Starting phenix.real_space_refine on Sun Jan 19 23:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmw_51456/01_2025/9gmw_51456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmw_51456/01_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_51456/01_2025/9gmw_51456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmw_51456/01_2025/9gmw_51456.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmw_51456/01_2025/9gmw_51456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmw_51456/01_2025/9gmw_51456.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.54, per 1000 atoms: 0.66 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 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: 4.89 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: 5.65 Time building geometry restraints manager: 4.07 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 899 or resid 1001 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.990 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.700 ------------------------------------------------------------------------------- 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 14959 Z= 0.245 Angle : 0.628 10.788 20467 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP B 332 HIS 0.005 0.001 HIS B 848 PHE 0.022 0.001 PHE B 435 TYR 0.026 0.001 TYR B 681 ARG 0.023 0.001 ARG B 690 *********************** 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 : 1.463 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: 1.6950 time to fit residues: 375.1250 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 : 1.619 ------------------------------------------------------------------------------- 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 142 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 B 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112613 restraints weight = 17780.086| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.92 r_work: 0.3087 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14959 Z= 0.321 Angle : 0.602 7.018 20467 Z= 0.310 Chirality : 0.043 0.183 2298 Planarity : 0.005 0.050 2418 Dihedral : 14.445 86.148 2711 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 14.07 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1638 helix: 1.09 (0.20), residues: 655 sheet: 0.33 (0.30), residues: 278 loop : 0.19 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 332 HIS 0.003 0.001 HIS A 664 PHE 0.014 0.002 PHE B 434 TYR 0.033 0.002 TYR B 681 ARG 0.009 0.001 ARG B 690 *********************** 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 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.662 Fit side-chains REVERT: A 68 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: A 124 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7838 (ttp80) REVERT: A 221 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7481 (mmtm) REVERT: A 228 LYS cc_start: 0.8747 (tttt) cc_final: 0.8184 (mppt) REVERT: A 657 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: B 583 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: B 590 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7552 (ttt-90) REVERT: B 617 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8138 (tpp80) REVERT: B 649 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 744 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: B 789 MET cc_start: 0.7300 (mmm) cc_final: 0.6164 (tpp) REVERT: B 830 MET cc_start: 0.6222 (tpp) cc_final: 0.5923 (ttt) outliers start: 32 outliers final: 8 residues processed: 205 average time/residue: 1.6140 time to fit residues: 358.3412 Evaluate side-chains 179 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 150 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114095 restraints weight = 17831.952| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.88 r_work: 0.3134 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14959 Z= 0.202 Angle : 0.541 7.703 20467 Z= 0.279 Chirality : 0.041 0.181 2298 Planarity : 0.004 0.066 2418 Dihedral : 14.282 84.459 2704 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.84 % Allowed : 13.94 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1638 helix: 1.19 (0.20), residues: 661 sheet: 0.44 (0.30), residues: 288 loop : 0.32 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.002 0.001 HIS B 821 PHE 0.017 0.001 PHE A 295 TYR 0.025 0.001 TYR B 681 ARG 0.005 0.000 ARG B 690 *********************** 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 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.618 Fit side-chains REVERT: A 66 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7975 (mttt) REVERT: A 68 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: A 124 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7816 (ttp80) REVERT: A 221 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7421 (mmtm) REVERT: A 228 LYS cc_start: 0.8724 (tttt) cc_final: 0.8157 (mppt) REVERT: A 229 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: A 657 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: A 780 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6272 (mttm) REVERT: B 335 GLU cc_start: 0.7773 (pp20) cc_final: 0.7559 (pt0) REVERT: B 583 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: B 590 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: B 617 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8061 (tpp80) REVERT: B 649 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 744 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 830 MET cc_start: 0.6231 (tpp) cc_final: 0.5887 (ttt) outliers start: 42 outliers final: 14 residues processed: 208 average time/residue: 1.6521 time to fit residues: 371.2091 Evaluate side-chains 189 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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 779 ILE Chi-restraints excluded: chain A residue 780 LYS 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 612 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.150580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113245 restraints weight = 17703.834| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.90 r_work: 0.3116 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14959 Z= 0.258 Angle : 0.560 10.263 20467 Z= 0.286 Chirality : 0.042 0.211 2298 Planarity : 0.004 0.040 2418 Dihedral : 14.290 81.440 2704 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.04 % Allowed : 14.14 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1638 helix: 1.20 (0.20), residues: 660 sheet: 0.38 (0.31), residues: 275 loop : 0.29 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS A 420 PHE 0.013 0.001 PHE A 295 TYR 0.026 0.002 TYR B 681 ARG 0.007 0.000 ARG A 617 *********************** 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 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8006 (mttt) REVERT: A 68 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 124 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7867 (ttp80) REVERT: A 146 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (mtp180) REVERT: A 221 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7480 (mmtm) REVERT: A 228 LYS cc_start: 0.8761 (tttt) cc_final: 0.8154 (mppt) REVERT: A 229 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6898 (ttp-170) REVERT: A 657 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 780 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6307 (mttm) REVERT: B 583 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: B 617 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8032 (tpp80) REVERT: B 649 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 744 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: B 830 MET cc_start: 0.6160 (tpp) cc_final: 0.5769 (ttt) outliers start: 45 outliers final: 16 residues processed: 205 average time/residue: 1.5848 time to fit residues: 351.3080 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR 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 63 MET 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 517 LEU Chi-restraints excluded: chain B residue 583 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114266 restraints weight = 17868.766| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.91 r_work: 0.3132 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14959 Z= 0.193 Angle : 0.524 6.995 20467 Z= 0.270 Chirality : 0.041 0.183 2298 Planarity : 0.004 0.044 2418 Dihedral : 14.275 80.097 2704 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.84 % Allowed : 15.29 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1638 helix: 1.33 (0.20), residues: 661 sheet: 0.37 (0.31), residues: 273 loop : 0.38 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 699 HIS 0.002 0.001 HIS B 848 PHE 0.011 0.001 PHE A 295 TYR 0.025 0.001 TYR B 681 ARG 0.007 0.000 ARG A 617 *********************** 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 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8029 (mttt) REVERT: A 68 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 124 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7865 (ttp80) REVERT: A 146 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: A 221 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7489 (mmtm) REVERT: A 228 LYS cc_start: 0.8745 (tttt) cc_final: 0.8143 (mppt) REVERT: A 229 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (ttp-170) REVERT: A 533 MET cc_start: 0.7947 (ttm) cc_final: 0.7257 (ttt) REVERT: A 657 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: B 44 GLU cc_start: 0.8046 (tp30) cc_final: 0.7673 (tt0) REVERT: B 583 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: B 590 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7322 (ttt-90) REVERT: B 617 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8013 (tpp80) REVERT: B 744 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: B 830 MET cc_start: 0.6091 (tpp) cc_final: 0.5704 (ttt) outliers start: 42 outliers final: 17 residues processed: 206 average time/residue: 1.6478 time to fit residues: 366.0958 Evaluate side-chains 186 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 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 786 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 93 optimal weight: 0.0000 chunk 133 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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 746 GLN B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114336 restraints weight = 17926.882| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.90 r_work: 0.3125 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14959 Z= 0.206 Angle : 0.526 10.746 20467 Z= 0.270 Chirality : 0.040 0.158 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.261 78.284 2704 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.64 % Allowed : 16.44 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1638 helix: 1.46 (0.21), residues: 649 sheet: 0.36 (0.31), residues: 273 loop : 0.38 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.002 0.001 HIS B 848 PHE 0.009 0.001 PHE B 434 TYR 0.023 0.001 TYR B 226 ARG 0.013 0.000 ARG A 617 *********************** 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 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8056 (mttt) REVERT: A 68 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 146 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: A 221 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7526 (mmtm) REVERT: A 228 LYS cc_start: 0.8777 (tttt) cc_final: 0.8189 (mppt) REVERT: A 229 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6921 (ttp-170) REVERT: A 657 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: B 300 VAL cc_start: 0.8607 (t) cc_final: 0.8179 (p) REVERT: B 583 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: B 617 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8017 (tpp80) REVERT: B 744 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: B 830 MET cc_start: 0.6081 (tpp) cc_final: 0.5725 (ttt) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 1.7370 time to fit residues: 365.0571 Evaluate side-chains 179 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 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 885 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 29 optimal weight: 0.4980 chunk 76 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 733 ASN B 891 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116675 restraints weight = 17850.869| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.91 r_work: 0.3163 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14959 Z= 0.153 Angle : 0.500 9.914 20467 Z= 0.258 Chirality : 0.039 0.156 2298 Planarity : 0.004 0.051 2418 Dihedral : 14.237 76.464 2704 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.50 % Allowed : 17.12 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1638 helix: 1.62 (0.21), residues: 649 sheet: 0.44 (0.32), residues: 273 loop : 0.48 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.005 0.001 HIS B 848 PHE 0.018 0.001 PHE B 435 TYR 0.020 0.001 TYR B 681 ARG 0.015 0.000 ARG A 617 *********************** 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: 37 poor density : 173 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8642 (mt) cc_final: 0.8350 (mp) REVERT: A 221 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7494 (mmtm) REVERT: A 228 LYS cc_start: 0.8749 (tttt) cc_final: 0.8139 (mppt) REVERT: A 229 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6792 (ttp-170) REVERT: A 657 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 766 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7063 (tm-30) REVERT: B 44 GLU cc_start: 0.8027 (tp30) cc_final: 0.7662 (tt0) REVERT: B 300 VAL cc_start: 0.8606 (t) cc_final: 0.8217 (p) REVERT: B 384 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7641 (mptt) REVERT: B 583 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: B 590 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7362 (ttt-90) REVERT: B 617 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7940 (tpp80) REVERT: B 744 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: B 830 MET cc_start: 0.5966 (tpp) cc_final: 0.5613 (ttt) outliers start: 37 outliers final: 14 residues processed: 195 average time/residue: 1.6732 time to fit residues: 351.8654 Evaluate side-chains 178 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 229 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 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 809 VAL 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 37 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 146 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.153708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116534 restraints weight = 17723.665| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.91 r_work: 0.3158 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14959 Z= 0.168 Angle : 0.516 12.320 20467 Z= 0.264 Chirality : 0.040 0.285 2298 Planarity : 0.004 0.053 2418 Dihedral : 14.216 74.253 2704 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1638 helix: 1.61 (0.21), residues: 649 sheet: 0.46 (0.32), residues: 273 loop : 0.48 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 389 PHE 0.011 0.001 PHE A 295 TYR 0.022 0.001 TYR B 226 ARG 0.011 0.000 ARG A 617 *********************** 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 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8640 (mt) cc_final: 0.8344 (mp) REVERT: A 228 LYS cc_start: 0.8788 (tttt) cc_final: 0.8207 (mppt) REVERT: A 229 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6734 (ttp-170) REVERT: A 657 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: B 44 GLU cc_start: 0.8038 (tp30) cc_final: 0.7671 (tt0) REVERT: B 300 VAL cc_start: 0.8616 (t) cc_final: 0.8222 (p) REVERT: B 384 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7659 (mptt) REVERT: B 583 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: B 656 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7249 (mtm110) REVERT: B 744 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: B 830 MET cc_start: 0.6020 (tpp) cc_final: 0.5606 (ttt) outliers start: 28 outliers final: 15 residues processed: 184 average time/residue: 1.6262 time to fit residues: 323.8803 Evaluate side-chains 179 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 241 THR 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 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 111 optimal weight: 0.0670 overall best weight: 1.0128 ------------------------------------------------------------------------------- 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 222 HIS B 891 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115666 restraints weight = 17639.520| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.92 r_work: 0.3148 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14959 Z= 0.201 Angle : 0.538 12.828 20467 Z= 0.272 Chirality : 0.040 0.278 2298 Planarity : 0.004 0.056 2418 Dihedral : 14.214 73.775 2704 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 17.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1638 helix: 1.56 (0.21), residues: 649 sheet: 0.43 (0.32), residues: 273 loop : 0.45 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 699 HIS 0.003 0.001 HIS A 389 PHE 0.011 0.001 PHE A 295 TYR 0.018 0.001 TYR B 309 ARG 0.009 0.000 ARG A 617 *********************** 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 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: A 228 LYS cc_start: 0.8777 (tttt) cc_final: 0.8188 (mppt) REVERT: A 229 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6804 (ttp-170) REVERT: A 657 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: B 44 GLU cc_start: 0.8034 (tp30) cc_final: 0.7670 (tt0) REVERT: B 300 VAL cc_start: 0.8668 (t) cc_final: 0.8287 (p) REVERT: B 384 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7647 (mptt) REVERT: B 583 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: B 656 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7256 (mtm110) REVERT: B 744 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 830 MET cc_start: 0.6072 (tpp) cc_final: 0.5593 (ttt) outliers start: 31 outliers final: 13 residues processed: 186 average time/residue: 1.6136 time to fit residues: 325.7721 Evaluate side-chains 178 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 229 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 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 153 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 222 HIS B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116770 restraints weight = 17650.434| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.92 r_work: 0.3161 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14959 Z= 0.172 Angle : 0.518 9.531 20467 Z= 0.266 Chirality : 0.040 0.252 2298 Planarity : 0.004 0.057 2418 Dihedral : 14.200 73.681 2704 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.56 % Allowed : 18.54 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1638 helix: 1.57 (0.21), residues: 649 sheet: 0.43 (0.33), residues: 263 loop : 0.49 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 699 HIS 0.003 0.001 HIS A 389 PHE 0.011 0.001 PHE A 295 TYR 0.019 0.001 TYR B 309 ARG 0.008 0.000 ARG A 617 ********************** 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 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: A 192 LEU cc_start: 0.8645 (mt) cc_final: 0.8367 (mp) REVERT: A 228 LYS cc_start: 0.8768 (tttt) cc_final: 0.8185 (mppt) REVERT: A 229 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6765 (ttp-170) REVERT: A 657 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: B 44 GLU cc_start: 0.8007 (tp30) cc_final: 0.7642 (tt0) REVERT: B 300 VAL cc_start: 0.8647 (t) cc_final: 0.8270 (p) REVERT: B 384 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7560 (mptt) REVERT: B 583 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: B 744 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 830 MET cc_start: 0.6004 (tpp) cc_final: 0.5654 (ttt) outliers start: 23 outliers final: 15 residues processed: 186 average time/residue: 1.6108 time to fit residues: 324.3660 Evaluate side-chains 183 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 533 MET 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 872 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 46 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 222 HIS B 891 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114790 restraints weight = 17739.794| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.91 r_work: 0.3134 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14959 Z= 0.227 Angle : 0.557 12.313 20467 Z= 0.283 Chirality : 0.041 0.222 2298 Planarity : 0.004 0.060 2418 Dihedral : 14.208 73.809 2704 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.49 % Allowed : 18.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1638 helix: 1.45 (0.21), residues: 650 sheet: 0.31 (0.33), residues: 263 loop : 0.46 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 PHE 0.012 0.001 PHE A 295 TYR 0.025 0.001 TYR B 226 ARG 0.016 0.000 ARG A 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11174.66 seconds wall clock time: 198 minutes 35.42 seconds (11915.42 seconds total)