Starting phenix.real_space_refine on Thu Sep 18 05:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmw_51456/09_2025/9gmw_51456.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 56 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 9043 2.51 5 N 2541 2.21 5 O 2806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.87, per 1000 atoms: 0.27 Number of scatterers: 14541 At special positions: 0 Unit cell: (95.964, 130.133, 146.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 3 24.99 S 86 16.00 P 56 15.00 Mg 4 11.99 O 2806 8.00 N 2541 7.00 C 9043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 517.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.25 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: 3.40 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2269 1.32 - 1.44: 4263 1.44 - 1.57: 8197 1.57 - 1.69: 108 1.69 - 1.82: 122 Bond restraints: 14959 Sorted by residual: bond pdb=" CA ARG B 637 " pdb=" C ARG B 637 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.27e-02 6.20e+03 2.36e+01 bond pdb=" C SER A 586 " pdb=" N ARG A 587 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.38e-02 5.25e+03 1.22e+01 bond pdb=" C MET B 63 " pdb=" O MET B 63 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" CA ARG A 124 " pdb=" C ARG A 124 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.66e+00 bond pdb=" N ARG A 587 " pdb=" CA ARG A 587 " ideal model delta sigma weight residual 1.457 1.415 0.042 1.35e-02 5.49e+03 9.56e+00 ... (remaining 14954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20161 2.16 - 4.32: 275 4.32 - 6.47: 26 6.47 - 8.63: 3 8.63 - 10.79: 2 Bond angle restraints: 20467 Sorted by residual: angle pdb=" N ASP A 336 " pdb=" CA ASP A 336 " pdb=" C ASP A 336 " ideal model delta sigma weight residual 108.67 97.88 10.79 1.67e+00 3.59e-01 4.17e+01 angle pdb=" N SER A 586 " pdb=" CA SER A 586 " pdb=" C SER A 586 " ideal model delta sigma weight residual 112.54 118.40 -5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" N SER A 588 " pdb=" CA SER A 588 " pdb=" C SER A 588 " ideal model delta sigma weight residual 113.01 107.28 5.73 1.20e+00 6.94e-01 2.28e+01 angle pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" CB LEU B 125 " ideal model delta sigma weight residual 111.08 104.17 6.91 1.71e+00 3.42e-01 1.63e+01 angle pdb=" O PRO A 123 " pdb=" C PRO A 123 " pdb=" N ARG A 124 " ideal model delta sigma weight residual 123.00 118.16 4.84 1.22e+00 6.72e-01 1.57e+01 ... (remaining 20462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 8160 18.01 - 36.03: 677 36.03 - 54.04: 231 54.04 - 72.06: 107 72.06 - 90.07: 27 Dihedral angle restraints: 9202 sinusoidal: 4370 harmonic: 4832 Sorted by residual: dihedral pdb=" CA CYS B 646 " pdb=" C CYS B 646 " pdb=" N ARG B 647 " pdb=" CA ARG B 647 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" O4' U T 16 " pdb=" C1' U T 16 " pdb=" N1 U T 16 " pdb=" C2 U T 16 " ideal model delta sinusoidal sigma weight residual 232.00 158.41 73.59 1 1.70e+01 3.46e-03 2.38e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1938 0.051 - 0.101: 259 0.101 - 0.152: 96 0.152 - 0.202: 2 0.202 - 0.253: 3 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA ILE A 756 " pdb=" N ILE A 756 " pdb=" C ILE A 756 " pdb=" CB ILE A 756 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO B 123 " pdb=" N PRO B 123 " pdb=" C PRO B 123 " pdb=" CB PRO B 123 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2295 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 690 " -0.210 9.50e-02 1.11e+02 9.48e-02 7.17e+00 pdb=" NE ARG B 690 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 690 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 690 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 690 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G T 6 " -0.031 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G T 6 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G T 6 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G T 6 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G T 6 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G T 6 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G T 6 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G T 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G T 6 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G T 6 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 231 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO B 232 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " -0.026 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 66 2.48 - 3.08: 9953 3.08 - 3.69: 22144 3.69 - 4.29: 34284 4.29 - 4.90: 56250 Nonbonded interactions: 122697 Sorted by model distance: nonbonded pdb=" OP1 C T 58 " pdb="MG MG T 101 " model vdw 1.874 2.170 nonbonded pdb=" OP2 U T 60 " pdb="MG MG T 101 " model vdw 1.914 2.170 nonbonded pdb=" OD2 ASP A 252 " pdb="MN MN A1002 " model vdw 1.999 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: 6.520 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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= 0.191 Angle : 0.629 10.788 20473 Z= 0.355 Chirality : 0.042 0.253 2298 Planarity : 0.004 0.095 2418 Dihedral : 16.814 90.074 6078 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.34 % Allowed : 13.80 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00378 (14959) covalent geometry : angle 0.62779 (20467) hydrogen bonds : bond 0.13175 ( 639) hydrogen bonds : angle 5.53927 ( 1747) metal coordination : bond 0.00852 ( 8) metal coordination : angle 2.24949 ( 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 : 0.591 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: 0.8888 time to fit residues: 195.8314 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 : 0.578 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3773 r_free = 0.3773 target = 0.151805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114729 restraints weight = 17794.598| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.92 r_work: 0.3119 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14967 Z= 0.156 Angle : 0.569 6.771 20473 Z= 0.293 Chirality : 0.042 0.177 2298 Planarity : 0.004 0.047 2418 Dihedral : 14.389 86.610 2711 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.89 % Allowed : 13.94 % 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 aren not related in a simple way. whole: 0.94 (0.21), residues: 1638 helix: 1.26 (0.21), residues: 655 sheet: 0.31 (0.30), residues: 279 loop : 0.32 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 690 TYR 0.029 0.002 TYR B 681 PHE 0.014 0.001 PHE B 434 TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00368 (14959) covalent geometry : angle 0.56688 (20467) hydrogen bonds : bond 0.04529 ( 639) hydrogen bonds : angle 4.55403 ( 1747) metal coordination : bond 0.00854 ( 8) metal coordination : angle 2.61097 ( 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: 28 poor density : 194 time to evaluate : 0.755 Fit side-chains REVERT: A 68 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 124 ARG cc_start: 0.8081 (ttp-170) cc_final: 0.7816 (ttp80) REVERT: A 221 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7455 (mmtm) REVERT: A 228 LYS cc_start: 0.8740 (tttt) cc_final: 0.8190 (mppt) REVERT: A 275 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8357 (mm-30) REVERT: A 533 MET cc_start: 0.8056 (mtt) cc_final: 0.7463 (ttt) REVERT: A 657 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: B 44 GLU cc_start: 0.8134 (tp30) cc_final: 0.7733 (tt0) REVERT: B 590 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7543 (ttt-90) REVERT: B 610 MET cc_start: 0.8867 (mtm) cc_final: 0.8622 (mtp) REVERT: B 617 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8123 (tpp80) REVERT: B 649 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 744 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 789 MET cc_start: 0.7316 (mmm) cc_final: 0.6266 (tpp) REVERT: B 830 MET cc_start: 0.6166 (tpp) cc_final: 0.5909 (ttt) outliers start: 28 outliers final: 6 residues processed: 209 average time/residue: 0.8385 time to fit residues: 189.2305 Evaluate side-chains 179 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 657 GLU Chi-restraints excluded: chain A residue 675 THR 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: 0.6980 chunk 152 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 35 GLN B 746 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112216 restraints weight = 18003.004| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.93 r_work: 0.3085 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14967 Z= 0.217 Angle : 0.594 8.004 20473 Z= 0.304 Chirality : 0.043 0.208 2298 Planarity : 0.005 0.065 2418 Dihedral : 14.325 82.984 2704 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.98 % Allowed : 14.34 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.21), residues: 1638 helix: 1.08 (0.20), residues: 656 sheet: 0.37 (0.30), residues: 289 loop : 0.16 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 690 TYR 0.029 0.002 TYR B 681 PHE 0.018 0.002 PHE A 295 TRP 0.012 0.002 TRP B 332 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00518 (14959) covalent geometry : angle 0.59349 (20467) hydrogen bonds : bond 0.04756 ( 639) hydrogen bonds : angle 4.54860 ( 1747) metal coordination : bond 0.01021 ( 8) metal coordination : angle 1.99139 ( 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 230 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.632 Fit side-chains REVERT: A 66 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8038 (mttt) REVERT: A 68 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: A 124 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7887 (ttp80) REVERT: A 134 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8365 (ptt180) REVERT: A 221 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7472 (mmtm) REVERT: A 228 LYS cc_start: 0.8765 (tttt) cc_final: 0.8165 (mppt) REVERT: A 229 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6975 (ttp-170) REVERT: A 275 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 657 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 735 ASP cc_start: 0.8331 (t0) cc_final: 0.8082 (m-30) REVERT: A 777 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8253 (tm) REVERT: A 780 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6306 (mttm) REVERT: B 262 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7907 (ptpt) REVERT: B 583 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: B 590 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7558 (ttt-90) REVERT: B 617 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8103 (tpp80) REVERT: B 649 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 744 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 830 MET cc_start: 0.6270 (tpp) cc_final: 0.5880 (ttt) outliers start: 44 outliers final: 14 residues processed: 210 average time/residue: 0.8670 time to fit residues: 195.6523 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 37 ILE 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 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 167 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3735 r_free = 0.3735 target = 0.148800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111462 restraints weight = 17979.556| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3087 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14967 Z= 0.228 Angle : 0.601 10.806 20473 Z= 0.306 Chirality : 0.044 0.248 2298 Planarity : 0.004 0.039 2418 Dihedral : 14.343 80.462 2704 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.86 % Allowed : 13.73 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1638 helix: 0.99 (0.20), residues: 655 sheet: 0.34 (0.30), residues: 282 loop : 0.11 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.026 0.002 TYR B 681 PHE 0.012 0.001 PHE A 295 TRP 0.013 0.002 TRP B 332 HIS 0.003 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00544 (14959) covalent geometry : angle 0.60044 (20467) hydrogen bonds : bond 0.04686 ( 639) hydrogen bonds : angle 4.55980 ( 1747) metal coordination : bond 0.01130 ( 8) metal coordination : angle 1.94571 ( 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 231 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.533 Fit side-chains REVERT: A 66 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8054 (mttt) REVERT: A 68 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: A 124 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7863 (ttp80) REVERT: A 134 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8386 (ptt180) REVERT: A 146 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8022 (mtp180) REVERT: A 221 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7511 (mmtm) REVERT: A 228 LYS cc_start: 0.8763 (tttt) cc_final: 0.8128 (mppt) REVERT: A 229 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6968 (ttp-170) REVERT: A 657 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: A 735 ASP cc_start: 0.8299 (t0) cc_final: 0.8029 (m-30) REVERT: A 780 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6295 (mttm) REVERT: B 253 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7960 (mppt) REVERT: B 340 CYS cc_start: 0.8870 (m) cc_final: 0.8669 (p) REVERT: B 583 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: B 590 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: B 617 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8041 (tpp80) REVERT: B 649 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 744 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: B 830 MET cc_start: 0.6259 (tpp) cc_final: 0.6037 (ttt) outliers start: 57 outliers final: 26 residues processed: 210 average time/residue: 0.8499 time to fit residues: 192.3720 Evaluate side-chains 204 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 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 35 GLN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 350 MET 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 809 VAL 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: 0.9980 chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3759 r_free = 0.3759 target = 0.150917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113809 restraints weight = 17873.204| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.90 r_work: 0.3128 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14967 Z= 0.127 Angle : 0.523 6.964 20473 Z= 0.269 Chirality : 0.041 0.175 2298 Planarity : 0.004 0.044 2418 Dihedral : 14.295 79.401 2704 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 15.63 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.21), residues: 1638 helix: 1.25 (0.21), residues: 656 sheet: 0.35 (0.30), residues: 284 loop : 0.26 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 690 TYR 0.022 0.001 TYR B 681 PHE 0.017 0.001 PHE B 435 TRP 0.011 0.001 TRP A 699 HIS 0.002 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00294 (14959) covalent geometry : angle 0.52185 (20467) hydrogen bonds : bond 0.04045 ( 639) hydrogen bonds : angle 4.39583 ( 1747) metal coordination : bond 0.00613 ( 8) metal coordination : angle 2.02901 ( 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: 40 poor density : 177 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8017 (mttt) REVERT: A 124 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7873 (ttp80) REVERT: A 146 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: A 221 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7524 (mmtm) REVERT: A 228 LYS cc_start: 0.8752 (tttt) cc_final: 0.8150 (mppt) REVERT: A 229 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6856 (ttp-170) REVERT: A 657 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: B 583 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: B 590 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7515 (ttt-90) REVERT: B 617 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8000 (tpp80) REVERT: B 649 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 744 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 830 MET cc_start: 0.6124 (tpp) cc_final: 0.5741 (ttt) outliers start: 40 outliers final: 13 residues processed: 202 average time/residue: 0.8609 time to fit residues: 187.4249 Evaluate side-chains 182 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 350 MET 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: 0.7980 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3730 r_free = 0.3730 target = 0.148564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111215 restraints weight = 17857.809| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.90 r_work: 0.3088 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14967 Z= 0.225 Angle : 0.588 11.778 20473 Z= 0.299 Chirality : 0.043 0.170 2298 Planarity : 0.004 0.042 2418 Dihedral : 14.322 75.974 2704 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.25 % Allowed : 16.31 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1638 helix: 1.06 (0.20), residues: 656 sheet: 0.26 (0.30), residues: 282 loop : 0.13 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 617 TYR 0.023 0.002 TYR B 681 PHE 0.011 0.001 PHE B 585 TRP 0.013 0.002 TRP A 699 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00536 (14959) covalent geometry : angle 0.58707 (20467) hydrogen bonds : bond 0.04596 ( 639) hydrogen bonds : angle 4.51435 ( 1747) metal coordination : bond 0.01116 ( 8) metal coordination : angle 1.87342 ( 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 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.624 Fit side-chains REVERT: A 66 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8069 (mttt) REVERT: A 68 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 134 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8392 (ptt180) REVERT: A 146 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (mtp180) REVERT: A 228 LYS cc_start: 0.8804 (tttt) cc_final: 0.8191 (mppt) REVERT: A 657 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 735 ASP cc_start: 0.8330 (t0) cc_final: 0.8083 (m-30) REVERT: B 144 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 253 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7981 (mppt) REVERT: B 583 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: B 590 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7607 (ttt-90) REVERT: B 617 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8038 (tpp80) REVERT: B 649 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 744 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 830 MET cc_start: 0.6210 (tpp) cc_final: 0.5815 (ttt) outliers start: 48 outliers final: 21 residues processed: 198 average time/residue: 0.8372 time to fit residues: 178.6485 Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 35 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 634 GLN A 880 ASN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111962 restraints weight = 17801.583| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.90 r_work: 0.3093 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14967 Z= 0.207 Angle : 0.576 12.449 20473 Z= 0.293 Chirality : 0.042 0.168 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.325 74.261 2704 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.52 % Allowed : 15.76 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.21), residues: 1638 helix: 1.09 (0.20), residues: 650 sheet: 0.15 (0.32), residues: 264 loop : 0.08 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.021 0.002 TYR B 681 PHE 0.010 0.001 PHE B 585 TRP 0.012 0.002 TRP B 332 HIS 0.002 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00493 (14959) covalent geometry : angle 0.57539 (20467) hydrogen bonds : bond 0.04494 ( 639) hydrogen bonds : angle 4.51170 ( 1747) metal coordination : bond 0.01026 ( 8) metal coordination : angle 1.87962 ( 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 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.744 Fit side-chains REVERT: A 66 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8068 (mttt) REVERT: A 68 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 134 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8358 (ptt180) REVERT: A 146 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: A 228 LYS cc_start: 0.8783 (tttt) cc_final: 0.8143 (mppt) REVERT: A 657 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 735 ASP cc_start: 0.8308 (t0) cc_final: 0.8036 (m-30) REVERT: B 144 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8277 (p0) REVERT: B 253 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7988 (mppt) REVERT: B 583 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 590 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7589 (ttt-90) REVERT: B 617 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7997 (tpp80) REVERT: B 649 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 744 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: B 830 MET cc_start: 0.6156 (tpp) cc_final: 0.5751 (ttt) outliers start: 52 outliers final: 24 residues processed: 191 average time/residue: 0.8330 time to fit residues: 171.5681 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 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 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 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 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: 10.0000 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3749 r_free = 0.3749 target = 0.150128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113136 restraints weight = 17752.924| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.89 r_work: 0.3110 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14967 Z= 0.160 Angle : 0.556 12.436 20473 Z= 0.283 Chirality : 0.041 0.236 2298 Planarity : 0.004 0.051 2418 Dihedral : 14.295 74.327 2704 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.37 % Allowed : 17.39 % 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 aren not related in a simple way. whole: 0.73 (0.21), residues: 1638 helix: 1.12 (0.20), residues: 656 sheet: 0.19 (0.32), residues: 261 loop : 0.14 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 690 TYR 0.023 0.001 TYR B 681 PHE 0.018 0.001 PHE B 435 TRP 0.013 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00380 (14959) covalent geometry : angle 0.55544 (20467) hydrogen bonds : bond 0.04187 ( 639) hydrogen bonds : angle 4.49049 ( 1747) metal coordination : bond 0.00605 ( 8) metal coordination : angle 1.89123 ( 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 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.586 Fit side-chains REVERT: A 66 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8046 (mttt) REVERT: A 68 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 134 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8388 (ptt180) REVERT: A 146 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: A 192 LEU cc_start: 0.8682 (mt) cc_final: 0.8448 (mp) REVERT: A 228 LYS cc_start: 0.8812 (tttt) cc_final: 0.8161 (mppt) REVERT: A 657 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: B 144 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8250 (p0) REVERT: B 262 LYS cc_start: 0.8268 (ptpt) cc_final: 0.8028 (ptpt) REVERT: B 583 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: B 590 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7564 (ttt-90) REVERT: B 617 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7983 (tpp80) REVERT: B 649 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 744 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: B 830 MET cc_start: 0.6129 (tpp) cc_final: 0.5747 (ttt) outliers start: 35 outliers final: 20 residues processed: 182 average time/residue: 0.7671 time to fit residues: 151.1707 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR 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 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 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 809 VAL 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: 0.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 161 optimal weight: 0.9980 chunk 46 optimal weight: 0.0010 chunk 67 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 733 ASN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116080 restraints weight = 17813.233| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2149 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= 0.113 Angle : 0.536 10.249 20473 Z= 0.273 Chirality : 0.040 0.231 2298 Planarity : 0.004 0.066 2418 Dihedral : 14.243 73.611 2704 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.89 % Allowed : 18.06 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.22), residues: 1638 helix: 1.42 (0.20), residues: 649 sheet: 0.31 (0.32), residues: 271 loop : 0.30 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 690 TYR 0.022 0.001 TYR B 226 PHE 0.009 0.001 PHE A 295 TRP 0.011 0.001 TRP A 413 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00262 (14959) covalent geometry : angle 0.53522 (20467) hydrogen bonds : bond 0.03778 ( 639) hydrogen bonds : angle 4.39598 ( 1747) metal coordination : bond 0.00733 ( 8) metal coordination : angle 2.00755 ( 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 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.586 Fit side-chains REVERT: A 68 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: A 146 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (mtp180) REVERT: A 192 LEU cc_start: 0.8625 (mt) cc_final: 0.8396 (mp) REVERT: A 228 LYS cc_start: 0.8784 (tttt) cc_final: 0.8166 (mppt) REVERT: A 657 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 745 MET cc_start: 0.7945 (mmm) cc_final: 0.7727 (mtt) REVERT: B 144 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8201 (p0) REVERT: B 300 VAL cc_start: 0.8625 (t) cc_final: 0.8244 (p) REVERT: B 489 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8387 (ttm170) REVERT: B 583 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: B 590 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7542 (ttt-90) REVERT: B 617 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7959 (tpp80) REVERT: B 649 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 656 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7256 (mtm110) REVERT: B 744 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: B 830 MET cc_start: 0.6074 (tpp) cc_final: 0.5584 (ttt) outliers start: 28 outliers final: 14 residues processed: 197 average time/residue: 0.8024 time to fit residues: 170.9654 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR 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 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3768 r_free = 0.3768 target = 0.151844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114608 restraints weight = 17842.897| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.90 r_work: 0.3131 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2236 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= 0.134 Angle : 0.545 10.118 20473 Z= 0.278 Chirality : 0.040 0.222 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.227 73.746 2704 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.89 % Allowed : 18.13 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.21), residues: 1638 helix: 1.42 (0.20), residues: 649 sheet: 0.32 (0.31), residues: 273 loop : 0.34 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 617 TYR 0.021 0.001 TYR B 681 PHE 0.017 0.001 PHE B 435 TRP 0.017 0.001 TRP A 699 HIS 0.004 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00319 (14959) covalent geometry : angle 0.54413 (20467) hydrogen bonds : bond 0.03948 ( 639) hydrogen bonds : angle 4.42710 ( 1747) metal coordination : bond 0.00533 ( 8) metal coordination : angle 1.86729 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.708 Fit side-chains REVERT: A 68 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 146 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: A 192 LEU cc_start: 0.8654 (mt) cc_final: 0.8418 (mp) REVERT: A 228 LYS cc_start: 0.8809 (tttt) cc_final: 0.8215 (mppt) REVERT: A 657 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: A 745 MET cc_start: 0.8053 (mmm) cc_final: 0.7755 (mtt) REVERT: B 44 GLU cc_start: 0.8041 (tp30) cc_final: 0.7701 (tt0) REVERT: B 144 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8242 (p0) REVERT: B 300 VAL cc_start: 0.8638 (t) cc_final: 0.8252 (p) REVERT: B 583 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 590 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7567 (ttt-90) REVERT: B 744 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: B 830 MET cc_start: 0.6182 (tpp) cc_final: 0.5683 (ttt) outliers start: 28 outliers final: 12 residues processed: 184 average time/residue: 0.7888 time to fit residues: 156.9974 Evaluate side-chains 176 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 408 THR 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.566 > 50: distance: 111 - 115: 33.908 distance: 115 - 116: 56.406 distance: 116 - 119: 6.761 distance: 117 - 118: 50.703 distance: 120 - 121: 13.764 distance: 121 - 122: 39.934 distance: 121 - 124: 49.139 distance: 122 - 123: 42.535 distance: 122 - 129: 42.441 distance: 124 - 125: 40.413 distance: 125 - 126: 10.142 distance: 126 - 127: 14.009 distance: 127 - 128: 4.431 distance: 130 - 131: 57.146 distance: 130 - 133: 15.709 distance: 133 - 134: 34.181 distance: 133 - 135: 48.056 distance: 138 - 139: 24.964 distance: 138 - 144: 39.796 distance: 140 - 141: 10.411 distance: 141 - 142: 7.053 distance: 141 - 143: 12.069 distance: 144 - 145: 23.854 distance: 145 - 146: 46.791 distance: 145 - 148: 54.454 distance: 146 - 147: 39.291 distance: 146 - 150: 56.936 distance: 148 - 149: 63.890 distance: 150 - 151: 57.298 distance: 151 - 152: 40.316 distance: 152 - 153: 39.541 distance: 155 - 156: 40.630 distance: 158 - 159: 25.506 distance: 159 - 160: 14.073 distance: 159 - 162: 15.519 distance: 160 - 164: 39.484 distance: 164 - 165: 27.638 distance: 164 - 170: 56.800 distance: 165 - 166: 25.099 distance: 165 - 168: 41.914 distance: 166 - 167: 40.428 distance: 168 - 169: 40.084 distance: 169 - 170: 39.760 distance: 171 - 172: 16.564 distance: 172 - 173: 59.282 distance: 172 - 175: 41.706 distance: 173 - 174: 38.870 distance: 175 - 176: 25.489 distance: 175 - 177: 40.271 distance: 178 - 179: 40.440 distance: 179 - 180: 39.400 distance: 180 - 181: 39.208 distance: 180 - 184: 35.406 distance: 182 - 183: 39.716