Starting phenix.real_space_refine on Fri Jul 3 19:39:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zgf_74190/07_2026/9zgf_74190.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.090 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 64 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 9536 2.51 5 N 2761 2.21 5 O 2947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15403 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7726 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 58, 'TRANS': 960} Chain breaks: 1 Chain: "C" Number of atoms: 6379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6379 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 776} Chain breaks: 1 Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 787 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "E" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 478 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3593 SG CYS A 499 18.117 62.941 85.029 1.00 80.69 S ATOM 3615 SG CYS A 502 16.924 66.610 85.004 1.00 68.62 S ATOM 3680 SG CYS A 510 19.897 65.623 87.139 1.00 72.63 S Time building chain proxies: 3.90, per 1000 atoms: 0.25 Number of scatterers: 15403 At special positions: 0 Unit cell: (101.376, 132.48, 154.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 64 15.00 Mg 1 11.99 O 2947 8.00 N 2761 7.00 C 9536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 737.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" ND1 HIS A 512 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 510 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 502 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 499 " Number of angles added : 3 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 13 sheets defined 48.4% alpha, 13.9% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 removed outlier: 3.756A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.823A pdb=" N LEU A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.951A pdb=" N GLU A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.560A pdb=" N LEU A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 178 through 181 removed outlier: 4.169A pdb=" N SER A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.939A pdb=" N GLY A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 270 Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.624A pdb=" N MET A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 removed outlier: 3.950A pdb=" N TRP A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.753A pdb=" N ALA A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.798A pdb=" N GLY A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 removed outlier: 3.566A pdb=" N CYS A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.538A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.733A pdb=" N ARG A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A 508 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 509 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 566 through 572 removed outlier: 3.580A pdb=" N ILE A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 609 through 638 removed outlier: 4.146A pdb=" N LEU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.554A pdb=" N LEU A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.974A pdb=" N SER A 687 " --> pdb=" O ASP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.653A pdb=" N VAL A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 717 Proline residue: A 709 - end of helix Processing helix chain 'A' and resid 787 through 798 removed outlier: 3.761A pdb=" N SER A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 797 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 815 through 827 removed outlier: 6.007A pdb=" N ALA A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 858 through 879 removed outlier: 3.632A pdb=" N ILE A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.540A pdb=" N CYS A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 4.327A pdb=" N ALA A 932 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 934 " --> pdb=" O ALA A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 940 through 951 Processing helix chain 'A' and resid 952 through 955 Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.560A pdb=" N ARG A 976 " --> pdb=" O MET A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1012 removed outlier: 3.723A pdb=" N ASN A1011 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A1012 " --> pdb=" O GLY A1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1012' Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 32 through 38 removed outlier: 3.634A pdb=" N TYR C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.970A pdb=" N VAL C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.744A pdb=" N ALA C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.562A pdb=" N HIS C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.848A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 228 removed outlier: 3.853A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 3.740A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 297 Processing helix chain 'C' and resid 306 through 319 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.987A pdb=" N GLY C 340 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 342 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 427 through 450 removed outlier: 3.555A pdb=" N SER C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.568A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 474 removed outlier: 4.346A pdb=" N HIS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.785A pdb=" N SER C 481 " --> pdb=" O CYS C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 531 removed outlier: 3.798A pdb=" N CYS C 511 " --> pdb=" O PRO C 507 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 512 " --> pdb=" O LYS C 508 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 removed outlier: 3.783A pdb=" N ALA C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 545 " --> pdb=" O PRO C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 563 through 575 Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.520A pdb=" N ARG C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.980A pdb=" N THR C 599 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 614 removed outlier: 3.595A pdb=" N PHE C 605 " --> pdb=" O SER C 601 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 614 " --> pdb=" O ASP C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 653 removed outlier: 3.937A pdb=" N ARG C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 677 removed outlier: 3.554A pdb=" N VAL C 672 " --> pdb=" O GLY C 668 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 673 " --> pdb=" O PRO C 669 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 674 " --> pdb=" O ASP C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 697 through 703 removed outlier: 3.676A pdb=" N LEU C 701 " --> pdb=" O ASP C 697 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 715 removed outlier: 3.601A pdb=" N LYS C 707 " --> pdb=" O GLU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 739 removed outlier: 3.630A pdb=" N HIS C 727 " --> pdb=" O SER C 723 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 739 " --> pdb=" O ILE C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 771 Processing helix chain 'C' and resid 775 through 779 removed outlier: 3.749A pdb=" N ALA C 778 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS C 779 " --> pdb=" O HIS C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 779' Processing helix chain 'C' and resid 781 through 792 Processing helix chain 'C' and resid 793 through 796 Processing helix chain 'C' and resid 806 through 812 removed outlier: 4.062A pdb=" N CYS C 811 " --> pdb=" O TRP C 808 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 812 " --> pdb=" O GLY C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 833 removed outlier: 4.053A pdb=" N GLU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 839 removed outlier: 6.058A pdb=" N GLU C 837 " --> pdb=" O LEU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 851 removed outlier: 3.549A pdb=" N THR C 850 " --> pdb=" O ASN C 847 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 851 " --> pdb=" O PHE C 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 847 through 851' Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.509A pdb=" N SER A 725 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 removed outlier: 7.263A pdb=" N GLY A 16 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLY A 70 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS A 84 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 71 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER A 82 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 83 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.494A pdb=" N VAL A 94 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL A 161 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 96 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 159 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 98 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 19 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 25 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU A 190 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.494A pdb=" N VAL A 94 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL A 161 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 96 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 159 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 98 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 19 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 25 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU A 190 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 390 Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 538 removed outlier: 5.546A pdb=" N GLY A 982 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE A1024 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 13.040A pdb=" N SER A 984 " --> pdb=" O ARG A1022 " (cutoff:3.500A) removed outlier: 15.866A pdb=" N ARG A1022 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A1023 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 538 removed outlier: 4.264A pdb=" N GLY A 982 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 984 " --> pdb=" O ASN A1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 58 removed outlier: 3.774A pdb=" N THR C 54 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 171 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N MET C 211 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 173 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 107 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASP C 174 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 109 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 327 removed outlier: 6.395A pdb=" N LEU C 325 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG C 248 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE C 398 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 250 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET C 400 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 616 through 620 Processing sheet with id=AB3, first strand: chain 'C' and resid 656 through 657 Processing sheet with id=AB4, first strand: chain 'C' and resid 743 through 746 634 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5109 1.36 - 1.50: 4471 1.50 - 1.64: 6150 1.64 - 1.78: 1 1.78 - 1.92: 140 Bond restraints: 15871 Sorted by residual: bond pdb=" O2G AGS C 902 " pdb=" PG AGS C 902 " ideal model delta sigma weight residual 1.604 1.489 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" O3B AGS C 902 " pdb=" PB AGS C 902 " ideal model delta sigma weight residual 1.673 1.591 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3G AGS C 902 " pdb=" PG AGS C 902 " ideal model delta sigma weight residual 1.570 1.493 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O3A AGS C 902 " pdb=" PA AGS C 902 " ideal model delta sigma weight residual 1.664 1.596 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C3' DT E 29 " pdb=" C2' DT E 29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 15866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 21231 1.55 - 3.10: 523 3.10 - 4.65: 57 4.65 - 6.19: 8 6.19 - 7.74: 4 Bond angle restraints: 21823 Sorted by residual: angle pdb=" N3 DT E 19 " pdb=" C4 DT E 19 " pdb=" O4 DT E 19 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT D 35 " pdb=" C4 DT D 35 " pdb=" O4 DT D 35 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 25 " pdb=" C4 DT D 25 " pdb=" O4 DT D 25 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 21818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.53: 8617 31.53 - 63.07: 695 63.07 - 94.60: 36 94.60 - 126.13: 1 126.13 - 157.66: 5 Dihedral angle restraints: 9354 sinusoidal: 4079 harmonic: 5275 Sorted by residual: dihedral pdb=" CA PHE C 320 " pdb=" C PHE C 320 " pdb=" N THR C 321 " pdb=" CA THR C 321 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" C4' DG D 2 " pdb=" C3' DG D 2 " pdb=" O3' DG D 2 " pdb=" P DA D 3 " ideal model delta sinusoidal sigma weight residual 220.00 62.34 157.66 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DA D 34 " pdb=" C3' DA D 34 " pdb=" O3' DA D 34 " pdb=" P DT D 35 " ideal model delta sinusoidal sigma weight residual 220.00 75.37 144.63 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 9351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2097 0.057 - 0.114: 337 0.114 - 0.172: 25 0.172 - 0.229: 1 0.229 - 0.286: 1 Chirality restraints: 2461 Sorted by residual: chirality pdb=" C3' AGS C 902 " pdb=" C2' AGS C 902 " pdb=" C4' AGS C 902 " pdb=" O3' AGS C 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" C3' DG D 2 " pdb=" C4' DG D 2 " pdb=" O3' DG D 2 " pdb=" C2' DG D 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 2458 not shown) Planarity restraints: 2626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 666 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 667 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 667 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 667 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC E 14 " -0.013 2.00e-02 2.50e+03 1.17e-02 3.08e+00 pdb=" N1 DC E 14 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DC E 14 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC E 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC E 14 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC E 14 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC E 14 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DC E 14 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC E 14 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 206 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.021 5.00e-02 4.00e+02 ... (remaining 2623 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 20 2.60 - 3.18: 11699 3.18 - 3.75: 22060 3.75 - 4.33: 29892 4.33 - 4.90: 51849 Nonbonded interactions: 115520 Sorted by model distance: nonbonded pdb="MG MG C 901 " pdb=" O2B AGS C 902 " model vdw 2.030 2.170 nonbonded pdb=" O THR A 74 " pdb=" C GLY A 75 " model vdw 2.458 3.270 nonbonded pdb=" O THR A 73 " pdb=" OG1 THR A 73 " model vdw 2.475 3.040 nonbonded pdb=" O THR A 74 " pdb=" N LEU A 76 " model vdw 2.521 3.120 nonbonded pdb=" O5' DA D 38 " pdb=" O4' DA D 38 " model vdw 2.522 2.432 ... (remaining 115515 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.360 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.115 15875 Z= 0.261 Angle : 0.552 7.742 21826 Z= 0.361 Chirality : 0.042 0.286 2461 Planarity : 0.004 0.051 2626 Dihedral : 19.980 157.663 5958 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 2.48 % Allowed : 21.46 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1826 helix: 1.44 (0.20), residues: 731 sheet: 0.12 (0.32), residues: 259 loop : -1.55 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 602 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE A 467 TRP 0.011 0.001 TRP A 959 HIS 0.006 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.26 (15871) covalent geometry : angle 0.55191 / 0.36 (21823) hydrogen bonds : bond 0.15447 / 10.93 ( 662) hydrogen bonds : angle 5.08638 / 3.60 ( 1886) metal coordination : bond 0.00261 / 0.12 ( 4) metal coordination : angle 1.34824 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.515 Fit side-chains REVERT: A 11 ILE cc_start: 0.7761 (mt) cc_final: 0.7211 (tt) REVERT: A 271 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: A 352 ASP cc_start: 0.8104 (m-30) cc_final: 0.7839 (m-30) REVERT: A 519 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6222 (ttm170) REVERT: A 602 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7631 (mtp85) REVERT: A 604 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8376 (mm-30) REVERT: A 629 GLU cc_start: 0.7798 (tp30) cc_final: 0.7571 (tp30) REVERT: C 56 GLU cc_start: 0.7882 (tt0) cc_final: 0.7678 (tt0) REVERT: C 75 CYS cc_start: 0.9063 (m) cc_final: 0.8736 (m) REVERT: C 508 LYS cc_start: 0.7628 (tppt) cc_final: 0.6917 (ttpt) REVERT: C 520 ASP cc_start: 0.8116 (t70) cc_final: 0.7786 (t0) REVERT: C 578 MET cc_start: 0.8131 (ttm) cc_final: 0.7828 (ttp) REVERT: C 748 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 833 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8316 (mp0) outliers start: 37 outliers final: 34 residues processed: 152 average time/residue: 0.1339 time to fit residues: 29.6741 Evaluate side-chains 156 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 743 GLN Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 758 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 850 ASN C 117 GLN C 743 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105907 restraints weight = 15999.300| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.33 r_work: 0.3028 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15875 Z= 0.135 Angle : 0.525 10.046 21826 Z= 0.287 Chirality : 0.042 0.313 2461 Planarity : 0.004 0.048 2626 Dihedral : 19.097 159.183 2809 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.68 % Allowed : 21.46 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1826 helix: 1.54 (0.20), residues: 745 sheet: 0.30 (0.33), residues: 238 loop : -1.44 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 633 TYR 0.010 0.001 TYR A 158 PHE 0.017 0.001 PHE A 467 TRP 0.011 0.001 TRP A 959 HIS 0.007 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15871) covalent geometry : angle 0.52519 / 0.29 (21823) hydrogen bonds : bond 0.04985 / 3.41 ( 662) hydrogen bonds : angle 4.10875 / 2.91 ( 1886) metal coordination : bond 0.00231 / 0.11 ( 4) metal coordination : angle 1.43355 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7751 (mt) cc_final: 0.7246 (tt) REVERT: A 223 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: A 245 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8488 (t) REVERT: A 336 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 602 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7659 (mtp85) REVERT: A 604 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8419 (mm-30) REVERT: A 634 ASN cc_start: 0.6848 (t0) cc_final: 0.6633 (t0) REVERT: C 37 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8824 (tp) REVERT: C 56 GLU cc_start: 0.7815 (tt0) cc_final: 0.7527 (tt0) REVERT: C 75 CYS cc_start: 0.9025 (m) cc_final: 0.8736 (m) REVERT: C 122 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (mtp180) REVERT: C 508 LYS cc_start: 0.7729 (tppt) cc_final: 0.7055 (ttpt) REVERT: C 520 ASP cc_start: 0.8178 (t70) cc_final: 0.7853 (t0) REVERT: C 578 MET cc_start: 0.8156 (ttm) cc_final: 0.7858 (ttp) REVERT: C 748 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8414 (m) REVERT: C 841 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7442 (tpt) outliers start: 40 outliers final: 20 residues processed: 145 average time/residue: 0.1315 time to fit residues: 28.1637 Evaluate side-chains 141 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 758 LYS Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 153 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN C 792 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110640 restraints weight = 16441.422| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.29 r_work: 0.3065 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15875 Z= 0.111 Angle : 0.483 9.363 21826 Z= 0.262 Chirality : 0.040 0.315 2461 Planarity : 0.004 0.042 2626 Dihedral : 18.591 159.787 2764 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.29 % Allowed : 21.40 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1826 helix: 1.69 (0.20), residues: 746 sheet: 0.30 (0.33), residues: 245 loop : -1.30 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.011 0.001 TYR A 364 PHE 0.013 0.001 PHE A 536 TRP 0.008 0.001 TRP A 959 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15871) covalent geometry : angle 0.48240 / 0.26 (21823) hydrogen bonds : bond 0.04061 / 2.80 ( 662) hydrogen bonds : angle 3.84211 / 2.72 ( 1886) metal coordination : bond 0.00391 / 0.19 ( 4) metal coordination : angle 1.10624 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.517 Fit side-chains REVERT: A 223 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: A 245 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 336 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 602 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7688 (mtp85) REVERT: A 604 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8397 (mm-30) REVERT: A 634 ASN cc_start: 0.6808 (t0) cc_final: 0.6603 (t0) REVERT: A 731 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8343 (m) REVERT: A 753 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: C 37 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8824 (tp) REVERT: C 56 GLU cc_start: 0.7684 (tt0) cc_final: 0.7351 (tt0) REVERT: C 75 CYS cc_start: 0.8973 (m) cc_final: 0.8691 (m) REVERT: C 122 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: C 343 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8276 (ttt90) REVERT: C 508 LYS cc_start: 0.7681 (tppt) cc_final: 0.6994 (ttpt) REVERT: C 520 ASP cc_start: 0.8093 (t70) cc_final: 0.7806 (t0) REVERT: C 529 ARG cc_start: 0.7941 (tpt90) cc_final: 0.6805 (ttp-110) REVERT: C 578 MET cc_start: 0.8093 (ttm) cc_final: 0.7806 (ttp) REVERT: C 689 GLU cc_start: 0.8149 (tt0) cc_final: 0.7893 (tt0) REVERT: C 748 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (m) REVERT: C 824 ASP cc_start: 0.5646 (OUTLIER) cc_final: 0.4563 (t0) REVERT: C 833 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8257 (mp0) REVERT: C 841 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7425 (tpt) outliers start: 49 outliers final: 27 residues processed: 160 average time/residue: 0.1281 time to fit residues: 30.4678 Evaluate side-chains 151 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 758 LYS Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 0.0470 chunk 173 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 160 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN C 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109576 restraints weight = 16415.429| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.26 r_work: 0.3048 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15875 Z= 0.127 Angle : 0.500 9.166 21826 Z= 0.269 Chirality : 0.041 0.314 2461 Planarity : 0.004 0.043 2626 Dihedral : 18.514 159.517 2762 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.49 % Allowed : 20.99 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1826 helix: 1.70 (0.20), residues: 746 sheet: 0.31 (0.33), residues: 245 loop : -1.29 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.010 0.001 TYR A 158 PHE 0.017 0.001 PHE A 467 TRP 0.010 0.001 TRP A 959 HIS 0.006 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15871) covalent geometry : angle 0.50035 / 0.27 (21823) hydrogen bonds : bond 0.04388 / 3.02 ( 662) hydrogen bonds : angle 3.79933 / 2.69 ( 1886) metal coordination : bond 0.00264 / 0.13 ( 4) metal coordination : angle 0.89821 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 0.425 Fit side-chains REVERT: A 215 ASN cc_start: 0.8594 (t0) cc_final: 0.8336 (t0) REVERT: A 217 ASN cc_start: 0.8505 (m-40) cc_final: 0.8268 (m110) REVERT: A 223 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: A 245 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 336 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7467 (t0) REVERT: A 602 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7712 (mtp85) REVERT: A 604 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8402 (mm-30) REVERT: A 634 ASN cc_start: 0.6805 (t0) cc_final: 0.6593 (t0) REVERT: A 753 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6703 (tt0) REVERT: C 37 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 56 GLU cc_start: 0.7704 (tt0) cc_final: 0.7403 (tt0) REVERT: C 75 CYS cc_start: 0.8980 (m) cc_final: 0.8705 (m) REVERT: C 122 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7714 (mtp180) REVERT: C 126 SER cc_start: 0.8102 (t) cc_final: 0.7780 (t) REVERT: C 343 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8250 (ttt90) REVERT: C 472 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8393 (mmp-170) REVERT: C 508 LYS cc_start: 0.7688 (tppt) cc_final: 0.6983 (ttpt) REVERT: C 520 ASP cc_start: 0.8108 (t70) cc_final: 0.7784 (t0) REVERT: C 529 ARG cc_start: 0.7930 (tpt90) cc_final: 0.6795 (ttp-110) REVERT: C 578 MET cc_start: 0.8065 (ttm) cc_final: 0.7763 (ttp) REVERT: C 748 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8383 (m) REVERT: C 841 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7374 (tpt) outliers start: 52 outliers final: 34 residues processed: 156 average time/residue: 0.1367 time to fit residues: 30.9566 Evaluate side-chains 159 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 758 LYS Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 185 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 815 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106008 restraints weight = 16370.424| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.25 r_work: 0.2998 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15875 Z= 0.214 Angle : 0.591 9.331 21826 Z= 0.312 Chirality : 0.045 0.313 2461 Planarity : 0.005 0.052 2626 Dihedral : 18.531 159.145 2761 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.09 % Allowed : 20.59 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1826 helix: 1.39 (0.20), residues: 744 sheet: 0.13 (0.33), residues: 247 loop : -1.42 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 203 TYR 0.018 0.002 TYR A 875 PHE 0.029 0.002 PHE A 467 TRP 0.018 0.002 TRP A 959 HIS 0.009 0.002 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.21 (15871) covalent geometry : angle 0.59039 / 0.31 (21823) hydrogen bonds : bond 0.06147 / 4.21 ( 662) hydrogen bonds : angle 4.03127 / 2.85 ( 1886) metal coordination : bond 0.00250 / 0.13 ( 4) metal coordination : angle 1.21231 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 183 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mtpp) REVERT: A 215 ASN cc_start: 0.8698 (t0) cc_final: 0.8387 (t0) REVERT: A 217 ASN cc_start: 0.8603 (m-40) cc_final: 0.8389 (m110) REVERT: A 223 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 245 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (t) REVERT: A 271 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: A 336 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7541 (t0) REVERT: A 602 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7756 (mtp85) REVERT: A 604 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8405 (mm-30) REVERT: A 634 ASN cc_start: 0.7141 (t0) cc_final: 0.6941 (t0) REVERT: A 753 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6804 (tt0) REVERT: A 798 GLN cc_start: 0.7596 (tt0) cc_final: 0.7246 (tp40) REVERT: C 37 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (tp) REVERT: C 56 GLU cc_start: 0.7831 (tt0) cc_final: 0.7591 (tt0) REVERT: C 75 CYS cc_start: 0.9016 (m) cc_final: 0.8756 (m) REVERT: C 122 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7765 (mtp180) REVERT: C 126 SER cc_start: 0.8274 (t) cc_final: 0.7941 (t) REVERT: C 343 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8340 (ttt90) REVERT: C 472 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8449 (mmp-170) REVERT: C 508 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7088 (ttpt) REVERT: C 515 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7789 (ttp80) REVERT: C 578 MET cc_start: 0.8149 (ttm) cc_final: 0.7798 (ttp) REVERT: C 653 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.7940 (ttt180) REVERT: C 748 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8490 (m) REVERT: C 841 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7098 (tpt) outliers start: 61 outliers final: 43 residues processed: 165 average time/residue: 0.1298 time to fit residues: 31.2177 Evaluate side-chains 173 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 758 LYS Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 126 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 164 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 999 GLN C 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108929 restraints weight = 16275.377| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.45 r_work: 0.3031 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15875 Z= 0.118 Angle : 0.493 9.044 21826 Z= 0.267 Chirality : 0.041 0.312 2461 Planarity : 0.004 0.045 2626 Dihedral : 18.424 159.185 2761 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.82 % Allowed : 21.26 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1826 helix: 1.62 (0.20), residues: 743 sheet: 0.25 (0.33), residues: 245 loop : -1.33 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.011 0.001 TYR A 364 PHE 0.014 0.001 PHE A 467 TRP 0.010 0.001 TRP A 959 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15871) covalent geometry : angle 0.49293 / 0.27 (21823) hydrogen bonds : bond 0.04293 / 2.95 ( 662) hydrogen bonds : angle 3.82441 / 2.71 ( 1886) metal coordination : bond 0.00194 / 0.09 ( 4) metal coordination : angle 1.37093 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (mtpp) REVERT: A 215 ASN cc_start: 0.8719 (t0) cc_final: 0.8410 (t0) REVERT: A 217 ASN cc_start: 0.8557 (m-40) cc_final: 0.8267 (m110) REVERT: A 223 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 245 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8416 (t) REVERT: A 271 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 542 MET cc_start: 0.8558 (mtt) cc_final: 0.8301 (mtt) REVERT: A 602 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7796 (mtp85) REVERT: A 604 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: A 731 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8359 (m) REVERT: A 753 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6641 (mt-10) REVERT: A 999 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: C 37 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8796 (tp) REVERT: C 56 GLU cc_start: 0.7698 (tt0) cc_final: 0.7432 (tt0) REVERT: C 75 CYS cc_start: 0.8967 (m) cc_final: 0.8704 (m) REVERT: C 122 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7819 (tpt170) REVERT: C 126 SER cc_start: 0.7921 (t) cc_final: 0.7622 (t) REVERT: C 343 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8274 (ttt90) REVERT: C 472 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8387 (mmp-170) REVERT: C 508 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6992 (ttpp) REVERT: C 515 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7680 (ttp80) REVERT: C 578 MET cc_start: 0.8104 (ttm) cc_final: 0.7811 (ttp) REVERT: C 689 GLU cc_start: 0.8324 (tt0) cc_final: 0.8014 (tt0) REVERT: C 711 ASP cc_start: 0.7473 (m-30) cc_final: 0.7176 (m-30) REVERT: C 748 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (m) REVERT: C 833 GLU cc_start: 0.8696 (mp0) cc_final: 0.8278 (mp0) REVERT: C 841 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7077 (tpt) outliers start: 57 outliers final: 34 residues processed: 162 average time/residue: 0.1304 time to fit residues: 30.8302 Evaluate side-chains 164 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 183 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108998 restraints weight = 16263.373| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.25 r_work: 0.3041 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15875 Z= 0.123 Angle : 0.497 9.131 21826 Z= 0.268 Chirality : 0.041 0.310 2461 Planarity : 0.004 0.045 2626 Dihedral : 18.342 159.088 2756 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.82 % Allowed : 21.46 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1826 helix: 1.65 (0.20), residues: 743 sheet: 0.27 (0.33), residues: 245 loop : -1.28 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.009 0.001 TYR A 364 PHE 0.016 0.001 PHE A 467 TRP 0.011 0.001 TRP A 959 HIS 0.006 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15871) covalent geometry : angle 0.49693 / 0.27 (21823) hydrogen bonds : bond 0.04360 / 3.00 ( 662) hydrogen bonds : angle 3.78627 / 2.68 ( 1886) metal coordination : bond 0.00209 / 0.10 ( 4) metal coordination : angle 1.18361 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8528 (mtpp) REVERT: A 215 ASN cc_start: 0.8733 (t0) cc_final: 0.8428 (t0) REVERT: A 217 ASN cc_start: 0.8562 (m-40) cc_final: 0.8285 (m110) REVERT: A 223 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: A 245 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8414 (t) REVERT: A 271 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: A 542 MET cc_start: 0.8554 (mtt) cc_final: 0.8323 (mtt) REVERT: A 602 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7793 (mtp85) REVERT: A 604 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: A 731 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8355 (m) REVERT: A 753 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: C 37 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8814 (tp) REVERT: C 56 GLU cc_start: 0.7722 (tt0) cc_final: 0.7458 (tt0) REVERT: C 75 CYS cc_start: 0.8961 (m) cc_final: 0.8694 (m) REVERT: C 122 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7807 (tpt170) REVERT: C 126 SER cc_start: 0.7932 (t) cc_final: 0.7681 (t) REVERT: C 343 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8266 (ttt90) REVERT: C 472 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8405 (mmp-170) REVERT: C 508 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6984 (ttpp) REVERT: C 515 ARG cc_start: 0.8180 (ptp-110) cc_final: 0.7667 (ttp80) REVERT: C 578 MET cc_start: 0.8105 (ttm) cc_final: 0.7811 (ttp) REVERT: C 689 GLU cc_start: 0.8341 (tt0) cc_final: 0.8028 (tt0) REVERT: C 748 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (m) REVERT: C 841 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7102 (tpt) outliers start: 57 outliers final: 38 residues processed: 159 average time/residue: 0.1295 time to fit residues: 29.7670 Evaluate side-chains 165 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 100 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 182 optimal weight: 50.0000 chunk 160 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110424 restraints weight = 16429.132| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.26 r_work: 0.3060 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15875 Z= 0.108 Angle : 0.475 9.140 21826 Z= 0.258 Chirality : 0.040 0.308 2461 Planarity : 0.004 0.044 2626 Dihedral : 18.255 159.094 2756 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.82 % Allowed : 21.40 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1826 helix: 1.73 (0.20), residues: 748 sheet: 0.33 (0.33), residues: 245 loop : -1.21 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.009 0.001 TYR A 364 PHE 0.012 0.001 PHE A 536 TRP 0.009 0.001 TRP A 844 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (15871) covalent geometry : angle 0.47533 / 0.26 (21823) hydrogen bonds : bond 0.03827 / 2.64 ( 662) hydrogen bonds : angle 3.68708 / 2.61 ( 1886) metal coordination : bond 0.00225 / 0.11 ( 4) metal coordination : angle 1.07708 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8516 (mtpp) REVERT: A 215 ASN cc_start: 0.8728 (t0) cc_final: 0.8389 (t0) REVERT: A 217 ASN cc_start: 0.8490 (m-40) cc_final: 0.8223 (m110) REVERT: A 223 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: A 245 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (t) REVERT: A 271 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: A 542 MET cc_start: 0.8526 (mtt) cc_final: 0.8296 (mtt) REVERT: A 602 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7772 (mtp85) REVERT: A 604 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: A 731 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8330 (m) REVERT: A 753 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6786 (tt0) REVERT: C 37 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8804 (tp) REVERT: C 56 GLU cc_start: 0.7685 (tt0) cc_final: 0.7421 (tt0) REVERT: C 75 CYS cc_start: 0.8962 (m) cc_final: 0.8692 (m) REVERT: C 122 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7813 (tpt170) REVERT: C 126 SER cc_start: 0.7975 (t) cc_final: 0.7774 (t) REVERT: C 343 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8223 (ttt90) REVERT: C 472 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8344 (mmp-170) REVERT: C 508 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6911 (ttpp) REVERT: C 515 ARG cc_start: 0.8120 (ptp-110) cc_final: 0.7609 (ttp80) REVERT: C 578 MET cc_start: 0.8115 (ttm) cc_final: 0.7815 (ttp) REVERT: C 689 GLU cc_start: 0.8294 (tt0) cc_final: 0.7749 (mt-10) REVERT: C 748 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8398 (m) REVERT: C 833 GLU cc_start: 0.8716 (mp0) cc_final: 0.8476 (mp0) REVERT: C 841 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7081 (tpt) outliers start: 57 outliers final: 36 residues processed: 166 average time/residue: 0.1164 time to fit residues: 28.2374 Evaluate side-chains 164 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 10 optimal weight: 0.0040 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108454 restraints weight = 16424.901| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.26 r_work: 0.3032 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15875 Z= 0.147 Angle : 0.518 9.118 21826 Z= 0.276 Chirality : 0.042 0.305 2461 Planarity : 0.004 0.047 2626 Dihedral : 18.280 158.942 2756 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.69 % Allowed : 21.60 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1826 helix: 1.69 (0.20), residues: 737 sheet: 0.27 (0.33), residues: 245 loop : -1.22 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.011 0.001 TYR C 382 PHE 0.021 0.001 PHE A 467 TRP 0.012 0.001 TRP A 959 HIS 0.007 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15871) covalent geometry : angle 0.51808 / 0.28 (21823) hydrogen bonds : bond 0.04693 / 3.22 ( 662) hydrogen bonds : angle 3.76937 / 2.66 ( 1886) metal coordination : bond 0.00180 / 0.09 ( 4) metal coordination : angle 1.20038 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: A 215 ASN cc_start: 0.8756 (t0) cc_final: 0.8433 (t0) REVERT: A 217 ASN cc_start: 0.8509 (m-40) cc_final: 0.8267 (m110) REVERT: A 223 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 245 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8409 (t) REVERT: A 271 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6648 (pm20) REVERT: A 542 MET cc_start: 0.8668 (mtt) cc_final: 0.8457 (mtt) REVERT: A 602 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7735 (mtp85) REVERT: A 604 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: A 727 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7810 (tttp) REVERT: A 731 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8261 (m) REVERT: A 753 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: C 37 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 56 GLU cc_start: 0.7750 (tt0) cc_final: 0.7491 (tt0) REVERT: C 75 CYS cc_start: 0.8973 (m) cc_final: 0.8708 (m) REVERT: C 122 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: C 343 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8301 (ttt90) REVERT: C 472 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8419 (mmp-170) REVERT: C 508 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.6966 (ttpp) REVERT: C 515 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7656 (ttp80) REVERT: C 578 MET cc_start: 0.8100 (ttm) cc_final: 0.7799 (ttp) REVERT: C 748 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8448 (m) REVERT: C 833 GLU cc_start: 0.8713 (mp0) cc_final: 0.8432 (mp0) REVERT: C 841 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7083 (tpt) outliers start: 55 outliers final: 40 residues processed: 158 average time/residue: 0.1380 time to fit residues: 31.9147 Evaluate side-chains 167 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1007 MET Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 117 optimal weight: 0.0270 chunk 113 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 999 GLN C 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110050 restraints weight = 16306.236| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.43 r_work: 0.3051 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15875 Z= 0.107 Angle : 0.479 9.101 21826 Z= 0.259 Chirality : 0.040 0.303 2461 Planarity : 0.004 0.045 2626 Dihedral : 18.210 159.028 2756 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.42 % Allowed : 21.93 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1826 helix: 1.78 (0.20), residues: 742 sheet: 0.35 (0.33), residues: 245 loop : -1.14 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.009 0.001 TYR A 364 PHE 0.012 0.001 PHE A 467 TRP 0.009 0.001 TRP A 844 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (15871) covalent geometry : angle 0.47905 / 0.26 (21823) hydrogen bonds : bond 0.03850 / 2.65 ( 662) hydrogen bonds : angle 3.67604 / 2.60 ( 1886) metal coordination : bond 0.00273 / 0.13 ( 4) metal coordination : angle 1.13384 / 0.72 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 117 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8503 (mtpp) REVERT: A 215 ASN cc_start: 0.8724 (t0) cc_final: 0.8416 (t0) REVERT: A 223 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 245 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 271 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: A 602 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7665 (mtp85) REVERT: A 604 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8377 (mm-30) REVERT: A 717 ASP cc_start: 0.7642 (m-30) cc_final: 0.7276 (t0) REVERT: A 731 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8315 (m) REVERT: A 753 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: A 999 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8575 (mp10) REVERT: C 37 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 56 GLU cc_start: 0.7673 (tt0) cc_final: 0.7415 (tt0) REVERT: C 75 CYS cc_start: 0.8952 (m) cc_final: 0.8709 (m) REVERT: C 122 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (tpt170) REVERT: C 343 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: C 472 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8338 (mmp-170) REVERT: C 508 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6894 (ttpp) REVERT: C 515 ARG cc_start: 0.8110 (ptp-110) cc_final: 0.7592 (ttp80) REVERT: C 578 MET cc_start: 0.8114 (ttm) cc_final: 0.7812 (ttp) REVERT: C 689 GLU cc_start: 0.8232 (tt0) cc_final: 0.7966 (mt-10) REVERT: C 748 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8420 (m) REVERT: C 833 GLU cc_start: 0.8706 (mp0) cc_final: 0.8435 (mp0) REVERT: C 841 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7067 (tpt) outliers start: 51 outliers final: 35 residues processed: 155 average time/residue: 0.1254 time to fit residues: 28.4833 Evaluate side-chains 165 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 115 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 555 GLU Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 841 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 174 optimal weight: 0.1980 chunk 118 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 172 optimal weight: 0.0030 chunk 39 optimal weight: 0.7980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 815 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110297 restraints weight = 16226.110| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.42 r_work: 0.3050 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.260 15875 Z= 0.183 Angle : 0.772 59.199 21826 Z= 0.434 Chirality : 0.040 0.303 2461 Planarity : 0.004 0.047 2626 Dihedral : 18.209 159.028 2756 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.22 % Allowed : 22.07 % Favored : 74.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1826 helix: 1.79 (0.20), residues: 742 sheet: 0.36 (0.33), residues: 245 loop : -1.14 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.009 0.001 TYR A 158 PHE 0.012 0.001 PHE A 467 TRP 0.008 0.001 TRP A 844 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (15871) covalent geometry : angle 0.77242 / 0.43 (21823) hydrogen bonds : bond 0.03804 / 2.62 ( 662) hydrogen bonds : angle 3.67495 / 2.60 ( 1886) metal coordination : bond 0.00267 / 0.13 ( 4) metal coordination : angle 1.12669 / 0.72 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.03 seconds wall clock time: 68 minutes 24.72 seconds (4104.72 seconds total)