 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.76 % Allowed : 18.47 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1638 helix: 1.19 (0.21), residues: 649 sheet: 0.11 (0.32), residues: 261 loop : 0.18 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 617 TYR 0.025 0.001 TYR B 681 PHE 0.010 0.001 PHE A 585 TRP 0.015 0.001 TRP A 699 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14959) covalent geometry : angle 0.56063 / 0.29 (20467) hydrogen bonds : bond 0.04187 / 2.76 ( 639) hydrogen bonds : angle 4.51346 / 3.12 ( 1747) metal coordination : bond 0.00669 / 0.34 ( 8) metal coordination : angle 1.91483 / 0.93 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4544.86 seconds wall clock time: 78 minutes 16.18 seconds (4696.18 seconds total)