Starting phenix.real_space_refine on Mon Jun 16 14:10:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga3_51170/06_2025/9ga3_51170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga3_51170/06_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_51170/06_2025/9ga3_51170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga3_51170/06_2025/9ga3_51170.map" model { file = "/net/cci-nas-00/data/ceres_data/9ga3_51170/06_2025/9ga3_51170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga3_51170/06_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-5710/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: 11.47, per 1000 atoms: 0.61 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: 4.84 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: 8.66 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: 8.08 Time building geometry restraints manager: 5.72 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: 3.000 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 54.530 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.300 ------------------------------------------------------------------------------- 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 : 1.816 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: 0.3330 time to fit residues: 51.6349 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 : 1.822 ------------------------------------------------------------------------------- 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 = 0.036480 restraints weight = 287257.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.036985 restraints weight = 214541.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.037289 restraints weight = 169266.776| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8137 (tpt) cc_final: 0.6713 (tmm) REVERT: A 108 TYR cc_start: 0.9773 (m-80) cc_final: 0.9513 (m-80) REVERT: A 773 TYR cc_start: 0.9616 (p90) cc_final: 0.9302 (m-80) REVERT: B 1 MET cc_start: 0.7780 (tpt) cc_final: 0.7478 (tpt) REVERT: E 216 PHE cc_start: 0.9123 (p90) cc_final: 0.8408 (p90) REVERT: E 430 PHE cc_start: 0.9448 (p90) cc_final: 0.9149 (p90) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.3581 time to fit residues: 49.0040 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 : 1.812 ------------------------------------------------------------------------------- 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: 5.9990 chunk 210 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 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: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.046619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.033357 restraints weight = 299267.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.033741 restraints weight = 231032.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.034068 restraints weight = 191513.634| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 19193 Z= 0.268 Angle : 0.825 14.388 26364 Z= 0.424 Chirality : 0.048 0.252 3009 Planarity : 0.007 0.062 3179 Dihedral : 20.533 179.762 3336 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 37.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.09 % 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: -1.92 (0.17), residues: 2191 helix: -0.81 (0.16), residues: 879 sheet: -1.67 (0.31), residues: 241 loop : -1.50 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 570 HIS 0.009 0.002 HIS E 334 PHE 0.028 0.003 PHE B 65 TYR 0.028 0.002 TYR B 605 ARG 0.016 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.06109 ( 802) hydrogen bonds : angle 6.62335 ( 2192) metal coordination : bond 0.01537 ( 20) metal coordination : angle 6.87412 ( 27) covalent geometry : bond 0.00561 (19173) covalent geometry : angle 0.79571 (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 71 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7945 (tpt) cc_final: 0.6947 (tmm) REVERT: A 773 TYR cc_start: 0.9503 (p90) cc_final: 0.9145 (m-80) REVERT: A 798 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9135 (t) REVERT: B 1 MET cc_start: 0.8447 (tpt) cc_final: 0.8013 (tpp) REVERT: E 430 PHE cc_start: 0.9432 (p90) cc_final: 0.9136 (p90) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.3348 time to fit residues: 38.1366 Evaluate side-chains 62 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 150 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 1.8582 ------------------------------------------------------------------------------- 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** 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 858 GLN E 299 GLN ** E 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.048753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.035232 restraints weight = 288337.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.035526 restraints weight = 222274.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.035922 restraints weight = 180202.112| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19193 Z= 0.150 Angle : 0.712 15.514 26364 Z= 0.354 Chirality : 0.045 0.233 3009 Planarity : 0.005 0.071 3179 Dihedral : 20.368 178.628 3336 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % 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: -1.36 (0.18), residues: 2191 helix: -0.23 (0.17), residues: 868 sheet: -1.23 (0.32), residues: 239 loop : -1.33 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 401 HIS 0.005 0.001 HIS A 587 PHE 0.019 0.002 PHE A 47 TYR 0.033 0.002 TYR E 131 ARG 0.010 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 802) hydrogen bonds : angle 5.93548 ( 2192) metal coordination : bond 0.00822 ( 20) metal coordination : angle 6.74862 ( 27) covalent geometry : bond 0.00333 (19173) covalent geometry : angle 0.67919 (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 85 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7957 (tpt) cc_final: 0.6987 (tmm) REVERT: A 773 TYR cc_start: 0.9603 (p90) cc_final: 0.9318 (m-80) REVERT: B 1 MET cc_start: 0.8364 (tpt) cc_final: 0.7897 (tpp) REVERT: E 229 TYR cc_start: 0.5915 (p90) cc_final: 0.5576 (p90) REVERT: E 430 PHE cc_start: 0.9473 (p90) cc_final: 0.9170 (p90) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3697 time to fit residues: 49.4956 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 : 3.192 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 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: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 534 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 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 = 0.3651 r_free = 0.3651 target = 0.046454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.033277 restraints weight = 299556.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.033673 restraints weight = 232150.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.034073 restraints weight = 191288.987| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19193 Z= 0.233 Angle : 0.765 13.920 26364 Z= 0.390 Chirality : 0.046 0.225 3009 Planarity : 0.006 0.056 3179 Dihedral : 20.470 179.348 3336 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 34.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -1.63 (0.18), residues: 2191 helix: -0.54 (0.17), residues: 878 sheet: -1.46 (0.32), residues: 242 loop : -1.38 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 570 HIS 0.010 0.002 HIS E 334 PHE 0.020 0.002 PHE B 65 TYR 0.024 0.002 TYR A 54 ARG 0.008 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05399 ( 802) hydrogen bonds : angle 6.34982 ( 2192) metal coordination : bond 0.00945 ( 20) metal coordination : angle 6.72261 ( 27) covalent geometry : bond 0.00493 (19173) covalent geometry : angle 0.73497 (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 71 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7888 (tpt) cc_final: 0.7075 (tmm) REVERT: A 108 TYR cc_start: 0.9729 (m-80) cc_final: 0.9508 (m-80) REVERT: A 399 MET cc_start: 0.5466 (mtt) cc_final: 0.5186 (mtt) REVERT: A 773 TYR cc_start: 0.9474 (p90) cc_final: 0.9173 (m-80) REVERT: B 1 MET cc_start: 0.8647 (tpt) cc_final: 0.8277 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.4318 time to fit residues: 47.3476 Evaluate side-chains 56 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 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** ** 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 = 0.3613 r_free = 0.3613 target = 0.045407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.033593 restraints weight = 304309.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.033119 restraints weight = 232465.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.033422 restraints weight = 210213.795| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19193 Z= 0.256 Angle : 0.806 16.298 26364 Z= 0.411 Chirality : 0.048 0.275 3009 Planarity : 0.007 0.099 3179 Dihedral : 20.682 179.487 3336 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 38.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -1.98 (0.17), residues: 2191 helix: -0.88 (0.16), residues: 880 sheet: -1.55 (0.34), residues: 219 loop : -1.58 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 401 HIS 0.010 0.002 HIS A 877 PHE 0.023 0.003 PHE A 744 TYR 0.026 0.002 TYR A 54 ARG 0.012 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05569 ( 802) hydrogen bonds : angle 6.57594 ( 2192) metal coordination : bond 0.01216 ( 20) metal coordination : angle 6.82235 ( 27) covalent geometry : bond 0.00537 (19173) covalent geometry : angle 0.77674 (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 70 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8297 (tpt) cc_final: 0.7002 (tmm) REVERT: A 108 TYR cc_start: 0.9555 (m-80) cc_final: 0.9312 (m-80) REVERT: B 66 LEU cc_start: 0.9547 (mp) cc_final: 0.9295 (tt) REVERT: E 86 MET cc_start: 0.4688 (mmm) cc_final: 0.4407 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3640 time to fit residues: 40.9630 Evaluate side-chains 58 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 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 = 0.3682 r_free = 0.3682 target = 0.047491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.034180 restraints weight = 288026.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.034488 restraints weight = 222250.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.034917 restraints weight = 184329.698| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19193 Z= 0.154 Angle : 0.713 14.749 26364 Z= 0.353 Chirality : 0.045 0.253 3009 Planarity : 0.005 0.080 3179 Dihedral : 20.496 179.807 3336 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -1.40 (0.18), residues: 2191 helix: -0.30 (0.17), residues: 876 sheet: -1.02 (0.34), residues: 238 loop : -1.39 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 401 HIS 0.006 0.001 HIS A 877 PHE 0.022 0.002 PHE A 30 TYR 0.032 0.002 TYR B 605 ARG 0.006 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 802) hydrogen bonds : angle 5.96628 ( 2192) metal coordination : bond 0.00753 ( 20) metal coordination : angle 6.69851 ( 27) covalent geometry : bond 0.00336 (19173) covalent geometry : angle 0.68031 (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 81 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7667 (tpt) cc_final: 0.7165 (tmm) REVERT: A 108 TYR cc_start: 0.9688 (m-80) cc_final: 0.9437 (m-80) REVERT: A 773 TYR cc_start: 0.9572 (p90) cc_final: 0.9297 (m-80) REVERT: B 1 MET cc_start: 0.8753 (tpt) cc_final: 0.8417 (tpt) REVERT: E 86 MET cc_start: 0.3522 (mmm) cc_final: 0.3238 (mmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3157 time to fit residues: 41.0372 Evaluate side-chains 62 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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: 7.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 ASN ** 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 = 0.3647 r_free = 0.3647 target = 0.046609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.033244 restraints weight = 290084.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.033795 restraints weight = 222226.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.033942 restraints weight = 182433.342| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5067 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= 0.184 Angle : 0.730 14.154 26364 Z= 0.367 Chirality : 0.045 0.232 3009 Planarity : 0.006 0.064 3179 Dihedral : 20.531 179.661 3336 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 29.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -1.46 (0.18), residues: 2191 helix: -0.43 (0.17), residues: 879 sheet: -0.97 (0.34), residues: 238 loop : -1.37 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 401 HIS 0.008 0.002 HIS E 334 PHE 0.021 0.002 PHE A 30 TYR 0.035 0.002 TYR E 487 ARG 0.007 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 802) hydrogen bonds : angle 6.08352 ( 2192) metal coordination : bond 0.00883 ( 20) metal coordination : angle 6.64065 ( 27) covalent geometry : bond 0.00396 (19173) covalent geometry : angle 0.69832 (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 74 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8252 (tpt) cc_final: 0.7224 (tmm) REVERT: A 108 TYR cc_start: 0.9623 (m-80) cc_final: 0.9360 (m-80) REVERT: A 743 ARG cc_start: 0.6014 (tpt170) cc_final: 0.5783 (tpt170) REVERT: A 773 TYR cc_start: 0.9527 (p90) cc_final: 0.9279 (m-80) REVERT: B 1 MET cc_start: 0.8341 (tpt) cc_final: 0.7846 (tpt) REVERT: E 86 MET cc_start: 0.4100 (mmm) cc_final: 0.3800 (mmm) REVERT: E 575 TYR cc_start: 0.6774 (m-80) cc_final: 0.6569 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3570 time to fit residues: 41.9800 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 : 1.970 ------------------------------------------------------------------------------- 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: 9.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 194 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 219 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- 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 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.047269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.034009 restraints weight = 288745.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.034316 restraints weight = 226046.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.034696 restraints weight = 185195.344| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19193 Z= 0.156 Angle : 0.704 13.420 26364 Z= 0.349 Chirality : 0.045 0.220 3009 Planarity : 0.005 0.061 3179 Dihedral : 20.486 179.923 3336 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -1.27 (0.18), residues: 2191 helix: -0.21 (0.17), residues: 877 sheet: -1.04 (0.33), residues: 255 loop : -1.27 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 401 HIS 0.008 0.001 HIS E 334 PHE 0.027 0.002 PHE E 211 TYR 0.024 0.002 TYR B 605 ARG 0.010 0.001 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 802) hydrogen bonds : angle 5.90282 ( 2192) metal coordination : bond 0.00706 ( 20) metal coordination : angle 6.38072 ( 27) covalent geometry : bond 0.00341 (19173) covalent geometry : angle 0.67375 (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 78 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7927 (tpt) cc_final: 0.7232 (tmm) REVERT: A 108 TYR cc_start: 0.9624 (m-80) cc_final: 0.9350 (m-80) REVERT: A 743 ARG cc_start: 0.5509 (tpt170) cc_final: 0.5308 (tpt170) REVERT: A 773 TYR cc_start: 0.9583 (p90) cc_final: 0.9372 (p90) REVERT: E 86 MET cc_start: 0.4104 (mmm) cc_final: 0.3789 (mmm) REVERT: E 540 VAL cc_start: 0.6896 (p) cc_final: 0.5790 (m) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3229 time to fit residues: 40.1937 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 : 2.127 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 50.0000 chunk 178 optimal weight: 0.0470 chunk 204 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 212 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- 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 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.048411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.035238 restraints weight = 280341.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.035671 restraints weight = 216377.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.036083 restraints weight = 174452.495| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19193 Z= 0.132 Angle : 0.686 12.885 26364 Z= 0.336 Chirality : 0.044 0.201 3009 Planarity : 0.005 0.057 3179 Dihedral : 20.347 179.887 3336 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -1.02 (0.18), residues: 2191 helix: 0.08 (0.17), residues: 877 sheet: -0.96 (0.32), residues: 277 loop : -1.19 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 401 HIS 0.008 0.001 HIS E 334 PHE 0.025 0.002 PHE E 211 TYR 0.021 0.001 TYR B 591 ARG 0.006 0.001 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 802) hydrogen bonds : angle 5.63020 ( 2192) metal coordination : bond 0.00532 ( 20) metal coordination : angle 6.20182 ( 27) covalent geometry : bond 0.00294 (19173) covalent geometry : angle 0.65653 (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 86 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8329 (tpt) cc_final: 0.6858 (tmm) REVERT: A 108 TYR cc_start: 0.9382 (m-80) cc_final: 0.9085 (m-80) REVERT: A 327 MET cc_start: 0.2608 (tmm) cc_final: 0.2092 (ptp) REVERT: A 328 MET cc_start: 0.2791 (mmt) cc_final: 0.1907 (mmp) REVERT: A 437 HIS cc_start: 0.9240 (t70) cc_final: 0.8941 (p-80) REVERT: A 743 ARG cc_start: 0.6581 (tpt170) cc_final: 0.6230 (tpt170) REVERT: A 773 TYR cc_start: 0.9614 (p90) cc_final: 0.9336 (m-80) REVERT: B 1 MET cc_start: 0.6912 (tpt) cc_final: 0.6324 (tpt) REVERT: B 69 MET cc_start: 0.6946 (mpp) cc_final: 0.6652 (mpp) REVERT: B 523 LEU cc_start: 0.9788 (tp) cc_final: 0.9404 (mp) REVERT: B 702 ASP cc_start: 0.9595 (m-30) cc_final: 0.9315 (m-30) REVERT: E 506 ARG cc_start: 0.8408 (tmt170) cc_final: 0.7985 (tpt170) REVERT: E 540 VAL cc_start: 0.7843 (p) cc_final: 0.7482 (m) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3276 time to fit residues: 44.3372 Evaluate side-chains 74 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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: 6.9990 chunk 148 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 150 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- 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 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** 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 = 0.3666 r_free = 0.3666 target = 0.047229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.034110 restraints weight = 285360.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.034441 restraints weight = 221276.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.034763 restraints weight = 180413.535| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19193 Z= 0.159 Angle : 0.693 12.796 26364 Z= 0.345 Chirality : 0.044 0.217 3009 Planarity : 0.005 0.058 3179 Dihedral : 20.370 178.171 3336 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.09 (0.18), residues: 2191 helix: -0.05 (0.17), residues: 879 sheet: -0.88 (0.33), residues: 256 loop : -1.20 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 401 HIS 0.010 0.001 HIS E 334 PHE 0.019 0.002 PHE E 211 TYR 0.039 0.002 TYR A 279 ARG 0.009 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 802) hydrogen bonds : angle 5.77240 ( 2192) metal coordination : bond 0.00677 ( 20) metal coordination : angle 6.15762 ( 27) covalent geometry : bond 0.00346 (19173) covalent geometry : angle 0.66453 (26337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7054.51 seconds wall clock time: 124 minutes 41.38 seconds (7481.38 seconds total)