Starting phenix.real_space_refine on Fri Aug 7 02:00:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga3_51170/08_2026/9ga3_51170.map" } resolution = 4.3 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= 0.002 sd= 0.025 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 82 5.49 5 S 52 5.16 5 C 11447 2.51 5 N 3340 2.21 5 O 3765 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: 18691 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6051 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 39, 'TRANS': 751} Chain breaks: 3 Chain: "B" Number of atoms: 6318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6318 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 40, 'TRANS': 786} Chain breaks: 2 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 756 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 847 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4660 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 28, 'TRANS': 560} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4533 SG CYS A 753 86.883 33.168 56.441 1.00293.98 S ATOM 4553 SG CYS A 756 89.395 34.321 53.617 1.00312.16 S ATOM 4706 SG CYS A 776 88.592 30.754 54.006 1.00332.08 S ATOM 4728 SG CYS A 779 85.877 33.207 52.846 1.00309.70 S ATOM 1034 SG CYS A 282 113.262 90.457 51.845 1.00616.18 S ATOM 1056 SG CYS A 285 111.217 87.387 51.288 1.00719.06 S ATOM 1951 SG CYS A 412 109.389 90.266 52.720 1.00721.65 S ATOM 1971 SG CYS A 415 110.493 90.768 49.283 1.00616.39 S ATOM 10851 SG CYS B 753 139.355 81.136 59.720 1.00562.15 S ATOM 10871 SG CYS B 756 137.982 78.623 57.286 1.00573.85 S ATOM 11024 SG CYS B 776 138.390 81.881 56.042 1.00596.17 S ATOM 11046 SG CYS B 779 141.514 79.769 56.528 1.00574.51 S ATOM 8186 SG CYS B 282 123.519 36.043 65.502 1.00578.49 S ATOM 8208 SG CYS B 285 125.466 39.197 64.700 1.00607.48 S ATOM 8269 SG CYS B 412 127.212 36.557 66.875 1.00612.52 S ATOM 8289 SG CYS B 415 126.517 35.770 63.330 1.00566.26 S ATOM 6994 SG CYS B 121 108.241 24.465 68.191 1.00501.32 S ATOM 7014 SG CYS B 124 106.831 21.126 69.550 1.00530.68 S ATOM 7999 SG CYS B 257 104.540 23.784 68.191 1.00499.46 S Time building chain proxies: 3.76, per 1000 atoms: 0.20 Number of scatterers: 18691 At special positions: 0 Unit cell: (192.36, 112.56, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 52 16.00 P 82 15.00 O 3765 8.00 N 3340 7.00 C 11447 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: 1.66 Conformation dependent library (CDL) restraints added in 670.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 776 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 779 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 756 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 753 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 412 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 285 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 415 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 282 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 776 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 779 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 753 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 415 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 285 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 282 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 412 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" ND1 HIS B 261 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 257 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 124 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 121 " Number of angles added : 27 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 45.4% alpha, 11.0% beta 28 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.894A pdb=" N MET A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.773A pdb=" N LYS A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.687A pdb=" N ALA A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 488 removed outlier: 5.321A pdb=" N GLN A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 534 through 551 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 719 through 730 removed outlier: 4.221A pdb=" N LYS A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.708A pdb=" N PHE A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 790 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 844 through 857 Processing helix chain 'A' and resid 877 through 894 Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 921 through 925 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 943 through 952 Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.846A pdb=" N ARG B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.751A pdb=" N ILE B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 214 through 229 removed outlier: 3.791A pdb=" N THR B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 449 through 459 removed outlier: 4.040A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 removed outlier: 5.321A pdb=" N GLN B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.616A pdb=" N GLY B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.786A pdb=" N LEU B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 659 through 666 Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 713 through 718 Processing helix chain 'B' and resid 719 through 730 removed outlier: 4.551A pdb=" N LYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 785 through 791 removed outlier: 4.133A pdb=" N VAL B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 796 Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 816 through 830 Processing helix chain 'B' and resid 844 through 858 removed outlier: 4.145A pdb=" N GLN B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 894 Processing helix chain 'B' and resid 904 through 911 removed outlier: 4.234A pdb=" N ILE B 908 " --> pdb=" O ASN B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 943 through 952 Processing helix chain 'E' and resid 39 through 53 Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.568A pdb=" N THR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.822A pdb=" N ALA E 93 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 154 Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 173 through 181 removed outlier: 3.606A pdb=" N SER E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 202 Processing helix chain 'E' and resid 274 through 300 Processing helix chain 'E' and resid 301 through 322 Processing helix chain 'E' and resid 327 through 330 Processing helix chain 'E' and resid 331 through 337 Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 361 through 381 Proline residue: E 367 - end of helix Processing helix chain 'E' and resid 390 through 396 removed outlier: 3.855A pdb=" N CYS E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 419 through 427 Processing helix chain 'E' and resid 453 through 467 removed outlier: 4.029A pdb=" N ALA E 467 " --> pdb=" O THR E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 491 Processing helix chain 'E' and resid 503 through 516 removed outlier: 4.032A pdb=" N ARG E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 553 through 565 Processing helix chain 'E' and resid 580 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.409A pdb=" N ARG A 16 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 11 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A 18 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.416A pdb=" N VAL A 29 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 574 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 31 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 86 removed outlier: 5.989A pdb=" N VAL A 84 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'A' and resid 640 through 645 removed outlier: 5.317A pdb=" N ILE A 640 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 631 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 650 through 653 removed outlier: 6.099A pdb=" N SER A 651 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU A 917 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 653 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 698 through 701 Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 23 removed outlier: 6.318A pdb=" N ARG B 16 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG B 11 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 18 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 156 removed outlier: 7.542A pdb=" N ILE B 201 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 235 removed outlier: 3.881A pdb=" N GLN B 249 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 867 through 869 removed outlier: 6.617A pdb=" N TYR B 867 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE B 901 " --> pdb=" O TYR B 867 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 869 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 652 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 916 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 930 " --> pdb=" O ASP B 916 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 761 through 766 removed outlier: 5.108A pdb=" N MET B 766 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 109 removed outlier: 6.975A pdb=" N ALA E 108 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL E 162 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU E 84 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP E 360 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET E 86 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E 412 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL E 58 " --> pdb=" O TYR E 413 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 120 Processing sheet with id=AB9, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'E' and resid 182 through 185 Processing sheet with id=AC2, first strand: chain 'E' and resid 205 through 206 removed outlier: 5.661A pdb=" N PHE E 239 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE E 243 " --> pdb=" O PHE E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 444 through 448 removed outlier: 6.175A pdb=" N LYS E 444 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N MET E 574 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 446 " --> pdb=" O MET E 574 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG E 470 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA E 541 " --> pdb=" O ARG E 470 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU E 472 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 543 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 474 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL E 471 " --> pdb=" O LEU E 522 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY E 524 " --> pdb=" O VAL E 471 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL E 473 " --> pdb=" O GLY E 524 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG E 496 " --> pdb=" O VAL E 523 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6099 1.34 - 1.46: 4220 1.46 - 1.58: 8616 1.58 - 1.70: 161 1.70 - 1.83: 77 Bond restraints: 19173 Sorted by residual: bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C1' DC D -23 " pdb=" N1 DC D -23 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" C1' DC C 34 " pdb=" N1 DC C 34 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" C1' DT D -10 " pdb=" N1 DT D -10 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" C1' DT D -13 " pdb=" N1 DT D -13 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.37e+01 ... (remaining 19168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 25220 1.68 - 3.36: 933 3.36 - 5.04: 163 5.04 - 6.71: 18 6.71 - 8.39: 3 Bond angle restraints: 26337 Sorted by residual: angle pdb=" O4' DC D -23 " pdb=" C4' DC D -23 " pdb=" C3' DC D -23 " ideal model delta sigma weight residual 106.00 101.56 4.44 6.00e-01 2.78e+00 5.49e+01 angle pdb=" O4' DG D -12 " pdb=" C4' DG D -12 " pdb=" C3' DG D -12 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.08e+01 angle pdb=" O4' DT D -13 " pdb=" C4' DT D -13 " pdb=" C3' DT D -13 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" N3 DT D -6 " pdb=" C4 DT D -6 " pdb=" O4 DT D -6 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.48e+01 ... (remaining 26332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 10799 35.33 - 70.67: 571 70.67 - 106.00: 21 106.00 - 141.34: 0 141.34 - 176.67: 11 Dihedral angle restraints: 11402 sinusoidal: 5117 harmonic: 6285 Sorted by residual: dihedral pdb=" CA LYS E 380 " pdb=" C LYS E 380 " pdb=" N ARG E 381 " pdb=" CA ARG E 381 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA MET E 318 " pdb=" C MET E 318 " pdb=" N MET E 319 " pdb=" CA MET E 319 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CD ARG A 96 " pdb=" NE ARG A 96 " pdb=" CZ ARG A 96 " pdb=" NH1 ARG A 96 " ideal model delta sinusoidal sigma weight residual 0.00 -42.71 42.71 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 11399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2170 0.041 - 0.082: 507 0.082 - 0.122: 241 0.122 - 0.163: 73 0.163 - 0.204: 18 Chirality restraints: 3009 Sorted by residual: chirality pdb=" C3' DC D -23 " pdb=" C4' DC D -23 " pdb=" O3' DC D -23 " pdb=" C2' DC D -23 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU A 293 " pdb=" N GLU A 293 " pdb=" C GLU A 293 " pdb=" CB GLU A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DG C 7 " pdb=" C4' DG C 7 " pdb=" O3' DG C 7 " pdb=" C2' DG C 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 3006 not shown) Planarity restraints: 3179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " 0.716 9.50e-02 1.11e+02 3.21e-01 6.31e+01 pdb=" NE ARG A 96 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 33 " 0.035 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" N1 DT C 33 " -0.035 2.00e-02 2.50e+03 pdb=" C2 DT C 33 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT C 33 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT C 33 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT C 33 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT C 33 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT C 33 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT C 33 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT C 33 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 153 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO B 154 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.035 5.00e-02 4.00e+02 ... (remaining 3176 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3490 2.76 - 3.29: 22664 3.29 - 3.83: 37126 3.83 - 4.36: 44209 4.36 - 4.90: 65774 Nonbonded interactions: 173263 Sorted by model distance: nonbonded pdb=" O ALA B 129 " pdb=" O ALA B 256 " model vdw 2.224 3.040 nonbonded pdb=" O GLU B 562 " pdb=" OE1 GLU B 566 " model vdw 2.342 3.040 nonbonded pdb=" OP1 DC D -22 " pdb=" O4' DC D -22 " model vdw 2.343 3.040 nonbonded pdb=" O THR A 650 " pdb=" O VAL A 898 " model vdw 2.349 3.040 nonbonded pdb=" O VAL B 671 " pdb=" OD1 ASN B 674 " model vdw 2.357 3.040 ... (remaining 173258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 122 or resid 269 or resid 289 or resid 291 or re \ sid 294 or resid 299 or resid 302 or resid 307 through 310 or resid 318 or resid \ 333 or resid 339 through 340 or resid 345 or resid 348 through 349 or resid 351 \ or resid 355 or resid 358 through 360 or resid 362 or resid 380 or resid 384 th \ rough 385 or resid 387 or resid 396 or resid 403 through 405 or resid 410 throug \ h 1002)) selection = (chain 'B' and (resid 1 through 63 or resid 70 through 122 or resid 126 or resid \ 146 or resid 148 or resid 151 or resid 156 or resid 165 or resid 170 or resid 1 \ 72 through 174 or resid 182 or resid 197 or resid 203 or resid 206 or resid 211 \ or resid 214 through 215 or resid 217 or resid 226 or resid 229 through 230 or r \ esid 236 or resid 238 or resid 251 or resid 255 through 256 or resid 263 or resi \ d 272 or resid 279 or resid 284 or resid 287 or resid 410 through 1002)) } ncs_group { reference = (chain 'C' and (resid 1 or (resid 2 and (name P or name OP1 or name OP2 or name \ O5' or name C5' or name C4' or name O4' or name C3' or name O3' or name C2' or n \ ame C1')) or resid 3 through 37)) selection = (chain 'D' and resid -42 through -6) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 21.090 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19193 Z= 0.301 Angle : 0.761 11.503 26364 Z= 0.499 Chirality : 0.048 0.204 3009 Planarity : 0.008 0.321 3179 Dihedral : 19.757 176.670 7386 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.97 % Allowed : 22.16 % Favored : 75.87 % 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: -1.90 (0.17), residues: 2191 helix: -0.46 (0.17), residues: 876 sheet: -2.12 (0.30), residues: 231 loop : -1.71 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.013 0.002 TYR E 487 PHE 0.012 0.001 PHE E 211 TRP 0.010 0.001 TRP E 401 HIS 0.012 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.30 (19173) covalent geometry : angle 0.74467 / 0.50 (26337) hydrogen bonds : bond 0.09686 / 6.54 ( 802) hydrogen bonds : angle 6.73566 / 4.73 ( 2192) metal coordination : bond 0.01008 / 0.71 ( 20) metal coordination : angle 4.99435 / 2.88 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.5254 (tmm) cc_final: 0.4763 (ptp) REVERT: A 728 PHE cc_start: 0.9682 (OUTLIER) cc_final: 0.9111 (t80) REVERT: A 743 ARG cc_start: 0.8096 (tpt170) cc_final: 0.7738 (tpt170) REVERT: A 773 TYR cc_start: 0.9519 (p90) cc_final: 0.9215 (m-80) REVERT: B 27 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8759 (tp) REVERT: E 216 PHE cc_start: 0.9592 (p90) cc_final: 0.9205 (p90) REVERT: E 229 TYR cc_start: 0.6933 (p90) cc_final: 0.6571 (p90) REVERT: E 430 PHE cc_start: 0.9546 (p90) cc_final: 0.9197 (p90) outliers start: 36 outliers final: 21 residues processed: 102 average time/residue: 0.1392 time to fit residues: 21.6575 Evaluate side-chains 88 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 388 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 299 GLN E 330 ASN E 368 GLN E 382 ASN E 433 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.048999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.036053 restraints weight = 289508.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.036460 restraints weight = 221798.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.036916 restraints weight = 174594.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.037241 restraints weight = 146212.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.037366 restraints weight = 131372.108| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 19193 Z= 0.246 Angle : 0.830 15.357 26364 Z= 0.431 Chirality : 0.051 0.368 3009 Planarity : 0.007 0.108 3179 Dihedral : 20.323 175.924 3336 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % 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: -1.97 (0.17), residues: 2191 helix: -0.69 (0.16), residues: 888 sheet: -1.70 (0.31), residues: 228 loop : -1.70 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 540 TYR 0.072 0.003 TYR B 605 PHE 0.027 0.003 PHE B 273 TRP 0.015 0.002 TRP E 401 HIS 0.016 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.25 (19173) covalent geometry : angle 0.80372 / 0.43 (26337) hydrogen bonds : bond 0.06701 / 4.46 ( 802) hydrogen bonds : angle 6.51494 / 4.60 ( 2192) metal coordination : bond 0.01288 / 0.76 ( 20) metal coordination : angle 6.49473 / 4.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8146 (tpt) cc_final: 0.6779 (tmm) REVERT: A 108 TYR cc_start: 0.9799 (m-80) cc_final: 0.9561 (m-80) REVERT: A 773 TYR cc_start: 0.9612 (p90) cc_final: 0.9268 (m-80) REVERT: B 1 MET cc_start: 0.7747 (tpt) cc_final: 0.7477 (tpt) REVERT: B 65 PHE cc_start: 0.7837 (m-80) cc_final: 0.7419 (m-80) REVERT: B 66 LEU cc_start: 0.9616 (mm) cc_final: 0.9344 (tp) REVERT: E 216 PHE cc_start: 0.9148 (p90) cc_final: 0.8449 (p90) REVERT: E 430 PHE cc_start: 0.9441 (p90) cc_final: 0.9153 (p90) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1483 time to fit residues: 18.9446 Evaluate side-chains 63 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 93 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 26 optimal weight: 10.0000 chunk 162 optimal weight: 50.0000 chunk 38 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.048746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.035257 restraints weight = 291936.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.035554 restraints weight = 226215.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.036022 restraints weight = 182564.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.036300 restraints weight = 158064.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.036409 restraints weight = 144267.912| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19193 Z= 0.220 Angle : 0.783 13.035 26364 Z= 0.407 Chirality : 0.050 0.350 3009 Planarity : 0.006 0.096 3179 Dihedral : 20.348 174.816 3336 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % 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: -1.85 (0.17), residues: 2191 helix: -0.69 (0.16), residues: 892 sheet: -1.59 (0.31), residues: 238 loop : -1.54 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 49 TYR 0.026 0.002 TYR B 605 PHE 0.021 0.002 PHE B 273 TRP 0.013 0.002 TRP E 401 HIS 0.012 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (19173) covalent geometry : angle 0.75990 / 0.41 (26337) hydrogen bonds : bond 0.06064 / 4.04 ( 802) hydrogen bonds : angle 6.42346 / 4.54 ( 2192) metal coordination : bond 0.00890 / 0.52 ( 20) metal coordination : angle 6.01031 / 3.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7986 (tpt) cc_final: 0.6876 (tmm) REVERT: A 108 TYR cc_start: 0.9788 (m-80) cc_final: 0.9535 (m-80) REVERT: A 399 MET cc_start: 0.3921 (mtt) cc_final: 0.3701 (mtt) REVERT: A 773 TYR cc_start: 0.9576 (p90) cc_final: 0.9243 (m-80) REVERT: B 1 MET cc_start: 0.8049 (tpt) cc_final: 0.7673 (tpt) REVERT: B 66 LEU cc_start: 0.9600 (mm) cc_final: 0.9338 (tt) REVERT: E 430 PHE cc_start: 0.9410 (p90) cc_final: 0.9136 (p90) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.1229 time to fit residues: 15.2454 Evaluate side-chains 65 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 116 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 165 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.048209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.034831 restraints weight = 291132.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.035104 restraints weight = 222481.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.035576 restraints weight = 183003.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.035921 restraints weight = 156884.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.035998 restraints weight = 140042.620| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19193 Z= 0.225 Angle : 0.785 15.992 26364 Z= 0.404 Chirality : 0.050 0.347 3009 Planarity : 0.006 0.069 3179 Dihedral : 20.366 174.995 3336 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 31.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -1.88 (0.17), residues: 2191 helix: -0.75 (0.16), residues: 888 sheet: -1.52 (0.31), residues: 239 loop : -1.54 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 49 TYR 0.047 0.002 TYR E 131 PHE 0.026 0.002 PHE A 30 TRP 0.012 0.002 TRP A 913 HIS 0.010 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (19173) covalent geometry : angle 0.75747 / 0.40 (26337) hydrogen bonds : bond 0.05905 / 3.92 ( 802) hydrogen bonds : angle 6.42369 / 4.54 ( 2192) metal coordination : bond 0.01038 / 0.60 ( 20) metal coordination : angle 6.49592 / 3.94 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7936 (tpt) cc_final: 0.6898 (tmm) REVERT: A 108 TYR cc_start: 0.9784 (m-80) cc_final: 0.9529 (m-80) REVERT: A 773 TYR cc_start: 0.9566 (p90) cc_final: 0.9219 (m-80) REVERT: B 1 MET cc_start: 0.8163 (tpt) cc_final: 0.7839 (tpp) REVERT: B 66 LEU cc_start: 0.9588 (mm) cc_final: 0.9364 (tp) REVERT: E 430 PHE cc_start: 0.9418 (p90) cc_final: 0.9145 (p90) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1350 time to fit residues: 16.1147 Evaluate side-chains 64 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 112 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 249 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.048337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.035128 restraints weight = 293959.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.035524 restraints weight = 224118.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.035780 restraints weight = 181412.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.036079 restraints weight = 155143.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.036250 restraints weight = 139550.024| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19193 Z= 0.185 Angle : 0.758 11.887 26364 Z= 0.387 Chirality : 0.050 0.338 3009 Planarity : 0.006 0.050 3179 Dihedral : 20.370 175.770 3336 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -1.73 (0.17), residues: 2191 helix: -0.62 (0.16), residues: 887 sheet: -1.45 (0.32), residues: 238 loop : -1.47 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 49 TYR 0.027 0.002 TYR E 131 PHE 0.020 0.002 PHE A 30 TRP 0.012 0.002 TRP A 570 HIS 0.008 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (19173) covalent geometry : angle 0.73347 / 0.39 (26337) hydrogen bonds : bond 0.05296 / 3.52 ( 802) hydrogen bonds : angle 6.31639 / 4.47 ( 2192) metal coordination : bond 0.00844 / 0.50 ( 20) metal coordination : angle 6.07787 / 3.81 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8122 (tpt) cc_final: 0.6806 (tmm) REVERT: A 108 TYR cc_start: 0.9743 (m-80) cc_final: 0.9473 (m-80) REVERT: A 773 TYR cc_start: 0.9586 (p90) cc_final: 0.9234 (m-80) REVERT: B 1 MET cc_start: 0.7964 (tpt) cc_final: 0.7569 (tpp) REVERT: B 30 PHE cc_start: 0.9364 (m-80) cc_final: 0.9159 (m-10) REVERT: B 69 MET cc_start: 0.6614 (mpp) cc_final: 0.6298 (mpp) REVERT: E 430 PHE cc_start: 0.9463 (p90) cc_final: 0.9162 (p90) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1633 time to fit residues: 20.9412 Evaluate side-chains 68 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 139 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 0.0270 chunk 79 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.049309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.035641 restraints weight = 285844.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.036106 restraints weight = 217829.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.036525 restraints weight = 176063.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.037008 restraints weight = 146536.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.037069 restraints weight = 130904.450| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19193 Z= 0.148 Angle : 0.740 12.142 26364 Z= 0.373 Chirality : 0.050 0.333 3009 Planarity : 0.005 0.085 3179 Dihedral : 20.328 176.144 3336 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -1.50 (0.18), residues: 2191 helix: -0.37 (0.17), residues: 873 sheet: -1.32 (0.32), residues: 240 loop : -1.38 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 49 TYR 0.028 0.002 TYR E 487 PHE 0.035 0.002 PHE A 30 TRP 0.010 0.002 TRP A 913 HIS 0.006 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (19173) covalent geometry : angle 0.71652 / 0.37 (26337) hydrogen bonds : bond 0.04731 / 3.15 ( 802) hydrogen bonds : angle 6.09677 / 4.30 ( 2192) metal coordination : bond 0.00625 / 0.40 ( 20) metal coordination : angle 5.76497 / 3.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8084 (tpt) cc_final: 0.6805 (tmm) REVERT: A 108 TYR cc_start: 0.9743 (m-80) cc_final: 0.9473 (m-80) REVERT: A 773 TYR cc_start: 0.9589 (p90) cc_final: 0.9263 (m-80) REVERT: B 1 MET cc_start: 0.8045 (tpt) cc_final: 0.7638 (tpp) REVERT: B 30 PHE cc_start: 0.9307 (m-80) cc_final: 0.9104 (m-10) REVERT: B 69 MET cc_start: 0.6553 (mpp) cc_final: 0.6339 (mpp) REVERT: E 430 PHE cc_start: 0.9459 (p90) cc_final: 0.9156 (p90) REVERT: E 521 VAL cc_start: 0.6303 (p) cc_final: 0.6055 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1537 time to fit residues: 21.1512 Evaluate side-chains 66 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 144 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 142 optimal weight: 40.0000 chunk 110 optimal weight: 0.5980 chunk 21 optimal weight: 40.0000 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.048304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.034765 restraints weight = 290279.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.035125 restraints weight = 222901.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.035538 restraints weight = 184873.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.035806 restraints weight = 155361.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.036236 restraints weight = 140416.806| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19193 Z= 0.187 Angle : 0.744 15.061 26364 Z= 0.378 Chirality : 0.048 0.324 3009 Planarity : 0.006 0.065 3179 Dihedral : 20.351 176.245 3336 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -1.51 (0.18), residues: 2191 helix: -0.38 (0.17), residues: 872 sheet: -1.20 (0.33), residues: 247 loop : -1.43 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 506 TYR 0.021 0.002 TYR E 487 PHE 0.023 0.002 PHE A 30 TRP 0.010 0.002 TRP E 401 HIS 0.007 0.002 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (19173) covalent geometry : angle 0.71536 / 0.38 (26337) hydrogen bonds : bond 0.04983 / 3.31 ( 802) hydrogen bonds : angle 6.17534 / 4.36 ( 2192) metal coordination : bond 0.01092 / 0.69 ( 20) metal coordination : angle 6.39575 / 4.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8376 (tpt) cc_final: 0.6637 (tmm) REVERT: A 437 HIS cc_start: 0.9476 (t70) cc_final: 0.9249 (p-80) REVERT: A 761 THR cc_start: 0.9199 (p) cc_final: 0.8895 (p) REVERT: A 763 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7986 (mmtm) REVERT: A 773 TYR cc_start: 0.9593 (p90) cc_final: 0.9207 (m-80) REVERT: B 1 MET cc_start: 0.7421 (tpt) cc_final: 0.6917 (tpp) REVERT: B 30 PHE cc_start: 0.9278 (m-80) cc_final: 0.9024 (m-10) REVERT: B 66 LEU cc_start: 0.9474 (mp) cc_final: 0.9147 (tt) REVERT: E 430 PHE cc_start: 0.9522 (p90) cc_final: 0.9186 (p90) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1632 time to fit residues: 20.4977 Evaluate side-chains 63 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 213 optimal weight: 20.0000 chunk 118 optimal weight: 0.0050 chunk 204 optimal weight: 8.9990 chunk 159 optimal weight: 0.0000 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.048917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.035100 restraints weight = 285625.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.035631 restraints weight = 218271.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.036002 restraints weight = 178802.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.036231 restraints weight = 153097.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.036548 restraints weight = 139217.640| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19193 Z= 0.151 Angle : 0.740 13.691 26364 Z= 0.371 Chirality : 0.049 0.327 3009 Planarity : 0.005 0.079 3179 Dihedral : 20.322 176.717 3336 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.05 % Allowed : 1.31 % Favored : 98.64 % 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: -1.40 (0.18), residues: 2191 helix: -0.32 (0.17), residues: 878 sheet: -1.19 (0.32), residues: 238 loop : -1.32 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 53 TYR 0.061 0.002 TYR B 605 PHE 0.030 0.002 PHE A 30 TRP 0.009 0.001 TRP A 913 HIS 0.006 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (19173) covalent geometry : angle 0.71366 / 0.37 (26337) hydrogen bonds : bond 0.04538 / 3.02 ( 802) hydrogen bonds : angle 6.05574 / 4.28 ( 2192) metal coordination : bond 0.00774 / 0.50 ( 20) metal coordination : angle 6.17102 / 4.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8006 (tpt) cc_final: 0.6926 (tmm) REVERT: A 773 TYR cc_start: 0.9579 (p90) cc_final: 0.9270 (m-80) REVERT: B 1 MET cc_start: 0.8285 (tpt) cc_final: 0.7836 (tpp) REVERT: B 30 PHE cc_start: 0.9330 (m-80) cc_final: 0.9126 (m-10) REVERT: E 430 PHE cc_start: 0.9464 (p90) cc_final: 0.9180 (p90) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1462 time to fit residues: 19.5338 Evaluate side-chains 67 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.047640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.034332 restraints weight = 293661.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.034703 restraints weight = 228392.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.035133 restraints weight = 187786.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.035419 restraints weight = 157351.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.035530 restraints weight = 143626.098| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19193 Z= 0.214 Angle : 0.771 12.954 26364 Z= 0.394 Chirality : 0.049 0.322 3009 Planarity : 0.006 0.071 3179 Dihedral : 20.360 176.898 3336 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.57 (0.18), residues: 2191 helix: -0.53 (0.16), residues: 884 sheet: -1.41 (0.32), residues: 245 loop : -1.32 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 470 TYR 0.045 0.002 TYR B 605 PHE 0.023 0.002 PHE A 30 TRP 0.010 0.002 TRP E 401 HIS 0.008 0.002 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (19173) covalent geometry : angle 0.74621 / 0.39 (26337) hydrogen bonds : bond 0.05212 / 3.46 ( 802) hydrogen bonds : angle 6.25844 / 4.41 ( 2192) metal coordination : bond 0.00969 / 0.56 ( 20) metal coordination : angle 6.05047 / 3.86 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8300 (tpt) cc_final: 0.6656 (tmm) REVERT: A 437 HIS cc_start: 0.9396 (p-80) cc_final: 0.9189 (p-80) REVERT: A 743 ARG cc_start: 0.6991 (tpt170) cc_final: 0.6679 (tpt170) REVERT: A 773 TYR cc_start: 0.9578 (p90) cc_final: 0.9263 (m-80) REVERT: B 1 MET cc_start: 0.7715 (tpt) cc_final: 0.7137 (tpp) REVERT: E 430 PHE cc_start: 0.9539 (p90) cc_final: 0.9208 (p90) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1539 time to fit residues: 18.0938 Evaluate side-chains 60 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 108 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 145 optimal weight: 0.0010 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.048239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.034522 restraints weight = 286273.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.035073 restraints weight = 216909.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.035412 restraints weight = 177627.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.035694 restraints weight = 155890.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.035861 restraints weight = 143298.884| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19193 Z= 0.158 Angle : 0.733 12.585 26364 Z= 0.368 Chirality : 0.048 0.332 3009 Planarity : 0.005 0.069 3179 Dihedral : 20.318 177.531 3336 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.40 (0.18), residues: 2191 helix: -0.34 (0.17), residues: 877 sheet: -1.33 (0.32), residues: 245 loop : -1.26 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 49 TYR 0.038 0.002 TYR B 605 PHE 0.021 0.002 PHE A 30 TRP 0.009 0.002 TRP A 913 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (19173) covalent geometry : angle 0.70591 / 0.37 (26337) hydrogen bonds : bond 0.04461 / 2.96 ( 802) hydrogen bonds : angle 6.04540 / 4.28 ( 2192) metal coordination : bond 0.00728 / 0.44 ( 20) metal coordination : angle 6.15482 / 3.97 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8261 (tpt) cc_final: 0.6756 (tmm) REVERT: A 437 HIS cc_start: 0.9412 (p-80) cc_final: 0.9206 (p-80) REVERT: A 743 ARG cc_start: 0.6671 (tpt170) cc_final: 0.6321 (tpt170) REVERT: A 773 TYR cc_start: 0.9586 (p90) cc_final: 0.9285 (m-80) REVERT: B 1 MET cc_start: 0.7956 (tpt) cc_final: 0.7386 (tpp) REVERT: B 30 PHE cc_start: 0.9281 (m-80) cc_final: 0.9044 (m-10) REVERT: E 430 PHE cc_start: 0.9502 (p90) cc_final: 0.9180 (p90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1498 time to fit residues: 17.8697 Evaluate side-chains 67 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 183 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 0.4980 chunk 57 optimal weight: 0.0170 chunk 217 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 163 optimal weight: 50.0000 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 overall best weight: 2.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.048362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.034990 restraints weight = 287856.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.035534 restraints weight = 214773.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.035922 restraints weight = 176296.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.036181 restraints weight = 151603.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.036224 restraints weight = 139001.184| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19193 Z= 0.155 Angle : 0.725 12.530 26364 Z= 0.364 Chirality : 0.048 0.334 3009 Planarity : 0.005 0.063 3179 Dihedral : 20.298 177.911 3336 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.30 (0.18), residues: 2191 helix: -0.26 (0.17), residues: 877 sheet: -1.29 (0.33), residues: 245 loop : -1.21 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 49 TYR 0.032 0.002 TYR B 605 PHE 0.021 0.002 PHE A 30 TRP 0.009 0.001 TRP E 401 HIS 0.006 0.001 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (19173) covalent geometry : angle 0.69927 / 0.36 (26337) hydrogen bonds : bond 0.04416 / 2.93 ( 802) hydrogen bonds : angle 5.98625 / 4.24 ( 2192) metal coordination : bond 0.00672 / 0.40 ( 20) metal coordination : angle 5.98918 / 3.87 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.20 seconds wall clock time: 65 minutes 39.51 seconds (3939.51 seconds total)