Starting phenix.real_space_refine on Mon May 19 16:13:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_51170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_51170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_51170.map" model { file = "/net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_51170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga3_51170/05_2025/9ga3_51170.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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:plan2': 1, ' DC:plan': 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: 10.74, per 1000 atoms: 0.57 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: 5.04 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 6.71 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: 7.08 Time building geometry restraints manager: 5.74 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=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.89e+00 bond pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.23e-02 6.61e+03 7.32e+00 bond pdb=" N GLU A 293 " pdb=" CA GLU A 293 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.17e-02 7.31e+03 5.87e+00 bond pdb=" N LYS B 71 " pdb=" CA LYS B 71 " ideal model delta sigma weight residual 1.453 1.482 -0.029 1.37e-02 5.33e+03 4.51e+00 bond pdb=" N ARG B 11 " pdb=" CA ARG B 11 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.46e-02 4.69e+03 4.35e+00 ... (remaining 19168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 25373 1.68 - 3.36: 813 3.36 - 5.04: 132 5.04 - 6.71: 16 6.71 - 8.39: 3 Bond angle restraints: 26337 Sorted by residual: angle pdb=" N VAL E 364 " pdb=" CA VAL E 364 " pdb=" C VAL E 364 " ideal model delta sigma weight residual 113.53 109.38 4.15 9.80e-01 1.04e+00 1.80e+01 angle pdb=" CA ARG B 11 " pdb=" CB ARG B 11 " pdb=" CG ARG B 11 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" O ARG A 96 " ideal model delta sigma weight residual 120.92 116.87 4.05 1.12e+00 7.97e-01 1.31e+01 angle pdb=" C LYS A 292 " pdb=" CA LYS A 292 " pdb=" CB LYS A 292 " ideal model delta sigma weight residual 111.41 117.37 -5.96 1.65e+00 3.67e-01 1.31e+01 angle pdb=" CA GLU A 293 " pdb=" C GLU A 293 " pdb=" O GLU A 293 " ideal model delta sigma weight residual 121.50 117.21 4.29 1.25e+00 6.40e-01 1.18e+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: 2195 0.041 - 0.081: 531 0.081 - 0.122: 251 0.122 - 0.162: 29 0.162 - 0.203: 3 Chirality restraints: 3009 Sorted by residual: 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=" CA VAL A 294 " pdb=" N VAL A 294 " pdb=" C VAL A 294 " pdb=" CB VAL A 294 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA PRO A 278 " pdb=" N PRO A 278 " pdb=" C PRO A 278 " pdb=" CB PRO A 278 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.07e-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 953 or resid 1001 through 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 953 or resid 1 \ 001 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 50.390 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 0.043 19193 Z= 0.174 Angle : 0.724 11.503 26364 Z= 0.402 Chirality : 0.044 0.203 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (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 TRP 0.010 0.001 TRP E 401 HIS 0.012 0.001 HIS A 587 PHE 0.012 0.001 PHE E 211 TYR 0.013 0.002 TYR E 487 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.09686 ( 802) hydrogen bonds : angle 6.73566 ( 2192) metal coordination : bond 0.01008 ( 20) metal coordination : angle 4.99435 ( 27) covalent geometry : bond 0.00350 (19173) covalent geometry : angle 0.70639 (26337) *********************** 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 : 1.982 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: 0.3365 time to fit residues: 52.1589 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 : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.049856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.036481 restraints weight = 287257.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.036975 restraints weight = 214427.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.037319 restraints weight = 169285.843| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19193 Z= 0.178 Angle : 0.742 14.053 26364 Z= 0.379 Chirality : 0.046 0.225 3009 Planarity : 0.006 0.082 3179 Dihedral : 20.281 175.325 3336 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2191 helix: -0.28 (0.17), residues: 882 sheet: -1.79 (0.30), residues: 242 loop : -1.49 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 401 HIS 0.010 0.002 HIS A 120 PHE 0.029 0.002 PHE B 273 TYR 0.049 0.002 TYR B 605 ARG 0.011 0.001 ARG B 540 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 802) hydrogen bonds : angle 6.15526 ( 2192) metal coordination : bond 0.00684 ( 20) metal coordination : angle 6.04250 ( 27) covalent geometry : bond 0.00395 (19173) covalent geometry : angle 0.71680 (26337) *********************** 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 90 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8139 (tpt) cc_final: 0.6711 (tmm) REVERT: A 108 TYR cc_start: 0.9773 (m-80) cc_final: 0.9512 (m-80) REVERT: A 773 TYR cc_start: 0.9617 (p90) cc_final: 0.9302 (m-80) REVERT: B 1 MET cc_start: 0.7776 (tpt) cc_final: 0.7474 (tpt) REVERT: E 216 PHE cc_start: 0.9126 (p90) cc_final: 0.8411 (p90) REVERT: E 430 PHE cc_start: 0.9447 (p90) cc_final: 0.9147 (p90) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.3625 time to fit residues: 49.3401 Evaluate side-chains 68 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 219 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 626 GLN ** 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 276 ASN ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 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 = 0.3665 r_free = 0.3665 target = 0.047007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.033792 restraints weight = 299051.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.034181 restraints weight = 231943.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.034555 restraints weight = 188909.966| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19193 Z= 0.252 Angle : 0.804 14.429 26364 Z= 0.412 Chirality : 0.047 0.254 3009 Planarity : 0.006 0.058 3179 Dihedral : 20.496 179.529 3336 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 35.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.05 % Allowed : 7.31 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.17), residues: 2191 helix: -0.77 (0.16), residues: 892 sheet: -1.66 (0.31), residues: 241 loop : -1.50 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 570 HIS 0.009 0.002 HIS E 334 PHE 0.026 0.003 PHE B 273 TYR 0.028 0.002 TYR B 605 ARG 0.012 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05887 ( 802) hydrogen bonds : angle 6.53955 ( 2192) metal coordination : bond 0.01114 ( 20) metal coordination : angle 6.71933 ( 27) covalent geometry : bond 0.00534 (19173) covalent geometry : angle 0.77512 (26337) *********************** 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 73 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8373 (tpt) cc_final: 0.6703 (tmm) REVERT: A 108 TYR cc_start: 0.9677 (m-80) cc_final: 0.9395 (m-80) REVERT: A 773 TYR cc_start: 0.9541 (p90) cc_final: 0.9186 (m-80) REVERT: B 1 MET cc_start: 0.7693 (tpt) cc_final: 0.7147 (tpp) REVERT: E 430 PHE cc_start: 0.9522 (p90) cc_final: 0.9193 (p90) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.3461 time to fit residues: 39.6377 Evaluate side-chains 61 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 150 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 507 GLN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** 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 514 GLN B 553 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN E 299 GLN ** E 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.050043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.036451 restraints weight = 284027.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.036943 restraints weight = 212466.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.037323 restraints weight = 169302.004| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19193 Z= 0.143 Angle : 0.714 15.031 26364 Z= 0.352 Chirality : 0.045 0.221 3009 Planarity : 0.005 0.071 3179 Dihedral : 20.308 179.069 3336 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2191 helix: -0.08 (0.17), residues: 875 sheet: -1.18 (0.32), residues: 241 loop : -1.26 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 401 HIS 0.005 0.001 HIS A 587 PHE 0.021 0.002 PHE A 47 TYR 0.032 0.002 TYR E 131 ARG 0.010 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 802) hydrogen bonds : angle 5.74644 ( 2192) metal coordination : bond 0.00801 ( 20) metal coordination : angle 6.57454 ( 27) covalent geometry : bond 0.00316 (19173) covalent geometry : angle 0.68270 (26337) *********************** 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 87 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7972 (tpt) cc_final: 0.6949 (tmm) REVERT: A 108 TYR cc_start: 0.9725 (m-80) cc_final: 0.9442 (m-80) REVERT: A 773 TYR cc_start: 0.9619 (p90) cc_final: 0.9349 (m-80) REVERT: B 1 MET cc_start: 0.8311 (tpt) cc_final: 0.7877 (tpp) REVERT: E 229 TYR cc_start: 0.5858 (p90) cc_final: 0.5535 (p90) REVERT: E 430 PHE cc_start: 0.9477 (p90) cc_final: 0.9179 (p90) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3384 time to fit residues: 45.5522 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 : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 96 optimal weight: 0.0980 chunk 215 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 overall best weight: 5.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 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 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 249 GLN B 514 GLN ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 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 = 0.3663 r_free = 0.3663 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.033783 restraints weight = 299314.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.034135 restraints weight = 231658.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.034500 restraints weight = 190694.915| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19193 Z= 0.232 Angle : 0.759 13.820 26364 Z= 0.387 Chirality : 0.046 0.228 3009 Planarity : 0.006 0.055 3179 Dihedral : 20.415 179.398 3336 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 32.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2191 helix: -0.46 (0.16), residues: 878 sheet: -1.31 (0.33), residues: 242 loop : -1.34 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 570 HIS 0.011 0.002 HIS E 334 PHE 0.022 0.002 PHE B 65 TYR 0.023 0.002 TYR E 487 ARG 0.008 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05288 ( 802) hydrogen bonds : angle 6.25671 ( 2192) metal coordination : bond 0.00893 ( 20) metal coordination : angle 6.68706 ( 27) covalent geometry : bond 0.00488 (19173) covalent geometry : angle 0.72826 (26337) *********************** 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 73 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7985 (tpt) cc_final: 0.7046 (tmm) REVERT: A 773 TYR cc_start: 0.9512 (p90) cc_final: 0.9217 (m-80) REVERT: B 1 MET cc_start: 0.8540 (tpt) cc_final: 0.8113 (tpp) REVERT: B 69 MET cc_start: 0.6644 (mpp) cc_final: 0.6416 (mpp) REVERT: E 86 MET cc_start: 0.2796 (mmp) cc_final: 0.2045 (mmt) REVERT: E 229 TYR cc_start: 0.5811 (p90) cc_final: 0.5509 (p90) REVERT: E 430 PHE cc_start: 0.9451 (p90) cc_final: 0.9181 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3319 time to fit residues: 37.5780 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 : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 6.9990 chunk 86 optimal weight: 0.0050 chunk 158 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 overall best weight: 2.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** 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 514 GLN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.047894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.034803 restraints weight = 287618.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.035102 restraints weight = 219369.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.035528 restraints weight = 177193.716| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19193 Z= 0.162 Angle : 0.692 14.265 26364 Z= 0.347 Chirality : 0.045 0.249 3009 Planarity : 0.005 0.054 3179 Dihedral : 20.372 179.090 3336 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2191 helix: -0.24 (0.17), residues: 878 sheet: -1.15 (0.33), residues: 240 loop : -1.27 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 401 HIS 0.006 0.001 HIS A 877 PHE 0.024 0.002 PHE A 30 TYR 0.019 0.002 TYR A 54 ARG 0.009 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 802) hydrogen bonds : angle 5.91069 ( 2192) metal coordination : bond 0.00686 ( 20) metal coordination : angle 6.06071 ( 27) covalent geometry : bond 0.00351 (19173) covalent geometry : angle 0.66436 (26337) *********************** 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 77 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8075 (tpt) cc_final: 0.7019 (tmm) REVERT: A 773 TYR cc_start: 0.9570 (p90) cc_final: 0.9287 (m-80) REVERT: B 1 MET cc_start: 0.8472 (tpt) cc_final: 0.7846 (tpt) REVERT: E 86 MET cc_start: 0.2651 (mmp) cc_final: 0.1948 (mmt) REVERT: E 229 TYR cc_start: 0.6071 (p90) cc_final: 0.5703 (p90) REVERT: E 529 ARG cc_start: 0.6513 (mtt-85) cc_final: 0.6024 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3658 time to fit residues: 42.7550 Evaluate side-chains 65 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 30 optimal weight: 0.0000 chunk 213 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.047356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.033989 restraints weight = 288287.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.034500 restraints weight = 226032.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.034882 restraints weight = 174783.839| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19193 Z= 0.171 Angle : 0.707 14.177 26364 Z= 0.354 Chirality : 0.045 0.247 3009 Planarity : 0.005 0.053 3179 Dihedral : 20.379 178.459 3336 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2191 helix: -0.20 (0.17), residues: 872 sheet: -1.25 (0.33), residues: 247 loop : -1.26 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 401 HIS 0.007 0.001 HIS E 334 PHE 0.030 0.002 PHE A 30 TYR 0.020 0.002 TYR A 54 ARG 0.008 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 802) hydrogen bonds : angle 5.92152 ( 2192) metal coordination : bond 0.00801 ( 20) metal coordination : angle 6.40818 ( 27) covalent geometry : bond 0.00371 (19173) covalent geometry : angle 0.67739 (26337) *********************** 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 79 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7851 (tpt) cc_final: 0.7035 (tmm) REVERT: A 108 TYR cc_start: 0.9719 (m-80) cc_final: 0.9476 (m-80) REVERT: A 773 TYR cc_start: 0.9538 (p90) cc_final: 0.9276 (m-80) REVERT: B 1 MET cc_start: 0.8693 (tpt) cc_final: 0.8227 (tpt) REVERT: E 86 MET cc_start: 0.3412 (mmp) cc_final: 0.2757 (mmt) REVERT: E 229 TYR cc_start: 0.6128 (p90) cc_final: 0.5783 (p90) REVERT: E 287 GLU cc_start: 0.9696 (mp0) cc_final: 0.9417 (pp20) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3293 time to fit residues: 40.5400 Evaluate side-chains 65 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 194 optimal weight: 0.9990 chunk 22 optimal weight: 0.0050 chunk 14 optimal weight: 30.0000 chunk 160 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 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 249 GLN ** B 581 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.049256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.036308 restraints weight = 277407.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.036853 restraints weight = 213114.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.037266 restraints weight = 167038.019| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19193 Z= 0.132 Angle : 0.693 15.096 26364 Z= 0.339 Chirality : 0.044 0.207 3009 Planarity : 0.005 0.057 3179 Dihedral : 20.302 178.053 3336 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2191 helix: -0.02 (0.17), residues: 877 sheet: -0.98 (0.32), residues: 267 loop : -1.15 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 401 HIS 0.004 0.001 HIS B 877 PHE 0.018 0.002 PHE A 47 TYR 0.023 0.001 TYR B 605 ARG 0.017 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 802) hydrogen bonds : angle 5.59933 ( 2192) metal coordination : bond 0.00633 ( 20) metal coordination : angle 6.47078 ( 27) covalent geometry : bond 0.00295 (19173) covalent geometry : angle 0.66117 (26337) *********************** 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 93 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7885 (tpt) cc_final: 0.7051 (tmm) REVERT: A 108 TYR cc_start: 0.9670 (m-80) cc_final: 0.9390 (m-80) REVERT: A 743 ARG cc_start: 0.5307 (tpt170) cc_final: 0.5023 (tpt170) REVERT: A 773 TYR cc_start: 0.9633 (p90) cc_final: 0.9365 (m-80) REVERT: B 1 MET cc_start: 0.8569 (tpt) cc_final: 0.8297 (tpp) REVERT: B 523 LEU cc_start: 0.9809 (tp) cc_final: 0.9534 (mt) REVERT: E 86 MET cc_start: 0.2701 (mmp) cc_final: 0.2034 (mmt) REVERT: E 229 TYR cc_start: 0.6222 (p90) cc_final: 0.5868 (p90) REVERT: E 287 GLU cc_start: 0.9683 (mp0) cc_final: 0.9444 (pp20) REVERT: E 430 PHE cc_start: 0.9523 (p90) cc_final: 0.9169 (p90) REVERT: E 540 VAL cc_start: 0.4599 (p) cc_final: 0.4040 (m) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3745 time to fit residues: 53.8462 Evaluate side-chains 71 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 50.0000 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 50.0000 chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** 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 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3655 r_free = 0.3655 target = 0.046646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.033415 restraints weight = 293948.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.033866 restraints weight = 226380.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.034132 restraints weight = 180975.449| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 19193 Z= 0.213 Angle : 0.750 14.409 26364 Z= 0.379 Chirality : 0.045 0.240 3009 Planarity : 0.006 0.054 3179 Dihedral : 20.435 179.786 3336 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2191 helix: -0.37 (0.16), residues: 883 sheet: -1.05 (0.34), residues: 235 loop : -1.23 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 570 HIS 0.009 0.002 HIS A 877 PHE 0.024 0.002 PHE B 878 TYR 0.033 0.002 TYR B 605 ARG 0.023 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 802) hydrogen bonds : angle 6.04265 ( 2192) metal coordination : bond 0.00988 ( 20) metal coordination : angle 6.66024 ( 27) covalent geometry : bond 0.00450 (19173) covalent geometry : angle 0.71947 (26337) *********************** 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 79 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8252 (tpt) cc_final: 0.6977 (tmm) REVERT: A 108 TYR cc_start: 0.9627 (m-80) cc_final: 0.9362 (m-80) REVERT: A 773 TYR cc_start: 0.9583 (p90) cc_final: 0.9307 (m-80) REVERT: B 523 LEU cc_start: 0.9844 (tp) cc_final: 0.9561 (mt) REVERT: E 86 MET cc_start: 0.3252 (mmp) cc_final: 0.2513 (mmp) REVERT: E 229 TYR cc_start: 0.6597 (p90) cc_final: 0.6194 (p90) REVERT: E 540 VAL cc_start: 0.6993 (p) cc_final: 0.6548 (m) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3152 time to fit residues: 39.3122 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 : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 50.0000 chunk 178 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** 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** ** A 849 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 553 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.048025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.034910 restraints weight = 281177.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.035278 restraints weight = 216322.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.035639 restraints weight = 174927.154| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19193 Z= 0.147 Angle : 0.701 13.209 26364 Z= 0.347 Chirality : 0.044 0.240 3009 Planarity : 0.005 0.056 3179 Dihedral : 20.376 178.591 3336 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2191 helix: -0.19 (0.17), residues: 877 sheet: -0.91 (0.33), residues: 257 loop : -1.18 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 401 HIS 0.006 0.001 HIS A 877 PHE 0.028 0.002 PHE E 211 TYR 0.025 0.001 TYR A 279 ARG 0.010 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 802) hydrogen bonds : angle 5.78737 ( 2192) metal coordination : bond 0.00620 ( 20) metal coordination : angle 6.35764 ( 27) covalent geometry : bond 0.00324 (19173) covalent geometry : angle 0.67093 (26337) ********************** 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 84 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8168 (tpt) cc_final: 0.7012 (tmm) REVERT: A 108 TYR cc_start: 0.9624 (m-80) cc_final: 0.9339 (m-80) REVERT: A 773 TYR cc_start: 0.9583 (p90) cc_final: 0.9326 (m-80) REVERT: B 523 LEU cc_start: 0.9828 (tp) cc_final: 0.9526 (mt) REVERT: E 86 MET cc_start: 0.3018 (mmp) cc_final: 0.2338 (mmp) REVERT: E 229 TYR cc_start: 0.6496 (p90) cc_final: 0.6122 (p90) REVERT: E 278 MET cc_start: 0.9214 (mpp) cc_final: 0.8995 (mpp) REVERT: E 540 VAL cc_start: 0.7489 (p) cc_final: 0.6520 (m) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3117 time to fit residues: 41.6659 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 : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 52 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 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** ** A 849 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 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 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 = 0.3649 r_free = 0.3649 target = 0.046438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.034236 restraints weight = 291630.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.034377 restraints weight = 196171.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.034404 restraints weight = 166573.938| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19193 Z= 0.199 Angle : 0.740 14.108 26364 Z= 0.371 Chirality : 0.046 0.238 3009 Planarity : 0.006 0.077 3179 Dihedral : 20.478 179.742 3336 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 31.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2191 helix: -0.44 (0.16), residues: 890 sheet: -1.01 (0.34), residues: 239 loop : -1.24 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 570 HIS 0.009 0.002 HIS E 334 PHE 0.022 0.002 PHE A 744 TYR 0.029 0.002 TYR B 605 ARG 0.011 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 802) hydrogen bonds : angle 6.06186 ( 2192) metal coordination : bond 0.00953 ( 20) metal coordination : angle 6.60825 ( 27) covalent geometry : bond 0.00426 (19173) covalent geometry : angle 0.70976 (26337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.81 seconds wall clock time: 115 minutes 42.10 seconds (6942.10 seconds total)