Starting phenix.real_space_refine on Tue Dec 31 01:09:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmw_51456/12_2024/9gmw_51456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmw_51456/12_2024/9gmw_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_51456/12_2024/9gmw_51456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmw_51456/12_2024/9gmw_51456.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmw_51456/12_2024/9gmw_51456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmw_51456/12_2024/9gmw_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.04, per 1000 atoms: 0.69 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: 4.13 Conformation dependent library (CDL) restraints added in 2.0 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: 5.61 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: 6.33 Time building geometry restraints manager: 4.68 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.700 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 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 : 1.618 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: 1.7949 time to fit residues: 397.1756 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 : 1.774 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 1.740 Fit side-chains REVERT: A 68 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: A 124 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7693 (ttp80) REVERT: A 221 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7446 (mmtm) REVERT: A 228 LYS cc_start: 0.8573 (tttt) cc_final: 0.8074 (mppt) REVERT: A 643 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7961 (mtp85) REVERT: A 657 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: B 583 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: B 590 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7285 (ttt-90) REVERT: B 617 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7813 (tpp80) REVERT: B 649 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 744 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 789 MET cc_start: 0.7377 (mmm) cc_final: 0.6252 (tpp) REVERT: B 830 MET cc_start: 0.6223 (tpp) cc_final: 0.5976 (ttt) outliers start: 32 outliers final: 8 residues processed: 205 average time/residue: 1.6422 time to fit residues: 364.3206 Evaluate side-chains 180 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 643 ARG 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 85 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14959 Z= 0.397 Angle : 0.626 7.940 20467 Z= 0.320 Chirality : 0.045 0.208 2298 Planarity : 0.005 0.064 2418 Dihedral : 14.365 82.897 2704 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 14.01 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.21), residues: 1638 helix: 0.85 (0.20), residues: 657 sheet: 0.40 (0.30), residues: 287 loop : 0.09 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.003 0.001 HIS B 420 PHE 0.016 0.002 PHE A 295 TYR 0.028 0.002 TYR B 681 ARG 0.005 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8111 (mttt) REVERT: A 68 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: A 124 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7748 (ttp80) REVERT: A 134 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8353 (ptt180) REVERT: A 146 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (mtp180) REVERT: A 221 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7437 (mmtm) REVERT: A 228 LYS cc_start: 0.8610 (tttt) cc_final: 0.8050 (mppt) REVERT: A 643 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7804 (mtp85) REVERT: A 657 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 735 ASP cc_start: 0.8023 (t0) cc_final: 0.7764 (m-30) REVERT: A 780 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6363 (mttm) REVERT: B 253 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7868 (mppt) REVERT: B 340 CYS cc_start: 0.8739 (m) cc_final: 0.8472 (p) REVERT: B 583 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: B 590 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7292 (ttt-90) REVERT: B 617 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7785 (tpp80) REVERT: B 649 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 744 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7776 (mp0) outliers start: 53 outliers final: 21 residues processed: 209 average time/residue: 1.6774 time to fit residues: 379.2194 Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 656 ARG Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14959 Z= 0.233 Angle : 0.552 8.970 20467 Z= 0.284 Chirality : 0.042 0.241 2298 Planarity : 0.004 0.040 2418 Dihedral : 14.327 81.417 2704 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.04 % Allowed : 14.95 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.21), residues: 1638 helix: 1.12 (0.20), residues: 655 sheet: 0.36 (0.30), residues: 281 loop : 0.19 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.002 0.001 HIS B 869 PHE 0.014 0.001 PHE B 435 TYR 0.026 0.001 TYR B 681 ARG 0.004 0.000 ARG B 690 *********************** 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 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8032 (mttt) REVERT: A 68 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: A 134 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8400 (ptt180) REVERT: A 221 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7452 (mmtm) REVERT: A 228 LYS cc_start: 0.8591 (tttt) cc_final: 0.8040 (mppt) REVERT: A 643 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (mtp85) REVERT: A 657 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: B 583 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: B 590 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7313 (ttt-90) REVERT: B 617 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7748 (tpp80) REVERT: B 649 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 744 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: B 830 MET cc_start: 0.6271 (tpp) cc_final: 0.5893 (ttt) outliers start: 45 outliers final: 15 residues processed: 210 average time/residue: 1.7296 time to fit residues: 391.2367 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 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 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 779 ILE 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 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 733 ASN B 746 GLN B 891 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1754 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 : 0.543 11.582 20467 Z= 0.276 Chirality : 0.041 0.234 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.277 78.935 2704 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.04 % Allowed : 15.90 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.21), residues: 1638 helix: 1.22 (0.20), residues: 656 sheet: 0.30 (0.31), residues: 273 loop : 0.27 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 PHE 0.011 0.001 PHE A 295 TYR 0.027 0.001 TYR B 681 ARG 0.006 0.000 ARG B 690 *********************** 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 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 2.176 Fit side-chains REVERT: A 66 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8117 (mttt) REVERT: A 68 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 134 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8456 (ptt180) REVERT: A 146 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7797 (mtp180) REVERT: A 221 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7457 (mmtm) REVERT: A 228 LYS cc_start: 0.8594 (tttt) cc_final: 0.8081 (mppt) REVERT: A 533 MET cc_start: 0.7816 (ttm) cc_final: 0.7175 (ttt) REVERT: A 643 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7802 (mtp85) REVERT: A 657 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: B 340 CYS cc_start: 0.8688 (m) cc_final: 0.8478 (p) REVERT: B 583 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: B 617 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7645 (tpp80) REVERT: B 649 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 744 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 830 MET cc_start: 0.6183 (tpp) cc_final: 0.5846 (ttt) outliers start: 45 outliers final: 16 residues processed: 200 average time/residue: 1.6962 time to fit residues: 368.3393 Evaluate side-chains 182 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER 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 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14959 Z= 0.336 Angle : 0.593 13.172 20467 Z= 0.302 Chirality : 0.043 0.169 2298 Planarity : 0.005 0.045 2418 Dihedral : 14.325 75.217 2704 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 15.63 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.21), residues: 1638 helix: 1.06 (0.20), residues: 656 sheet: 0.18 (0.31), residues: 269 loop : 0.12 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 699 HIS 0.003 0.001 HIS A 420 PHE 0.011 0.001 PHE B 585 TYR 0.027 0.002 TYR B 681 ARG 0.007 0.001 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 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8140 (mttt) REVERT: A 68 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: A 134 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8348 (ptt180) REVERT: A 146 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7843 (mtp180) REVERT: A 228 LYS cc_start: 0.8634 (tttt) cc_final: 0.8073 (mppt) REVERT: A 642 ASP cc_start: 0.7811 (p0) cc_final: 0.7601 (p0) REVERT: A 643 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7744 (mtp85) REVERT: A 657 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: B 144 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8231 (p0) REVERT: B 253 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7917 (mppt) REVERT: B 583 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: B 590 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7136 (ttt-90) REVERT: B 617 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7721 (tpp80) REVERT: B 649 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 744 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 830 MET cc_start: 0.6216 (tpp) cc_final: 0.5857 (ttt) outliers start: 53 outliers final: 24 residues processed: 193 average time/residue: 1.6745 time to fit residues: 351.9441 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 819 VAL 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 144 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14959 Z= 0.195 Angle : 0.528 7.589 20467 Z= 0.272 Chirality : 0.040 0.155 2298 Planarity : 0.004 0.050 2418 Dihedral : 14.278 75.476 2704 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 17.05 % Favored : 80.51 % 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: 0.87 (0.21), residues: 1638 helix: 1.27 (0.20), residues: 656 sheet: 0.21 (0.32), residues: 263 loop : 0.23 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 699 HIS 0.003 0.001 HIS B 848 PHE 0.010 0.001 PHE B 434 TYR 0.025 0.001 TYR B 681 ARG 0.007 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 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 2.071 Fit side-chains REVERT: A 66 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8097 (mttt) REVERT: A 68 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 146 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7794 (mtp180) REVERT: A 192 LEU cc_start: 0.8680 (mt) cc_final: 0.8444 (mp) REVERT: A 228 LYS cc_start: 0.8639 (tttt) cc_final: 0.8068 (mppt) REVERT: A 642 ASP cc_start: 0.7770 (p0) cc_final: 0.7552 (p0) REVERT: A 643 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: A 657 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 44 GLU cc_start: 0.7819 (tp30) cc_final: 0.7506 (tt0) REVERT: B 144 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 300 VAL cc_start: 0.8665 (t) cc_final: 0.8247 (p) REVERT: B 583 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: B 617 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7711 (tpp80) REVERT: B 649 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 744 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 830 MET cc_start: 0.6118 (tpp) cc_final: 0.5779 (ttt) outliers start: 36 outliers final: 17 residues processed: 194 average time/residue: 1.6938 time to fit residues: 355.6037 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 643 ARG 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 779 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14959 Z= 0.340 Angle : 0.591 9.968 20467 Z= 0.301 Chirality : 0.043 0.162 2298 Planarity : 0.004 0.046 2418 Dihedral : 14.313 74.733 2704 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.98 % Allowed : 17.46 % Favored : 79.57 % 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: 0.64 (0.21), residues: 1638 helix: 1.05 (0.20), residues: 657 sheet: 0.07 (0.31), residues: 274 loop : 0.14 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 332 HIS 0.003 0.001 HIS B 848 PHE 0.020 0.002 PHE A 295 TYR 0.029 0.002 TYR B 226 ARG 0.011 0.001 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 203 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.681 Fit side-chains REVERT: A 66 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8138 (mttt) REVERT: A 68 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 134 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8372 (ptt180) REVERT: A 146 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7851 (mtp180) REVERT: A 228 LYS cc_start: 0.8668 (tttt) cc_final: 0.8074 (mppt) REVERT: A 642 ASP cc_start: 0.7791 (p0) cc_final: 0.7585 (p0) REVERT: A 643 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7777 (mtp85) REVERT: A 657 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: A 735 ASP cc_start: 0.8126 (t0) cc_final: 0.7866 (m-30) REVERT: A 745 MET cc_start: 0.8094 (mmm) cc_final: 0.7838 (mtp) REVERT: B 144 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8256 (p0) REVERT: B 253 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (mppt) REVERT: B 583 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: B 590 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7165 (ttt-90) REVERT: B 617 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7698 (tpp80) REVERT: B 649 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 744 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 830 MET cc_start: 0.6225 (tpp) cc_final: 0.5846 (ttt) outliers start: 44 outliers final: 22 residues processed: 185 average time/residue: 1.6047 time to fit residues: 321.5117 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 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 156 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 151 optimal weight: 0.0000 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14959 Z= 0.165 Angle : 0.528 11.035 20467 Z= 0.272 Chirality : 0.040 0.156 2298 Planarity : 0.004 0.063 2418 Dihedral : 14.248 75.224 2704 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 18.47 % Favored : 79.30 % 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: 1.03 (0.22), residues: 1638 helix: 1.42 (0.21), residues: 650 sheet: 0.23 (0.32), residues: 275 loop : 0.33 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 699 HIS 0.002 0.001 HIS B 869 PHE 0.017 0.001 PHE B 435 TYR 0.019 0.001 TYR B 309 ARG 0.018 0.001 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 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.623 Fit side-chains REVERT: A 66 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8087 (mttt) REVERT: A 192 LEU cc_start: 0.8662 (mt) cc_final: 0.8429 (mp) REVERT: A 228 LYS cc_start: 0.8656 (tttt) cc_final: 0.8098 (mppt) REVERT: A 642 ASP cc_start: 0.7779 (p0) cc_final: 0.7555 (p0) REVERT: A 643 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7762 (mtp85) REVERT: A 657 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: A 789 MET cc_start: 0.5901 (ttm) cc_final: 0.5521 (ttm) REVERT: B 44 GLU cc_start: 0.7815 (tp30) cc_final: 0.7504 (tt0) REVERT: B 144 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8190 (p0) REVERT: B 300 VAL cc_start: 0.8640 (t) cc_final: 0.8251 (p) REVERT: B 384 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7567 (mptt) REVERT: B 583 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: B 617 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7689 (tpp80) REVERT: B 744 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: B 830 MET cc_start: 0.6078 (tpp) cc_final: 0.5752 (ttt) outliers start: 33 outliers final: 17 residues processed: 200 average time/residue: 1.6490 time to fit residues: 361.0407 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS 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 643 ARG 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 779 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 880 ASN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14959 Z= 0.277 Angle : 0.583 12.667 20467 Z= 0.296 Chirality : 0.042 0.153 2298 Planarity : 0.004 0.056 2418 Dihedral : 14.264 73.933 2704 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.89 % Allowed : 19.01 % Favored : 79.09 % 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: 0.84 (0.21), residues: 1638 helix: 1.23 (0.20), residues: 656 sheet: 0.14 (0.32), residues: 268 loop : 0.25 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 699 HIS 0.005 0.001 HIS B 848 PHE 0.015 0.001 PHE A 295 TYR 0.025 0.002 TYR B 226 ARG 0.019 0.001 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 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.668 Fit side-chains REVERT: A 66 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8123 (mttt) REVERT: A 192 LEU cc_start: 0.8695 (mt) cc_final: 0.8460 (mp) REVERT: A 228 LYS cc_start: 0.8660 (tttt) cc_final: 0.8079 (mppt) REVERT: A 642 ASP cc_start: 0.7795 (p0) cc_final: 0.7573 (p0) REVERT: A 643 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7771 (mtp85) REVERT: A 657 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: B 44 GLU cc_start: 0.7870 (tp30) cc_final: 0.7531 (tt0) REVERT: B 144 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8250 (p0) REVERT: B 300 VAL cc_start: 0.8686 (t) cc_final: 0.8285 (p) REVERT: B 583 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7502 (tp30) REVERT: B 617 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7681 (tpp80) REVERT: B 744 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 830 MET cc_start: 0.6223 (tpp) cc_final: 0.5741 (ttt) outliers start: 28 outliers final: 15 residues processed: 178 average time/residue: 1.6109 time to fit residues: 310.9416 Evaluate side-chains 180 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.152345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115015 restraints weight = 17704.269| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.89 r_work: 0.3140 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14959 Z= 0.199 Angle : 0.555 11.771 20467 Z= 0.284 Chirality : 0.040 0.155 2298 Planarity : 0.004 0.075 2418 Dihedral : 14.246 74.540 2704 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.76 % Allowed : 19.15 % Favored : 79.09 % 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: 0.99 (0.22), residues: 1638 helix: 1.39 (0.21), residues: 650 sheet: 0.20 (0.32), residues: 265 loop : 0.31 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 699 HIS 0.006 0.001 HIS B 848 PHE 0.014 0.001 PHE A 295 TYR 0.022 0.001 TYR B 681 ARG 0.018 0.001 ARG A 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5986.68 seconds wall clock time: 108 minutes 9.56 seconds (6489.56 seconds total)