Starting phenix.real_space_refine on Thu Sep 18 17:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga3_51170/09_2025/9ga3_51170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga3_51170/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ga3_51170/09_2025/9ga3_51170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga3_51170/09_2025/9ga3_51170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga3_51170/09_2025/9ga3_51170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga3_51170/09_2025/9ga3_51170.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 82 5.49 5 S 52 5.16 5 C 11447 2.51 5 N 3340 2.21 5 O 3765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18691 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6051 Classifications: {'peptide': 791} Link IDs: {'PTRANS': 39, 'TRANS': 751} Chain breaks: 3 Chain: "B" Number of atoms: 6318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6318 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 40, 'TRANS': 786} Chain breaks: 2 Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 756 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 847 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4660 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 28, 'TRANS': 560} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4533 SG CYS A 753 86.883 33.168 56.441 1.00293.98 S ATOM 4553 SG CYS A 756 89.395 34.321 53.617 1.00312.16 S ATOM 4706 SG CYS A 776 88.592 30.754 54.006 1.00332.08 S ATOM 4728 SG CYS A 779 85.877 33.207 52.846 1.00309.70 S ATOM 1034 SG CYS A 282 113.262 90.457 51.845 1.00616.18 S ATOM 1056 SG CYS A 285 111.217 87.387 51.288 1.00719.06 S ATOM 1951 SG CYS A 412 109.389 90.266 52.720 1.00721.65 S ATOM 1971 SG CYS A 415 110.493 90.768 49.283 1.00616.39 S ATOM 10851 SG CYS B 753 139.355 81.136 59.720 1.00562.15 S ATOM 10871 SG CYS B 756 137.982 78.623 57.286 1.00573.85 S ATOM 11024 SG CYS B 776 138.390 81.881 56.042 1.00596.17 S ATOM 11046 SG CYS B 779 141.514 79.769 56.528 1.00574.51 S ATOM 8186 SG CYS B 282 123.519 36.043 65.502 1.00578.49 S ATOM 8208 SG CYS B 285 125.466 39.197 64.700 1.00607.48 S ATOM 8269 SG CYS B 412 127.212 36.557 66.875 1.00612.52 S ATOM 8289 SG CYS B 415 126.517 35.770 63.330 1.00566.26 S ATOM 6994 SG CYS B 121 108.241 24.465 68.191 1.00501.32 S ATOM 7014 SG CYS B 124 106.831 21.126 69.550 1.00530.68 S ATOM 7999 SG CYS B 257 104.540 23.784 68.191 1.00499.46 S Time building chain proxies: 4.47, per 1000 atoms: 0.24 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: 2.23 Conformation dependent library (CDL) restraints added in 941.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 776 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 779 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 756 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 753 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 412 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 285 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 415 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 282 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 776 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 779 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 753 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 415 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 285 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 282 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 412 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" ND1 HIS B 261 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 257 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 124 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 121 " Number of angles added : 27 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 45.4% alpha, 11.0% beta 28 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 2.71 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: 3.57 Time building geometry restraints manager: 2.84 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 1002)) selection = (chain 'B' and (resid 1 through 63 or resid 70 through 122 or resid 126 or resid \ 146 or resid 148 or resid 151 or resid 156 or resid 165 or resid 170 or resid 1 \ 72 through 174 or resid 182 or resid 197 or resid 203 or resid 206 or resid 211 \ or resid 214 through 215 or resid 217 or resid 226 or resid 229 through 230 or r \ esid 236 or resid 238 or resid 251 or resid 255 through 256 or resid 263 or resi \ d 272 or resid 279 or resid 284 or resid 287 or resid 410 through 1002)) } ncs_group { reference = (chain 'C' and (resid 1 or (resid 2 and (name P or name OP1 or name OP2 or name \ O5' or name C5' or name C4' or name O4' or name C3' or name O3' or name C2' or n \ ame C1')) or resid 3 through 37)) selection = (chain 'D' and resid -42 through -6) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.860 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 2191 helix: -0.46 (0.17), residues: 876 sheet: -2.12 (0.30), residues: 231 loop : -1.71 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.013 0.002 TYR E 487 PHE 0.012 0.001 PHE E 211 TRP 0.010 0.001 TRP E 401 HIS 0.012 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00350 (19173) covalent geometry : angle 0.70639 (26337) hydrogen bonds : bond 0.09686 ( 802) hydrogen bonds : angle 6.73566 ( 2192) metal coordination : bond 0.01008 ( 20) metal coordination : angle 4.99435 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.647 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: 0.1537 time to fit residues: 23.7611 Evaluate side-chains 88 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 382 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.047928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.034431 restraints weight = 294736.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.034917 restraints weight = 226182.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.035301 restraints weight = 184528.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.035608 restraints weight = 160917.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.035721 restraints weight = 144478.836| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 19193 Z= 0.250 Angle : 0.814 14.458 26364 Z= 0.421 Chirality : 0.048 0.224 3009 Planarity : 0.007 0.066 3179 Dihedral : 20.425 175.980 3336 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.17), residues: 2191 helix: -0.77 (0.16), residues: 895 sheet: -1.89 (0.30), residues: 240 loop : -1.63 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 540 TYR 0.052 0.002 TYR B 605 PHE 0.032 0.003 PHE B 273 TRP 0.017 0.003 TRP E 401 HIS 0.010 0.002 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00537 (19173) covalent geometry : angle 0.78869 (26337) hydrogen bonds : bond 0.06024 ( 802) hydrogen bonds : angle 6.56730 ( 2192) metal coordination : bond 0.01061 ( 20) metal coordination : angle 6.38122 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8052 (tpt) cc_final: 0.6812 (tmm) REVERT: A 108 TYR cc_start: 0.9769 (m-80) cc_final: 0.9512 (m-80) REVERT: A 773 TYR cc_start: 0.9566 (p90) cc_final: 0.9210 (m-80) REVERT: B 1 MET cc_start: 0.7956 (tpt) cc_final: 0.7627 (tpp) REVERT: B 61 TYR cc_start: 0.7883 (m-10) cc_final: 0.7578 (m-80) REVERT: E 430 PHE cc_start: 0.9420 (p90) cc_final: 0.9140 (p90) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1653 time to fit residues: 20.6985 Evaluate side-chains 64 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 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 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 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 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 = 0.3668 r_free = 0.3668 target = 0.047085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.033921 restraints weight = 297845.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.034053 restraints weight = 231380.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.034512 restraints weight = 188385.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.034792 restraints weight = 160254.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.034966 restraints weight = 146882.259| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19193 Z= 0.233 Angle : 0.781 15.586 26364 Z= 0.400 Chirality : 0.047 0.250 3009 Planarity : 0.006 0.053 3179 Dihedral : 20.514 178.442 3336 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 32.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.11 % Allowed : 7.42 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.17), residues: 2191 helix: -0.75 (0.16), residues: 884 sheet: -1.76 (0.32), residues: 231 loop : -1.55 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 49 TYR 0.033 0.002 TYR E 131 PHE 0.025 0.002 PHE B 273 TRP 0.012 0.002 TRP E 401 HIS 0.009 0.002 HIS A 877 Details of bonding type rmsd covalent geometry : bond 0.00498 (19173) covalent geometry : angle 0.75141 (26337) hydrogen bonds : bond 0.05380 ( 802) hydrogen bonds : angle 6.49589 ( 2192) metal coordination : bond 0.01058 ( 20) metal coordination : angle 6.67569 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8327 (tpt) cc_final: 0.6721 (tmm) REVERT: A 327 MET cc_start: 0.4922 (tmm) cc_final: 0.4715 (tmm) REVERT: A 773 TYR cc_start: 0.9558 (p90) cc_final: 0.9210 (m-80) REVERT: B 1 MET cc_start: 0.7760 (tpt) cc_final: 0.7135 (tpp) REVERT: B 66 LEU cc_start: 0.9552 (mp) cc_final: 0.9294 (tt) REVERT: E 216 PHE cc_start: 0.9071 (p90) cc_final: 0.8670 (p90) REVERT: E 430 PHE cc_start: 0.9514 (p90) cc_final: 0.9178 (p90) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.1562 time to fit residues: 19.4088 Evaluate side-chains 64 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 116 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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 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 858 GLN E 330 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.047160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.033729 restraints weight = 296946.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.034136 restraints weight = 228165.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.034518 restraints weight = 185418.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.034689 restraints weight = 160796.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.034979 restraints weight = 146146.008| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19193 Z= 0.197 Angle : 0.743 15.641 26364 Z= 0.375 Chirality : 0.046 0.245 3009 Planarity : 0.006 0.070 3179 Dihedral : 20.466 177.105 3336 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 28.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.18), residues: 2191 helix: -0.57 (0.17), residues: 870 sheet: -1.50 (0.32), residues: 240 loop : -1.49 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 49 TYR 0.021 0.002 TYR A 54 PHE 0.020 0.002 PHE B 237 TRP 0.010 0.002 TRP E 401 HIS 0.008 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00425 (19173) covalent geometry : angle 0.70773 (26337) hydrogen bonds : bond 0.04908 ( 802) hydrogen bonds : angle 6.29794 ( 2192) metal coordination : bond 0.00939 ( 20) metal coordination : angle 7.08395 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8320 (tpt) cc_final: 0.6835 (tmm) REVERT: A 773 TYR cc_start: 0.9565 (p90) cc_final: 0.9235 (m-80) REVERT: B 1 MET cc_start: 0.7763 (tpt) cc_final: 0.7304 (tpp) REVERT: B 66 LEU cc_start: 0.9542 (mp) cc_final: 0.9255 (tt) REVERT: B 69 MET cc_start: 0.6491 (mpp) cc_final: 0.6211 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1629 time to fit residues: 19.1919 Evaluate side-chains 60 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 214 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 393 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** ** A 849 GLN ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.046458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.033363 restraints weight = 295548.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.033690 restraints weight = 226945.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.034044 restraints weight = 185694.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.034346 restraints weight = 157725.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.034562 restraints weight = 143898.543| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19193 Z= 0.212 Angle : 0.748 14.325 26364 Z= 0.381 Chirality : 0.046 0.235 3009 Planarity : 0.006 0.057 3179 Dihedral : 20.519 177.069 3336 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.17), residues: 2191 helix: -0.66 (0.16), residues: 869 sheet: -1.47 (0.33), residues: 239 loop : -1.53 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 53 TYR 0.023 0.002 TYR A 54 PHE 0.016 0.002 PHE B 237 TRP 0.010 0.002 TRP E 401 HIS 0.008 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00453 (19173) covalent geometry : angle 0.71796 (26337) hydrogen bonds : bond 0.05029 ( 802) hydrogen bonds : angle 6.36224 ( 2192) metal coordination : bond 0.00911 ( 20) metal coordination : angle 6.54736 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8331 (tpt) cc_final: 0.6946 (tmm) REVERT: A 108 TYR cc_start: 0.9669 (m-80) cc_final: 0.9417 (m-80) REVERT: A 773 TYR cc_start: 0.9529 (p90) cc_final: 0.9231 (m-80) REVERT: B 1 MET cc_start: 0.8172 (tpt) cc_final: 0.7557 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1676 time to fit residues: 19.8559 Evaluate side-chains 60 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 139 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 177 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 173 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.046289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.033078 restraints weight = 295678.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.033422 restraints weight = 227630.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.033847 restraints weight = 188528.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.034168 restraints weight = 159770.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.034448 restraints weight = 140669.649| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19193 Z= 0.206 Angle : 0.741 14.920 26364 Z= 0.376 Chirality : 0.046 0.271 3009 Planarity : 0.006 0.075 3179 Dihedral : 20.517 177.788 3336 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.17), residues: 2191 helix: -0.67 (0.16), residues: 875 sheet: -1.27 (0.34), residues: 229 loop : -1.55 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 515 TYR 0.024 0.002 TYR E 487 PHE 0.020 0.002 PHE A 744 TRP 0.011 0.002 TRP E 401 HIS 0.007 0.002 HIS A 877 Details of bonding type rmsd covalent geometry : bond 0.00437 (19173) covalent geometry : angle 0.71247 (26337) hydrogen bonds : bond 0.04893 ( 802) hydrogen bonds : angle 6.35439 ( 2192) metal coordination : bond 0.00923 ( 20) metal coordination : angle 6.39432 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8234 (tpt) cc_final: 0.7041 (tmm) REVERT: A 108 TYR cc_start: 0.9636 (m-80) cc_final: 0.9373 (m-80) REVERT: A 399 MET cc_start: 0.4449 (mtt) cc_final: 0.4091 (mtt) REVERT: A 773 TYR cc_start: 0.9540 (p90) cc_final: 0.9242 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1716 time to fit residues: 20.0768 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 : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 144 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 chunk 21 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- 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 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.046361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.034347 restraints weight = 293591.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.033860 restraints weight = 222671.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.034155 restraints weight = 193150.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.034210 restraints weight = 166506.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.034329 restraints weight = 161070.502| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.004 0.066 19193 Z= 0.194 Angle : 0.741 14.615 26364 Z= 0.372 Chirality : 0.046 0.246 3009 Planarity : 0.006 0.074 3179 Dihedral : 20.546 179.393 3336 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2191 helix: -0.59 (0.16), residues: 882 sheet: -1.16 (0.34), residues: 228 loop : -1.52 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 49 TYR 0.045 0.002 TYR B 605 PHE 0.021 0.002 PHE A 744 TRP 0.011 0.002 TRP E 401 HIS 0.008 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00417 (19173) covalent geometry : angle 0.70816 (26337) hydrogen bonds : bond 0.04722 ( 802) hydrogen bonds : angle 6.26379 ( 2192) metal coordination : bond 0.00999 ( 20) metal coordination : angle 6.81863 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8241 (tpt) cc_final: 0.7323 (tmm) REVERT: A 108 TYR cc_start: 0.9623 (m-80) cc_final: 0.9356 (m-80) REVERT: A 773 TYR cc_start: 0.9509 (p90) cc_final: 0.9252 (m-80) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1687 time to fit residues: 20.4947 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 213 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.045478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.032526 restraints weight = 294504.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.032776 restraints weight = 228936.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.033125 restraints weight = 186003.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.033414 restraints weight = 161819.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.033686 restraints weight = 145453.775| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19193 Z= 0.225 Angle : 0.773 15.099 26364 Z= 0.391 Chirality : 0.047 0.267 3009 Planarity : 0.006 0.069 3179 Dihedral : 20.634 179.352 3336 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 35.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2191 helix: -0.82 (0.16), residues: 888 sheet: -1.34 (0.33), residues: 237 loop : -1.61 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 743 TYR 0.035 0.002 TYR B 605 PHE 0.027 0.002 PHE A 744 TRP 0.011 0.002 TRP E 401 HIS 0.009 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00475 (19173) covalent geometry : angle 0.73968 (26337) hydrogen bonds : bond 0.05224 ( 802) hydrogen bonds : angle 6.44842 ( 2192) metal coordination : bond 0.01153 ( 20) metal coordination : angle 7.01593 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8131 (tpt) cc_final: 0.7156 (tmm) REVERT: A 108 TYR cc_start: 0.9599 (m-80) cc_final: 0.9359 (m-80) REVERT: A 773 TYR cc_start: 0.9549 (p90) cc_final: 0.9313 (p90) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1719 time to fit residues: 20.1891 Evaluate side-chains 59 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.047624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.034017 restraints weight = 283070.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.034462 restraints weight = 216694.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.034830 restraints weight = 177507.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.035173 restraints weight = 155037.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.035258 restraints weight = 140745.074| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19193 Z= 0.139 Angle : 0.709 13.116 26364 Z= 0.349 Chirality : 0.045 0.224 3009 Planarity : 0.005 0.057 3179 Dihedral : 20.458 179.548 3336 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.18), residues: 2191 helix: -0.27 (0.17), residues: 871 sheet: -1.00 (0.33), residues: 247 loop : -1.30 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 555 TYR 0.020 0.002 TYR B 605 PHE 0.018 0.002 PHE A 47 TRP 0.011 0.002 TRP E 401 HIS 0.005 0.001 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00310 (19173) covalent geometry : angle 0.67951 (26337) hydrogen bonds : bond 0.04058 ( 802) hydrogen bonds : angle 5.91813 ( 2192) metal coordination : bond 0.00657 ( 20) metal coordination : angle 6.41185 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.9698 (m-80) cc_final: 0.9446 (m-80) REVERT: A 743 ARG cc_start: 0.5535 (tpt170) cc_final: 0.5300 (tpm170) REVERT: A 773 TYR cc_start: 0.9533 (p90) cc_final: 0.9274 (m-80) REVERT: E 473 VAL cc_start: 0.8810 (t) cc_final: 0.8361 (t) REVERT: E 540 VAL cc_start: 0.3603 (p) cc_final: 0.2897 (m) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1526 time to fit residues: 21.2841 Evaluate side-chains 64 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 108 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 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 = 0.045539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.032579 restraints weight = 291645.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.032928 restraints weight = 225545.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.033247 restraints weight = 185197.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.033491 restraints weight = 159936.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.033827 restraints weight = 143388.001| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19193 Z= 0.232 Angle : 0.769 14.147 26364 Z= 0.390 Chirality : 0.046 0.249 3009 Planarity : 0.006 0.063 3179 Dihedral : 20.586 178.251 3336 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 34.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.18), residues: 2191 helix: -0.71 (0.16), residues: 895 sheet: -1.35 (0.33), residues: 244 loop : -1.43 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 529 TYR 0.032 0.002 TYR B 605 PHE 0.025 0.002 PHE E 211 TRP 0.011 0.002 TRP A 570 HIS 0.013 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00485 (19173) covalent geometry : angle 0.73955 (26337) hydrogen bonds : bond 0.05178 ( 802) hydrogen bonds : angle 6.36169 ( 2192) metal coordination : bond 0.01093 ( 20) metal coordination : angle 6.63675 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 LEU cc_start: 0.8809 (mm) cc_final: 0.8567 (tp) REVERT: A 773 TYR cc_start: 0.9537 (p90) cc_final: 0.9297 (p90) REVERT: E 86 MET cc_start: 0.3292 (mmm) cc_final: 0.3007 (mmm) REVERT: E 278 MET cc_start: 0.9473 (mpp) cc_final: 0.9208 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1614 time to fit residues: 19.3312 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 : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 183 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 177 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 131 optimal weight: 40.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 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 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.046171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.033012 restraints weight = 290432.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.033358 restraints weight = 225455.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.033674 restraints weight = 182764.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.033800 restraints weight = 158731.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.034107 restraints weight = 147610.380| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19193 Z= 0.179 Angle : 0.730 13.669 26364 Z= 0.364 Chirality : 0.045 0.228 3009 Planarity : 0.005 0.060 3179 Dihedral : 20.558 177.835 3336 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2191 helix: -0.58 (0.16), residues: 882 sheet: -1.20 (0.33), residues: 246 loop : -1.37 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 49 TYR 0.028 0.002 TYR B 605 PHE 0.023 0.002 PHE E 211 TRP 0.013 0.002 TRP E 401 HIS 0.011 0.002 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00386 (19173) covalent geometry : angle 0.69937 (26337) hydrogen bonds : bond 0.04540 ( 802) hydrogen bonds : angle 6.19142 ( 2192) metal coordination : bond 0.00859 ( 20) metal coordination : angle 6.55035 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.69 seconds wall clock time: 71 minutes 56.86 seconds (4316.86 seconds total)