Starting phenix.real_space_refine on Thu Aug 6 15:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zgf_74190/08_2026/9zgf_74190.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zgf_74190/08_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_74190/08_2026/9zgf_74190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zgf_74190/08_2026/9zgf_74190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zgf_74190/08_2026/9zgf_74190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zgf_74190/08_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-2.2rc3-6140/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: 2.84, per 1000 atoms: 0.18 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: 1.20 Conformation dependent library (CDL) restraints added in 464.3 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: 1.47 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: 2.86 Time building geometry restraints manager: 1.57 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- 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 : 0.554 7.742 21826 Z= 0.363 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 0.55367 / 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 : 0.439 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: 0.1252 time to fit residues: 28.3082 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 : 0.329 ------------------------------------------------------------------------------- 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 = 0.157005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105886 restraints weight = 15997.920| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.33 r_work: 0.3027 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0382 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= 0.136 Angle : 0.529 9.766 21826 Z= 0.287 Chirality : 0.042 0.336 2461 Planarity : 0.004 0.048 2626 Dihedral : 19.071 157.861 2809 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.68 % Allowed : 21.40 % Favored : 75.92 % 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: 0.08 (0.20), residues: 1826 helix: 1.54 (0.20), residues: 745 sheet: 0.30 (0.34), residues: 238 loop : -1.43 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 602 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 0.00297 / 0.14 (15871) covalent geometry : angle 0.52896 / 0.29 (21823) hydrogen bonds : bond 0.05024 / 3.44 ( 662) hydrogen bonds : angle 4.11133 / 2.91 ( 1886) metal coordination : bond 0.00226 / 0.11 ( 4) metal coordination : angle 1.49630 / 0.95 ( 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 157 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7758 (mt) cc_final: 0.7260 (tt) REVERT: A 223 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: A 245 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8476 (t) REVERT: A 336 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 602 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7714 (mtp85) REVERT: A 604 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8419 (mm-30) REVERT: A 634 ASN cc_start: 0.6830 (t0) cc_final: 0.6616 (t0) REVERT: C 37 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 56 GLU cc_start: 0.7813 (tt0) cc_final: 0.7517 (tt0) REVERT: C 75 CYS cc_start: 0.9026 (m) cc_final: 0.8739 (m) REVERT: C 122 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: C 508 LYS cc_start: 0.7731 (tppt) cc_final: 0.7055 (ttpt) REVERT: C 520 ASP cc_start: 0.8180 (t70) cc_final: 0.7856 (t0) REVERT: C 578 MET cc_start: 0.8159 (ttm) cc_final: 0.7861 (ttp) REVERT: C 748 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8415 (m) REVERT: C 841 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7556 (tpt) outliers start: 40 outliers final: 20 residues processed: 146 average time/residue: 0.1115 time to fit residues: 24.1176 Evaluate side-chains 140 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 562 VAL 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: 1.9990 chunk 159 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111593 restraints weight = 16441.636| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.28 r_work: 0.3078 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15875 Z= 0.104 Angle : 0.476 9.165 21826 Z= 0.259 Chirality : 0.040 0.339 2461 Planarity : 0.004 0.040 2626 Dihedral : 18.530 158.543 2763 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.95 % Allowed : 21.66 % Favored : 75.39 % 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: 0.33 (0.20), residues: 1826 helix: 1.73 (0.20), residues: 746 sheet: 0.37 (0.33), residues: 242 loop : -1.28 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.010 0.001 TYR A 364 PHE 0.012 0.001 PHE A 536 TRP 0.007 0.001 TRP A 844 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (15871) covalent geometry : angle 0.47558 / 0.26 (21823) hydrogen bonds : bond 0.03807 / 2.63 ( 662) hydrogen bonds : angle 3.81800 / 2.71 ( 1886) metal coordination : bond 0.00404 / 0.19 ( 4) metal coordination : angle 1.07981 / 0.59 ( 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 163 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.339 Fit side-chains REVERT: A 223 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 336 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7460 (t0) REVERT: A 602 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7668 (mtp85) REVERT: A 604 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8392 (mm-30) REVERT: A 731 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 753 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: C 56 GLU cc_start: 0.7678 (tt0) cc_final: 0.7360 (tt0) REVERT: C 122 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7758 (mtp180) REVERT: C 343 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8245 (ttt90) REVERT: C 508 LYS cc_start: 0.7701 (tppt) cc_final: 0.6971 (ttpt) REVERT: C 520 ASP cc_start: 0.8068 (t70) cc_final: 0.7787 (t0) REVERT: C 529 ARG cc_start: 0.7938 (tpt90) cc_final: 0.6804 (ttp-110) REVERT: C 578 MET cc_start: 0.8078 (ttm) cc_final: 0.7793 (ttp) REVERT: C 689 GLU cc_start: 0.8090 (tt0) cc_final: 0.7864 (tt0) REVERT: C 748 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8386 (m) REVERT: C 824 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.4533 (t0) REVERT: C 833 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8256 (mp0) outliers start: 44 outliers final: 25 residues processed: 153 average time/residue: 0.1074 time to fit residues: 24.2203 Evaluate side-chains 147 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 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 27 TYR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 MET 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 390 THR Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 522 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 173 optimal weight: 0.0870 chunk 175 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.160405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108693 restraints weight = 16432.239| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.27 r_work: 0.3034 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15875 Z= 0.148 Angle : 0.527 9.528 21826 Z= 0.281 Chirality : 0.042 0.339 2461 Planarity : 0.004 0.045 2626 Dihedral : 18.490 158.122 2761 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.69 % Allowed : 20.86 % Favored : 75.45 % 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: 0.23 (0.20), residues: 1826 helix: 1.67 (0.20), residues: 742 sheet: 0.30 (0.33), residues: 245 loop : -1.33 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.011 0.001 TYR A 875 PHE 0.020 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 0.00346 / 0.15 (15871) covalent geometry : angle 0.52710 / 0.28 (21823) hydrogen bonds : bond 0.04849 / 3.33 ( 662) hydrogen bonds : angle 3.84727 / 2.73 ( 1886) metal coordination : bond 0.00214 / 0.11 ( 4) metal coordination : angle 0.93420 / 0.59 ( 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 173 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.344 Fit side-chains REVERT: A 183 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8559 (mtpp) REVERT: A 215 ASN cc_start: 0.8620 (t0) cc_final: 0.8353 (t0) REVERT: A 217 ASN cc_start: 0.8577 (m-40) cc_final: 0.8318 (m110) REVERT: A 223 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: A 336 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7491 (t0) REVERT: A 602 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7697 (mtp85) REVERT: A 604 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8410 (mm-30) REVERT: A 731 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8373 (m) REVERT: A 753 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: C 37 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8821 (tp) REVERT: C 56 GLU cc_start: 0.7734 (tt0) cc_final: 0.7442 (tt0) REVERT: C 75 CYS cc_start: 0.8985 (m) cc_final: 0.8711 (m) REVERT: C 122 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7731 (mtp180) REVERT: C 343 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8263 (ttt90) REVERT: C 472 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8420 (mmp-170) REVERT: C 508 LYS cc_start: 0.7729 (tppt) cc_final: 0.7027 (ttpt) REVERT: C 520 ASP cc_start: 0.8155 (t70) cc_final: 0.7829 (t0) REVERT: C 529 ARG cc_start: 0.7950 (tpt90) cc_final: 0.6824 (ttp-110) REVERT: C 578 MET cc_start: 0.8094 (ttm) cc_final: 0.7795 (ttp) REVERT: C 748 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8413 (m) REVERT: C 824 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.5493 (m-30) REVERT: C 841 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7583 (tpt) outliers start: 55 outliers final: 34 residues processed: 158 average time/residue: 0.1164 time to fit residues: 26.7466 Evaluate side-chains 159 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 731 VAL Chi-restraints excluded: chain A residue 753 GLU 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 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 198 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 515 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 824 ASP 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: 1.9990 chunk 0 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 185 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 162 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.159309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107755 restraints weight = 16331.372| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.26 r_work: 0.3021 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15875 Z= 0.163 Angle : 0.535 9.446 21826 Z= 0.285 Chirality : 0.043 0.337 2461 Planarity : 0.004 0.047 2626 Dihedral : 18.432 157.924 2760 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.16 % Allowed : 20.59 % Favored : 75.25 % 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: 0.18 (0.20), residues: 1826 helix: 1.61 (0.20), residues: 736 sheet: 0.26 (0.33), residues: 245 loop : -1.32 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.012 0.001 TYR A 875 PHE 0.022 0.002 PHE A 467 TRP 0.014 0.001 TRP A 959 HIS 0.007 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (15871) covalent geometry : angle 0.53448 / 0.29 (21823) hydrogen bonds : bond 0.05138 / 3.52 ( 662) hydrogen bonds : angle 3.89162 / 2.76 ( 1886) metal coordination : bond 0.00208 / 0.11 ( 4) metal coordination : angle 1.19352 / 0.77 ( 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 178 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 116 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: A 215 ASN cc_start: 0.8668 (t0) cc_final: 0.8319 (t0) REVERT: A 217 ASN cc_start: 0.8597 (m-40) cc_final: 0.8281 (m110) REVERT: A 223 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 245 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8444 (t) REVERT: A 271 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: A 336 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 602 ARG cc_start: 0.8322 (ttm110) cc_final: 0.7753 (mtp85) REVERT: A 604 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8404 (mm-30) REVERT: A 727 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7844 (tttp) REVERT: A 731 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8367 (m) REVERT: A 753 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: C 37 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8859 (tp) REVERT: C 56 GLU cc_start: 0.7764 (tt0) cc_final: 0.7505 (tt0) REVERT: C 75 CYS cc_start: 0.8976 (m) cc_final: 0.8717 (m) REVERT: C 122 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (tpt170) REVERT: C 126 SER cc_start: 0.8221 (t) cc_final: 0.7883 (t) REVERT: C 343 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8305 (ttt90) REVERT: C 472 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8429 (mmp-170) REVERT: C 508 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7076 (ttpt) REVERT: C 515 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: C 578 MET cc_start: 0.8107 (ttm) cc_final: 0.7778 (ttp) REVERT: C 841 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7342 (tpt) outliers start: 62 outliers final: 42 residues processed: 164 average time/residue: 0.1344 time to fit residues: 32.5088 Evaluate side-chains 170 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 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 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 198 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 515 ARG Chi-restraints excluded: chain C residue 522 LEU 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 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: 0.9980 chunk 71 optimal weight: 0.0970 chunk 145 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 117 optimal weight: 0.0020 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.162435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110680 restraints weight = 16272.465| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.47 r_work: 0.3055 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0782 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= 0.103 Angle : 0.474 9.306 21826 Z= 0.257 Chirality : 0.040 0.335 2461 Planarity : 0.004 0.041 2626 Dihedral : 18.286 157.861 2759 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.09 % Allowed : 21.80 % Favored : 75.12 % 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: 0.37 (0.33), residues: 245 loop : -1.22 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.010 0.001 TYR A 364 PHE 0.012 0.001 PHE C 286 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 0.00205 / 0.10 (15871) covalent geometry : angle 0.47348 / 0.26 (21823) hydrogen bonds : bond 0.03713 / 2.56 ( 662) hydrogen bonds : angle 3.70668 / 2.62 ( 1886) metal coordination : bond 0.00291 / 0.14 ( 4) metal coordination : angle 1.24301 / 0.74 ( 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 167 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8610 (t0) cc_final: 0.8276 (t0) REVERT: A 217 ASN cc_start: 0.8540 (m-40) cc_final: 0.8228 (m110) REVERT: A 223 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 245 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 271 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: A 602 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7786 (mtp85) REVERT: A 604 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: A 634 ASN cc_start: 0.6943 (t0) cc_final: 0.6722 (t0) REVERT: A 731 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 753 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6755 (tt0) REVERT: A 999 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: C 37 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (tp) REVERT: C 56 GLU cc_start: 0.7666 (tt0) cc_final: 0.7327 (tt0) REVERT: C 75 CYS cc_start: 0.8943 (m) cc_final: 0.8697 (m) REVERT: C 122 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7826 (tpt170) REVERT: C 126 SER cc_start: 0.7843 (t) cc_final: 0.7572 (t) REVERT: C 343 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8209 (ttt90) REVERT: C 472 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8312 (mmp-170) REVERT: C 508 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6909 (ttpp) REVERT: C 520 ASP cc_start: 0.8110 (t70) cc_final: 0.7826 (t0) REVERT: C 578 MET cc_start: 0.8097 (ttm) cc_final: 0.7794 (ttp) REVERT: C 833 GLU cc_start: 0.8672 (mp0) cc_final: 0.8263 (mp0) REVERT: C 841 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7095 (tpt) outliers start: 46 outliers final: 25 residues processed: 154 average time/residue: 0.1262 time to fit residues: 28.2117 Evaluate side-chains 155 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 201 LEU 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 328 SER Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 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 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 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 198 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 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 699 LEU Chi-restraints excluded: chain C residue 742 VAL 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: 2.9990 chunk 23 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 151 optimal weight: 0.4980 chunk 183 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.159060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107604 restraints weight = 16304.878| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.26 r_work: 0.3019 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15875 Z= 0.186 Angle : 0.548 9.329 21826 Z= 0.291 Chirality : 0.043 0.333 2461 Planarity : 0.004 0.047 2626 Dihedral : 18.300 157.584 2755 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.96 % Allowed : 20.93 % Favored : 75.12 % 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: 0.21 (0.20), residues: 1826 helix: 1.60 (0.20), residues: 737 sheet: 0.26 (0.33), residues: 245 loop : -1.27 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 323 TYR 0.013 0.002 TYR A 875 PHE 0.025 0.002 PHE A 467 TRP 0.013 0.001 TRP A 959 HIS 0.008 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (15871) covalent geometry : angle 0.54737 / 0.29 (21823) hydrogen bonds : bond 0.05206 / 3.58 ( 662) hydrogen bonds : angle 3.84122 / 2.72 ( 1886) metal coordination : bond 0.00200 / 0.10 ( 4) metal coordination : angle 1.18016 / 0.77 ( 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 174 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8741 (t0) cc_final: 0.8420 (t0) REVERT: A 217 ASN cc_start: 0.8590 (m-40) cc_final: 0.8294 (m110) REVERT: A 223 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: A 245 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (t) REVERT: A 271 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: A 542 MET cc_start: 0.8680 (mtt) cc_final: 0.8451 (mtt) REVERT: A 602 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7792 (mtp85) REVERT: A 604 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8403 (mm-30) REVERT: A 731 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 753 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: C 37 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8828 (tp) REVERT: C 56 GLU cc_start: 0.7751 (tt0) cc_final: 0.7492 (tt0) REVERT: C 75 CYS cc_start: 0.8977 (m) cc_final: 0.8718 (m) REVERT: C 122 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7727 (mtp180) REVERT: C 126 SER cc_start: 0.7988 (t) cc_final: 0.7755 (t) REVERT: C 343 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8289 (ttt90) REVERT: C 472 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8423 (mmp-170) REVERT: C 508 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6995 (ttpp) REVERT: C 515 ARG cc_start: 0.8190 (ptp-110) cc_final: 0.7682 (ttp80) REVERT: C 578 MET cc_start: 0.8080 (ttm) cc_final: 0.7773 (ttp) REVERT: C 841 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7072 (tpt) outliers start: 59 outliers final: 42 residues processed: 157 average time/residue: 0.1167 time to fit residues: 27.1699 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 : 0.522 ------------------------------------------------------------------------------- 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 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 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 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 31 VAL 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 122 ARG 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 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 562 VAL 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 841 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 182 optimal weight: 50.0000 chunk 160 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.161378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109873 restraints weight = 16395.474| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.26 r_work: 0.3054 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0824 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= 0.110 Angle : 0.485 9.292 21826 Z= 0.262 Chirality : 0.041 0.330 2461 Planarity : 0.004 0.043 2626 Dihedral : 18.231 157.609 2755 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.55 % Allowed : 21.40 % Favored : 75.05 % 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: 0.39 (0.20), residues: 1826 helix: 1.78 (0.20), residues: 736 sheet: 0.33 (0.33), residues: 245 loop : -1.19 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.010 0.001 TYR A 364 PHE 0.013 0.001 PHE C 286 TRP 0.009 0.001 TRP A 959 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15871) covalent geometry : angle 0.48440 / 0.26 (21823) hydrogen bonds : bond 0.03960 / 2.73 ( 662) hydrogen bonds : angle 3.72675 / 2.64 ( 1886) metal coordination : bond 0.00173 / 0.09 ( 4) metal coordination : angle 1.22114 / 0.78 ( 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 170 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8719 (t0) cc_final: 0.8408 (t0) REVERT: A 217 ASN cc_start: 0.8560 (m-40) cc_final: 0.8255 (m110) REVERT: A 223 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 245 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8457 (t) REVERT: A 271 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: A 542 MET cc_start: 0.8547 (mtt) cc_final: 0.8323 (mtt) REVERT: A 602 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7795 (mtp85) REVERT: A 604 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: A 731 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (m) REVERT: A 753 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: C 37 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8795 (tp) REVERT: C 56 GLU cc_start: 0.7679 (tt0) cc_final: 0.7422 (tt0) REVERT: C 75 CYS cc_start: 0.8938 (m) cc_final: 0.8699 (m) REVERT: C 122 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7815 (tpt170) REVERT: C 126 SER cc_start: 0.7944 (t) cc_final: 0.7719 (t) REVERT: C 343 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8254 (ttt90) REVERT: C 472 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (mmp-170) REVERT: C 508 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6936 (ttpp) REVERT: C 520 ASP cc_start: 0.8137 (t70) cc_final: 0.7846 (t0) REVERT: C 578 MET cc_start: 0.8124 (ttm) cc_final: 0.7829 (ttp) REVERT: C 833 GLU cc_start: 0.8691 (mp0) cc_final: 0.8435 (mp0) REVERT: C 841 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7109 (tpt) outliers start: 53 outliers final: 33 residues processed: 159 average time/residue: 0.1185 time to fit residues: 27.8336 Evaluate side-chains 159 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 156 LEU 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 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 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 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 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 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 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL 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: 1.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.161296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109791 restraints weight = 16415.277| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.25 r_work: 0.3054 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15875 Z= 0.116 Angle : 0.490 9.289 21826 Z= 0.263 Chirality : 0.041 0.327 2461 Planarity : 0.004 0.044 2626 Dihedral : 18.199 157.476 2755 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.22 % Allowed : 21.80 % Favored : 74.98 % 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: 0.41 (0.20), residues: 1826 helix: 1.78 (0.20), residues: 742 sheet: 0.35 (0.33), residues: 245 loop : -1.17 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.009 0.001 TYR C 382 PHE 0.015 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 0.00251 / 0.12 (15871) covalent geometry : angle 0.49000 / 0.26 (21823) hydrogen bonds : bond 0.04057 / 2.79 ( 662) hydrogen bonds : angle 3.69729 / 2.61 ( 1886) metal coordination : bond 0.00188 / 0.09 ( 4) metal coordination : angle 1.11875 / 0.71 ( 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 166 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8707 (t0) cc_final: 0.8371 (t0) REVERT: A 223 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: A 245 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 271 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: A 542 MET cc_start: 0.8548 (mtt) cc_final: 0.8327 (mtt) REVERT: A 602 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7657 (mtp85) REVERT: A 604 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: A 731 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (m) REVERT: A 753 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: C 37 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8807 (tp) REVERT: C 56 GLU cc_start: 0.7691 (tt0) cc_final: 0.7435 (tt0) REVERT: C 75 CYS cc_start: 0.8950 (m) cc_final: 0.8678 (m) REVERT: C 122 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7821 (tpt170) REVERT: C 343 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8217 (ttt90) REVERT: C 472 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8354 (mmp-170) REVERT: C 508 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6914 (ttpp) REVERT: C 520 ASP cc_start: 0.8115 (t70) cc_final: 0.7793 (t0) REVERT: C 578 MET cc_start: 0.8112 (ttm) cc_final: 0.7807 (ttp) REVERT: C 689 GLU cc_start: 0.8314 (tt0) cc_final: 0.8049 (mt-10) REVERT: C 833 GLU cc_start: 0.8704 (mp0) cc_final: 0.8433 (mp0) REVERT: C 841 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7087 (tpt) outliers start: 48 outliers final: 35 residues processed: 156 average time/residue: 0.1015 time to fit residues: 23.3082 Evaluate side-chains 163 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 156 LEU 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 1007 MET 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 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 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 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 VAL 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: 0.9980 chunk 83 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 165 optimal weight: 0.0470 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.160773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109294 restraints weight = 16330.084| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.25 r_work: 0.3046 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0875 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= 0.127 Angle : 0.500 9.324 21826 Z= 0.267 Chirality : 0.041 0.323 2461 Planarity : 0.004 0.045 2626 Dihedral : 18.188 157.377 2755 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.29 % Allowed : 21.80 % 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: 0.38 (0.20), residues: 1826 helix: 1.77 (0.20), residues: 737 sheet: 0.33 (0.33), residues: 245 loop : -1.19 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.006 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15871) covalent geometry : angle 0.50023 / 0.27 (21823) hydrogen bonds : bond 0.04327 / 2.98 ( 662) hydrogen bonds : angle 3.73242 / 2.64 ( 1886) metal coordination : bond 0.00179 / 0.09 ( 4) metal coordination : angle 1.16838 / 0.76 ( 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 170 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 215 ASN cc_start: 0.8708 (t0) cc_final: 0.8407 (t0) REVERT: A 223 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: A 245 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 271 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: A 602 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7714 (mtp85) REVERT: A 604 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: A 717 ASP cc_start: 0.7654 (m-30) cc_final: 0.7292 (t0) REVERT: A 727 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7709 (tttp) REVERT: A 753 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: C 37 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8790 (tp) REVERT: C 56 GLU cc_start: 0.7713 (tt0) cc_final: 0.7457 (tt0) REVERT: C 75 CYS cc_start: 0.8951 (m) cc_final: 0.8678 (m) REVERT: C 122 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7676 (mtp180) REVERT: C 343 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: C 472 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8385 (mmp-170) REVERT: C 508 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6907 (ttpp) REVERT: C 520 ASP cc_start: 0.8112 (t70) cc_final: 0.7808 (t0) REVERT: C 578 MET cc_start: 0.8063 (ttm) cc_final: 0.7759 (ttp) REVERT: C 689 GLU cc_start: 0.8320 (tt0) cc_final: 0.7956 (mt-10) REVERT: C 833 GLU cc_start: 0.8691 (mp0) cc_final: 0.8416 (mp0) REVERT: C 841 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7090 (tpt) outliers start: 49 outliers final: 36 residues processed: 159 average time/residue: 0.1061 time to fit residues: 24.9547 Evaluate side-chains 166 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 156 LEU 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 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 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 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 584 ILE 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 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: 0.4980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.161479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110141 restraints weight = 16213.004| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.25 r_work: 0.3058 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0919 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= 0.114 Angle : 0.485 9.288 21826 Z= 0.260 Chirality : 0.040 0.319 2461 Planarity : 0.004 0.044 2626 Dihedral : 18.126 157.355 2755 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.22 % Allowed : 21.93 % Favored : 74.85 % 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: 0.39 (0.20), residues: 1826 helix: 1.73 (0.20), residues: 749 sheet: 0.37 (0.33), residues: 245 loop : -1.20 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.009 0.001 TYR A 364 PHE 0.014 0.001 PHE A 467 TRP 0.009 0.001 TRP A 959 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15871) covalent geometry : angle 0.48526 / 0.26 (21823) hydrogen bonds : bond 0.03963 / 2.73 ( 662) hydrogen bonds : angle 3.67820 / 2.60 ( 1886) metal coordination : bond 0.00255 / 0.13 ( 4) metal coordination : angle 1.15219 / 0.73 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.68 seconds wall clock time: 58 minutes 28.68 seconds (3508.68 seconds total)