Starting phenix.real_space_refine on Thu Aug 6 08:38:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmw_51456/08_2026/9gmw_51456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmw_51456/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gmw_51456/08_2026/9gmw_51456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmw_51456/08_2026/9gmw_51456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gmw_51456/08_2026/9gmw_51456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmw_51456/08_2026/9gmw_51456.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 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: 3.24, per 1000 atoms: 0.22 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: 0.88 Conformation dependent library (CDL) restraints added in 467.3 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: 1.85 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: 2.75 Time building geometry restraints manager: 1.20 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: 20122 2.16 - 4.32: 314 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=" O5' G T 17 " pdb=" C5' G T 17 " pdb=" C4' G T 17 " ideal model delta sigma weight residual 109.40 112.76 -3.36 8.00e-01 1.56e+00 1.77e+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 ... (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: 1877 0.051 - 0.101: 303 0.101 - 0.152: 113 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 2.320 nonbonded pdb=" OE1 GLU B 209 " pdb="MN MN B1003 " model vdw 2.001 2.320 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- 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= 0.211 Angle : 0.653 10.788 20473 Z= 0.420 Chirality : 0.044 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 0.00381 / 0.21 (14959) covalent geometry : angle 0.65205 / 0.42 (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 : 0.496 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: 0.7629 time to fit residues: 168.7218 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 : 0.447 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.151536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115048 restraints weight = 17773.650| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.85 r_work: 0.3136 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14967 Z= 0.159 Angle : 0.573 7.600 20473 Z= 0.302 Chirality : 0.043 0.233 2298 Planarity : 0.004 0.040 2418 Dihedral : 14.425 86.324 2711 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.03 % Allowed : 13.80 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1638 helix: 1.21 (0.21), residues: 653 sheet: 0.32 (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 0.034 0.002 TYR B 681 PHE 0.013 0.001 PHE B 434 TRP 0.010 0.001 TRP A 413 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (14959) covalent geometry : angle 0.57106 / 0.30 (20467) hydrogen bonds : bond 0.04998 / 3.31 ( 639) hydrogen bonds : angle 4.62692 / 3.17 ( 1747) metal coordination : bond 0.00818 / 0.41 ( 8) metal coordination : angle 2.83830 / 1.42 ( 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 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.345 Fit side-chains REVERT: A 68 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: A 124 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7781 (ttp80) REVERT: A 221 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7449 (mmtm) REVERT: A 228 LYS cc_start: 0.8728 (tttt) cc_final: 0.8205 (mppt) REVERT: A 275 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 657 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: B 44 GLU cc_start: 0.8078 (tp30) cc_final: 0.7678 (tt0) REVERT: B 590 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7504 (ttt-90) REVERT: B 610 MET cc_start: 0.8847 (mtm) cc_final: 0.8593 (mtp) REVERT: B 617 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8106 (tpp80) REVERT: B 649 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 744 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 789 MET cc_start: 0.7214 (mmm) cc_final: 0.6061 (tpp) REVERT: B 830 MET cc_start: 0.6269 (tpp) cc_final: 0.6017 (ttt) outliers start: 30 outliers final: 8 residues processed: 208 average time/residue: 0.7049 time to fit residues: 158.4686 Evaluate side-chains 176 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 252 ASP 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: 0.5980 chunk 152 optimal weight: 3.9990 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: 20.0000 chunk 46 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.151651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114214 restraints weight = 17945.627| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.98 r_work: 0.3141 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14967 Z= 0.150 Angle : 0.547 9.717 20473 Z= 0.285 Chirality : 0.042 0.298 2298 Planarity : 0.004 0.082 2418 Dihedral : 14.285 84.649 2704 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 13.94 % Favored : 83.29 % 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: 0.89 (0.21), residues: 1638 helix: 1.17 (0.21), residues: 661 sheet: 0.37 (0.30), residues: 277 loop : 0.28 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.029 0.001 TYR B 681 PHE 0.023 0.001 PHE A 295 TRP 0.009 0.001 TRP B 332 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14959) covalent geometry : angle 0.54534 / 0.28 (20467) hydrogen bonds : bond 0.04674 / 3.07 ( 639) hydrogen bonds : angle 4.48685 / 3.07 ( 1747) metal coordination : bond 0.00622 / 0.32 ( 8) metal coordination : angle 2.26835 / 1.13 ( 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: 41 poor density : 181 time to evaluate : 0.579 Fit side-chains REVERT: A 68 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: A 124 ARG cc_start: 0.8067 (ttp-170) cc_final: 0.7789 (ttp80) REVERT: A 221 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7423 (mmtm) REVERT: A 228 LYS cc_start: 0.8730 (tttt) cc_final: 0.8167 (mppt) REVERT: A 229 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6847 (ttp-170) REVERT: A 275 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 657 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: B 44 GLU cc_start: 0.8059 (tp30) cc_final: 0.7671 (tt0) REVERT: B 583 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: B 590 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7481 (ttt-90) REVERT: B 617 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8070 (tpp80) REVERT: B 649 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 744 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 788 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7155 (mp) REVERT: B 789 MET cc_start: 0.7335 (mmm) cc_final: 0.6245 (tpp) REVERT: B 830 MET cc_start: 0.6257 (tpp) cc_final: 0.5951 (ttt) outliers start: 41 outliers final: 12 residues processed: 204 average time/residue: 0.6951 time to fit residues: 153.6950 Evaluate side-chains 182 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 B residue 35 GLN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER 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 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: 4.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110188 restraints weight = 17973.018| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.89 r_work: 0.3063 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14967 Z= 0.305 Angle : 0.663 11.092 20473 Z= 0.340 Chirality : 0.047 0.289 2298 Planarity : 0.005 0.049 2418 Dihedral : 14.400 80.886 2704 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.52 % Allowed : 14.48 % Favored : 82.00 % 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: 0.46 (0.21), residues: 1638 helix: 0.80 (0.20), residues: 659 sheet: 0.22 (0.31), residues: 274 loop : 0.02 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 617 TYR 0.026 0.002 TYR B 681 PHE 0.015 0.002 PHE A 896 TRP 0.016 0.002 TRP B 332 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.30 (14959) covalent geometry : angle 0.66262 / 0.34 (20467) hydrogen bonds : bond 0.05399 / 3.62 ( 639) hydrogen bonds : angle 4.70108 / 3.23 ( 1747) metal coordination : bond 0.01943 / 1.26 ( 8) metal coordination : angle 1.84456 / 1.10 ( 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 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 0.453 Fit side-chains REVERT: A 66 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8146 (mttt) REVERT: A 68 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: A 124 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7864 (ttp80) REVERT: A 134 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8324 (ptt180) REVERT: A 146 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7960 (mtp180) REVERT: A 221 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7476 (mmtm) REVERT: A 228 LYS cc_start: 0.8773 (tttt) cc_final: 0.8144 (mppt) REVERT: A 657 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 735 ASP cc_start: 0.8307 (t0) cc_final: 0.8026 (m-30) REVERT: A 780 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6325 (mttm) REVERT: B 144 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8257 (p0) REVERT: B 583 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: B 590 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7539 (ttt-90) REVERT: B 617 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8072 (tpp80) REVERT: B 646 CYS cc_start: 0.8270 (p) cc_final: 0.8063 (p) REVERT: B 649 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 744 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: B 788 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7187 (mp) REVERT: B 830 MET cc_start: 0.6315 (tpp) cc_final: 0.5900 (ttt) outliers start: 52 outliers final: 23 residues processed: 206 average time/residue: 0.6598 time to fit residues: 147.3985 Evaluate side-chains 201 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 656 ARG 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 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP 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 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 618 ASN 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 Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115081 restraints weight = 17808.953| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.92 r_work: 0.3108 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14967 Z= 0.129 Angle : 0.539 11.409 20473 Z= 0.280 Chirality : 0.041 0.287 2298 Planarity : 0.004 0.059 2418 Dihedral : 14.325 81.247 2704 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.57 % Allowed : 15.90 % Favored : 81.53 % 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: 0.89 (0.21), residues: 1638 helix: 1.20 (0.21), residues: 654 sheet: 0.34 (0.30), residues: 281 loop : 0.27 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 617 TYR 0.021 0.001 TYR B 681 PHE 0.012 0.001 PHE A 295 TRP 0.011 0.001 TRP A 413 HIS 0.003 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14959) covalent geometry : angle 0.53832 / 0.28 (20467) hydrogen bonds : bond 0.04352 / 2.87 ( 639) hydrogen bonds : angle 4.47065 / 3.07 ( 1747) metal coordination : bond 0.00723 / 0.37 ( 8) metal coordination : angle 2.01322 / 0.92 ( 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 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.350 Fit side-chains REVERT: A 66 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7961 (mttt) REVERT: A 68 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: A 124 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7860 (ttp80) REVERT: A 134 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8309 (ptt180) REVERT: A 146 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: A 221 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7524 (mmtm) REVERT: A 228 LYS cc_start: 0.8756 (tttt) cc_final: 0.8160 (mppt) REVERT: A 533 MET cc_start: 0.7904 (ttm) cc_final: 0.7268 (ttt) REVERT: A 657 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: B 253 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (mppt) REVERT: B 340 CYS cc_start: 0.8898 (m) cc_final: 0.8690 (p) REVERT: B 583 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: B 590 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7550 (ttt-90) REVERT: B 617 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8037 (tpp80) REVERT: B 649 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 744 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 788 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (mp) REVERT: B 830 MET cc_start: 0.6311 (tpp) cc_final: 0.5855 (ttt) outliers start: 38 outliers final: 14 residues processed: 206 average time/residue: 0.7178 time to fit residues: 159.9105 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU 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 686 SER 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 B residue 37 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 444 SER 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: 2.9990 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 746 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 = 0.3751 r_free = 0.3751 target = 0.150184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113918 restraints weight = 17781.778| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.91 r_work: 0.3086 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14967 Z= 0.173 Angle : 0.547 7.485 20473 Z= 0.285 Chirality : 0.042 0.163 2298 Planarity : 0.004 0.058 2418 Dihedral : 14.306 79.406 2704 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.91 % Allowed : 16.24 % Favored : 80.85 % 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: 0.79 (0.21), residues: 1638 helix: 1.12 (0.21), residues: 654 sheet: 0.24 (0.31), residues: 274 loop : 0.23 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 617 TYR 0.021 0.002 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.012 0.001 TRP A 699 HIS 0.002 0.001 HIS A 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (14959) covalent geometry : angle 0.54597 / 0.28 (20467) hydrogen bonds : bond 0.04518 / 3.00 ( 639) hydrogen bonds : angle 4.49002 / 3.08 ( 1747) metal coordination : bond 0.00595 / 0.37 ( 8) metal coordination : angle 1.82579 / 0.91 ( 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 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.362 Fit side-chains REVERT: A 66 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8051 (mttt) REVERT: A 68 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 134 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8287 (ptt180) REVERT: A 146 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8067 (mtp180) REVERT: A 221 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7519 (mmtm) REVERT: A 228 LYS cc_start: 0.8767 (tttt) cc_final: 0.8173 (mppt) REVERT: A 656 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7213 (ptp-110) REVERT: A 657 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 745 MET cc_start: 0.8143 (mmm) cc_final: 0.7901 (mtp) REVERT: B 44 GLU cc_start: 0.8108 (tp30) cc_final: 0.7713 (tt0) REVERT: B 253 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (mppt) REVERT: B 453 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 583 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: B 590 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7569 (ttt-90) REVERT: B 617 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8009 (tpp80) REVERT: B 649 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 744 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 788 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7090 (mp) REVERT: B 830 MET cc_start: 0.6198 (tpp) cc_final: 0.5793 (ttt) outliers start: 43 outliers final: 14 residues processed: 196 average time/residue: 0.6973 time to fit residues: 148.1304 Evaluate side-chains 186 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 134 ARG Chi-restraints excluded: chain A residue 146 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.149267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111925 restraints weight = 17802.756| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.89 r_work: 0.3092 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14967 Z= 0.213 Angle : 0.585 10.830 20473 Z= 0.302 Chirality : 0.043 0.161 2298 Planarity : 0.004 0.037 2418 Dihedral : 14.314 77.099 2704 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.38 % Allowed : 16.24 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.21), residues: 1638 helix: 1.05 (0.21), residues: 650 sheet: 0.09 (0.31), residues: 264 loop : 0.14 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 617 TYR 0.024 0.002 TYR B 681 PHE 0.011 0.001 PHE B 585 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 0.00509 / 0.21 (14959) covalent geometry : angle 0.58402 / 0.30 (20467) hydrogen bonds : bond 0.04741 / 3.16 ( 639) hydrogen bonds : angle 4.55144 / 3.12 ( 1747) metal coordination : bond 0.00938 / 0.61 ( 8) metal coordination : angle 1.78764 / 0.96 ( 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 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.564 Fit side-chains REVERT: A 66 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8088 (mttt) REVERT: A 68 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: A 146 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8059 (mtp180) REVERT: A 228 LYS cc_start: 0.8780 (tttt) cc_final: 0.8156 (mppt) REVERT: A 656 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7254 (ptp-110) REVERT: A 657 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: A 735 ASP cc_start: 0.8319 (t0) cc_final: 0.8048 (m-30) REVERT: A 745 MET cc_start: 0.8147 (mmm) cc_final: 0.7933 (mtp) REVERT: B 44 GLU cc_start: 0.8055 (tp30) cc_final: 0.7695 (tt0) REVERT: B 144 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8238 (p0) REVERT: B 253 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7966 (mppt) REVERT: B 340 CYS cc_start: 0.8873 (m) cc_final: 0.8671 (p) REVERT: B 453 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: B 583 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: B 590 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7598 (ttt-90) REVERT: B 617 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8008 (tpp80) REVERT: B 649 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8077 (mm-30) REVERT: B 744 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 788 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7102 (mp) REVERT: B 830 MET cc_start: 0.6189 (tpp) cc_final: 0.5782 (ttt) outliers start: 50 outliers final: 23 residues processed: 202 average time/residue: 0.7166 time to fit residues: 157.2599 Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 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 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS 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 612 ILE 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 713 SER 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: 0.9990 chunk 164 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 880 ASN B 746 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 = 0.3757 r_free = 0.3757 target = 0.150766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113501 restraints weight = 17732.009| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.91 r_work: 0.3113 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14967 Z= 0.143 Angle : 0.549 15.435 20473 Z= 0.284 Chirality : 0.041 0.153 2298 Planarity : 0.004 0.063 2418 Dihedral : 14.292 76.672 2704 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.91 % Allowed : 16.85 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1638 helix: 1.13 (0.20), residues: 656 sheet: 0.10 (0.31), residues: 263 loop : 0.19 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 690 TYR 0.024 0.001 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.015 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (14959) covalent geometry : angle 0.54819 / 0.28 (20467) hydrogen bonds : bond 0.04367 / 2.90 ( 639) hydrogen bonds : angle 4.50786 / 3.10 ( 1747) metal coordination : bond 0.00494 / 0.26 ( 8) metal coordination : angle 1.77510 / 0.87 ( 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 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.583 Fit side-chains REVERT: A 66 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8034 (mttt) REVERT: A 68 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: A 134 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8329 (ptt180) REVERT: A 146 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8026 (mtp180) REVERT: A 228 LYS cc_start: 0.8778 (tttt) cc_final: 0.8148 (mppt) REVERT: A 656 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7046 (ptp-110) REVERT: A 657 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: B 44 GLU cc_start: 0.8049 (tp30) cc_final: 0.7668 (tt0) REVERT: B 144 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8206 (p0) REVERT: B 253 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7951 (mppt) REVERT: B 335 GLU cc_start: 0.8106 (tt0) cc_final: 0.7822 (pp20) REVERT: B 453 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 583 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 590 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7571 (ttt-90) REVERT: B 617 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7972 (tpp80) REVERT: B 646 CYS cc_start: 0.8117 (p) cc_final: 0.7911 (p) REVERT: B 649 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8096 (mm-30) REVERT: B 744 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 786 GLU cc_start: 0.8089 (mp0) cc_final: 0.7706 (mm-30) REVERT: B 830 MET cc_start: 0.6147 (tpp) cc_final: 0.5750 (ttt) outliers start: 43 outliers final: 17 residues processed: 191 average time/residue: 0.7693 time to fit residues: 159.3914 Evaluate side-chains 186 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 662 ILE Chi-restraints excluded: chain A residue 675 THR 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 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS 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 650 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU 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: 0.8980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.151941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114662 restraints weight = 17780.910| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.91 r_work: 0.3130 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14967 Z= 0.130 Angle : 0.543 12.604 20473 Z= 0.280 Chirality : 0.040 0.154 2298 Planarity : 0.004 0.039 2418 Dihedral : 14.258 75.635 2704 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.23 % Allowed : 17.59 % 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: 0.90 (0.21), residues: 1638 helix: 1.30 (0.21), residues: 649 sheet: 0.12 (0.31), residues: 263 loop : 0.29 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 690 TYR 0.022 0.001 TYR B 681 PHE 0.020 0.001 PHE B 435 TRP 0.013 0.001 TRP A 699 HIS 0.002 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14959) covalent geometry : angle 0.54170 / 0.28 (20467) hydrogen bonds : bond 0.04181 / 2.75 ( 639) hydrogen bonds : angle 4.45219 / 3.06 ( 1747) metal coordination : bond 0.00551 / 0.28 ( 8) metal coordination : angle 1.86945 / 0.93 ( 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 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.596 Fit side-chains REVERT: A 66 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8056 (mttt) REVERT: A 68 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 146 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (mtp180) REVERT: A 192 LEU cc_start: 0.8666 (mt) cc_final: 0.8425 (mp) REVERT: A 228 LYS cc_start: 0.8784 (tttt) cc_final: 0.8154 (mppt) REVERT: A 656 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7014 (ptp-110) REVERT: A 657 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: B 44 GLU cc_start: 0.8029 (tp30) cc_final: 0.7660 (tt0) REVERT: B 144 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8205 (p0) REVERT: B 335 GLU cc_start: 0.8094 (tt0) cc_final: 0.7791 (pp20) REVERT: B 583 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: B 590 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7552 (ttt-90) REVERT: B 617 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7949 (tpp80) REVERT: B 646 CYS cc_start: 0.8096 (p) cc_final: 0.7884 (p) REVERT: B 649 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 744 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 786 GLU cc_start: 0.8078 (mp0) cc_final: 0.7766 (mm-30) REVERT: B 830 MET cc_start: 0.6061 (tpp) cc_final: 0.5671 (ttt) outliers start: 33 outliers final: 15 residues processed: 188 average time/residue: 0.7652 time to fit residues: 155.3109 Evaluate side-chains 185 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 779 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 252 ASP 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 650 THR Chi-restraints excluded: chain B residue 713 SER 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: 3.9990 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 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: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN A 634 GLN A 880 ASN B 35 GLN B 891 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109817 restraints weight = 18028.824| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.91 r_work: 0.3040 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 14967 Z= 0.334 Angle : 0.679 12.373 20473 Z= 0.348 Chirality : 0.048 0.161 2298 Planarity : 0.005 0.058 2418 Dihedral : 14.356 74.231 2704 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.44 % Allowed : 17.73 % Favored : 79.84 % 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: 0.35 (0.21), residues: 1638 helix: 0.78 (0.20), residues: 651 sheet: -0.01 (0.31), residues: 274 loop : -0.02 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 617 TYR 0.030 0.002 TYR B 226 PHE 0.022 0.002 PHE B 435 TRP 0.017 0.002 TRP B 332 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.33 (14959) covalent geometry : angle 0.67850 / 0.35 (20467) hydrogen bonds : bond 0.05379 / 3.60 ( 639) hydrogen bonds : angle 4.76001 / 3.27 ( 1747) metal coordination : bond 0.02043 / 1.31 ( 8) metal coordination : angle 1.78997 / 1.13 ( 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 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.413 Fit side-chains REVERT: A 66 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8174 (mttt) REVERT: A 68 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: A 146 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8017 (mtp180) REVERT: A 228 LYS cc_start: 0.8808 (tttt) cc_final: 0.8144 (mppt) REVERT: A 656 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7222 (ptp-110) REVERT: A 657 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: A 735 ASP cc_start: 0.8362 (t0) cc_final: 0.8075 (m-30) REVERT: A 745 MET cc_start: 0.8188 (mmm) cc_final: 0.7931 (mtp) REVERT: B 44 GLU cc_start: 0.8088 (tp30) cc_final: 0.7716 (tt0) REVERT: B 144 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8328 (p0) REVERT: B 253 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7993 (mppt) REVERT: B 340 CYS cc_start: 0.9023 (m) cc_final: 0.8664 (p) REVERT: B 583 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: B 590 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7627 (ttt-90) REVERT: B 617 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7991 (tpp80) REVERT: B 649 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 744 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 786 GLU cc_start: 0.8155 (mp0) cc_final: 0.7869 (mm-30) REVERT: B 789 MET cc_start: 0.7082 (mmt) cc_final: 0.6859 (tpp) REVERT: B 830 MET cc_start: 0.6354 (tpp) cc_final: 0.5784 (ttt) outliers start: 36 outliers final: 18 residues processed: 182 average time/residue: 0.7203 time to fit residues: 142.2355 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 789 MET Chi-restraints excluded: chain A residue 819 VAL 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 144 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS 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 650 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU 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: 0.6980 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.151593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114449 restraints weight = 17651.538| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.90 r_work: 0.3123 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14967 Z= 0.129 Angle : 0.548 10.486 20473 Z= 0.286 Chirality : 0.040 0.154 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.265 73.655 2704 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 18.20 % Favored : 79.84 % 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: 1.20 (0.21), residues: 644 sheet: 0.12 (0.32), residues: 261 loop : 0.18 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 617 TYR 0.021 0.001 TYR B 629 PHE 0.020 0.001 PHE B 435 TRP 0.013 0.001 TRP A 413 HIS 0.006 0.001 HIS B 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14959) covalent geometry : angle 0.54712 / 0.29 (20467) hydrogen bonds : bond 0.04179 / 2.75 ( 639) hydrogen bonds : angle 4.50331 / 3.10 ( 1747) metal coordination : bond 0.00601 / 0.31 ( 8) metal coordination : angle 2.03924 / 0.98 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5253.60 seconds wall clock time: 90 minutes 11.71 seconds (5411.71 seconds total)