Starting phenix.real_space_refine on Sat Jul 4 14:00:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.map" model { file = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p91_13257/07_2026/7p91_13257.cif" } resolution = 2.8 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 62 7.16 5 Zn 2 6.06 5 P 2 5.49 5 S 219 5.16 5 C 13304 2.51 5 N 3525 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21419 Number of models: 1 Model: "" Number of chains: 18 Chain: "a" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5037 Classifications: {'peptide': 642} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 616} Chain: "b" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4320 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 532} Chain breaks: 1 Chain: "c" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "A" Number of atoms: 4376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 4425 Chain: "B" Number of atoms: 4716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 613, 4708 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 31, 'TRANS': 581} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 613, 4708 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 31, 'TRANS': 581} Chain breaks: 1 bond proxies already assigned to first conformer: 4787 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "a" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 40 Unusual residues: {'FES': 2, 'SF4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "b" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "c" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4818 SG CYS a 612 50.942 88.423 34.824 1.00 27.14 S ATOM 4848 SG CYS a 616 48.073 88.389 32.503 1.00 36.72 S ATOM 4528 SG CYS a 575 54.288 87.219 30.790 1.00 29.12 S ATOM 4559 SG CYS a 580 51.868 87.717 28.285 1.00 31.77 S ATOM 2747 SG CYS a 350 75.420 88.863 68.749 1.00 8.79 S ATOM 2305 SG CYS a 295 69.843 91.274 70.272 1.00 16.50 S ATOM 3795 SG CYS a 486 74.226 90.178 74.981 1.00 16.50 S ATOM 3765 SG CYS a 482 71.286 85.277 71.266 1.00 9.41 S ATOM 1464 SG CYS a 186 70.382 84.592 59.972 1.00 16.50 S ATOM 1485 SG CYS a 189 69.287 83.660 66.309 1.00 16.50 S ATOM 1504 SG CYS a 192 71.681 79.105 62.941 1.00 16.50 S ATOM 1211 SG CYS a 153 65.493 80.666 62.024 1.00 16.50 S ATOM 1180 SG CYS a 149 68.952 73.464 61.116 1.00 16.50 S ATOM 1162 SG CYS a 146 70.029 68.006 64.159 1.00 16.50 S ATOM 1534 SG CYS a 196 74.747 72.042 63.219 1.00 16.50 S ATOM 1140 SG CYS a 143 71.815 68.987 57.941 1.00 16.50 S ATOM 782 SG CYS a 99 83.141 69.859 61.975 1.00 16.50 S ATOM 825 SG CYS a 105 80.445 65.144 65.319 1.00 16.50 S ATOM 762 SG CYS a 96 86.033 64.231 61.720 1.00 16.50 S ATOM 377 SG CYS a 48 65.456 54.353 69.520 1.00 9.24 S ATOM 464 SG CYS a 60 62.829 56.855 69.455 1.00 10.72 S ATOM 271 SG CYS a 34 66.504 60.378 66.875 1.00 10.87 S ATOM 352 SG CYS a 45 68.633 57.461 66.614 1.00 16.50 S ATOM 8691 SG CYS b 485 59.829 60.976 55.037 1.00 7.98 S ATOM 8730 SG CYS b 491 62.851 55.464 53.001 1.00 11.24 S ATOM 9049 SG CYS b 531 57.076 55.563 56.017 1.00 9.30 S ATOM 8710 SG CYS b 488 63.447 56.390 58.256 1.00 16.50 S ATOM 5293 SG CYS b 31 35.252 53.197 29.539 1.00 26.40 S ATOM 5321 SG CYS b 36 38.027 52.639 27.207 1.00 24.25 S ATOM 5564 SG CYS b 78 37.721 50.295 33.385 1.00 29.04 S ATOM 5591 SG CYS b 82 40.655 50.157 31.270 1.00 29.41 S ATOM 8547 SG CYS b 468 67.917 41.130 34.548 1.00 23.29 S ATOM 9273 SG CYS b 560 70.423 40.306 31.676 1.00 30.69 S ATOM 9304 SG CYS b 565 70.257 43.844 33.139 1.00 33.07 S ATOM 10272 SG CYS c 119 49.011 53.082 35.116 1.00 15.53 S ATOM 10295 SG CYS c 123 48.779 50.271 33.197 1.00 17.33 S ATOM 9978 SG CYS c 78 53.439 55.211 32.964 1.00 16.71 S ATOM 10008 SG CYS c 83 53.525 52.882 30.377 1.00 15.89 S ATOM 13333 SG CYS A 350 101.102 39.250 69.129 1.00 7.37 S ATOM 12891 SG CYS A 295 106.640 36.774 70.674 1.00 16.50 S ATOM 14381 SG CYS A 486 102.177 37.905 75.350 1.00 16.50 S ATOM 14351 SG CYS A 482 105.158 42.785 71.651 1.00 10.37 S ATOM 12090 SG CYS A 192 104.810 48.977 63.224 1.00 16.50 S ATOM 12050 SG CYS A 186 106.057 43.372 60.288 1.00 16.50 S ATOM 12071 SG CYS A 189 107.120 44.186 66.518 1.00 16.50 S ATOM 11797 SG CYS A 153 110.903 47.333 62.188 1.00 16.50 S ATOM 11766 SG CYS A 149 107.527 54.577 61.263 1.00 16.50 S ATOM 11748 SG CYS A 146 106.477 60.079 64.172 1.00 16.50 S ATOM 12120 SG CYS A 196 101.711 55.990 63.254 1.00 16.50 S ATOM 11726 SG CYS A 143 104.647 59.117 58.041 1.00 16.50 S ATOM 11400 SG CYS A 105 96.077 62.739 65.350 1.00 16.50 S ATOM 11337 SG CYS A 96 90.415 63.703 61.971 1.00 16.50 S ATOM 11357 SG CYS A 99 93.343 58.085 62.205 1.00 16.50 S ATOM 10952 SG CYS A 48 110.963 73.672 69.360 1.00 7.10 S ATOM 11039 SG CYS A 60 113.584 71.282 69.216 1.00 9.93 S ATOM 10846 SG CYS A 34 110.094 67.607 66.718 1.00 9.02 S ATOM 10927 SG CYS A 45 107.842 70.549 66.345 1.00 16.50 S ATOM 19574 SG CYS B 611 95.206 90.539 23.743 1.00 42.65 S ATOM 19592 SG CYS B 614 90.916 86.828 24.887 1.00 46.54 S ATOM 19552 SG CYS B 608 95.862 84.198 21.328 1.00 48.74 S ATOM 19396 SG CYS B 588 90.988 88.629 19.705 1.00 45.94 S ATOM 19331 SG CYS B 578 83.019 80.019 27.690 1.00 43.58 S ATOM 19368 SG CYS B 584 85.964 85.713 25.772 1.00 43.64 S ATOM 19618 SG CYS B 618 86.125 84.529 31.296 1.00 41.14 S ATOM 19350 SG CYS B 581 80.316 85.827 28.903 1.00 38.79 S ATOM 18613 SG CYS B 485 116.527 66.878 54.975 1.00 11.06 S ATOM 18652 SG CYS B 491 113.616 72.543 52.837 1.00 8.58 S ATOM 18971 SG CYS B 531 119.345 72.357 55.809 1.00 16.50 S ATOM 18632 SG CYS B 488 113.018 71.598 58.042 1.00 16.50 S ATOM 15207 SG CYS B 31 140.893 74.109 28.870 1.00 30.10 S ATOM 15235 SG CYS B 36 138.137 75.154 26.670 1.00 27.51 S ATOM 15478 SG CYS B 78 138.765 77.421 32.811 1.00 30.90 S ATOM 15505 SG CYS B 82 135.907 78.002 30.838 1.00 31.26 S ATOM 18469 SG CYS B 468 108.426 86.182 34.641 1.00 22.52 S ATOM 19195 SG CYS B 560 106.557 87.111 31.464 1.00 29.09 S ATOM 19226 SG CYS B 565 106.060 83.657 33.051 1.00 28.48 S ATOM 20582 SG CYS C 119 127.039 74.727 34.959 1.00 20.24 S ATOM 20605 SG CYS C 123 127.180 77.219 32.671 1.00 22.24 S ATOM 20288 SG CYS C 78 122.911 72.216 32.525 1.00 19.40 S ATOM 20318 SG CYS C 83 122.587 74.495 29.869 1.00 18.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 Time building chain proxies: 6.29, per 1000 atoms: 0.29 Number of scatterers: 21419 At special positions: 0 Unit cell: (177.16, 128.544, 104.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 62 26.01 S 219 16.00 P 2 15.00 O 4305 8.00 N 3525 7.00 C 13304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 705 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 48 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 60 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 45 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 34 " pdb=" FES B 705 " pdb="FE2 FES B 705 " - pdb=" SG CYS B 78 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 36 " pdb="FE2 FES B 705 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 31 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb=" FES a 701 " pdb="FE2 FES a 701 " - pdb=" SG CYS a 580 " pdb="FE2 FES a 701 " - pdb=" SG CYS a 575 " pdb="FE1 FES a 701 " - pdb=" SG CYS a 616 " pdb="FE1 FES a 701 " - pdb=" SG CYS a 612 " pdb=" FES a 706 " pdb="FE1 FES a 706 " - pdb=" SG CYS a 48 " pdb="FE2 FES a 706 " - pdb=" SG CYS a 45 " pdb="FE1 FES a 706 " - pdb=" SG CYS a 60 " pdb="FE2 FES a 706 " - pdb=" SG CYS a 34 " pdb=" FES b 703 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 82 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 36 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 78 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 31 " pdb=" FES c 201 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 78 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 83 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 119 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 123 " pdb=" SF4 A 701 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 153 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 189 " pdb=" SF4 A 703 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 149 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 143 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 196 " pdb=" SF4 A 704 " pdb="FE4 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 105 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 99 " pdb=" SF4 B 701 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 614 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 588 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 611 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 608 " pdb=" SF4 B 702 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 584 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 581 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 618 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 578 " pdb=" SF4 B 703 " pdb="FE1 SF4 B 703 " - pdb=" SG CYS B 485 " pdb="FE4 SF4 B 703 " - pdb=" SG CYS B 488 " pdb="FE3 SF4 B 703 " - pdb=" SG CYS B 531 " pdb="FE2 SF4 B 703 " - pdb=" SG CYS B 491 " pdb=" SF4 a 702 " pdb="FE1 SF4 a 702 " - pdb=" SG CYS a 350 " pdb="FE4 SF4 a 702 " - pdb=" SG CYS a 482 " pdb="FE2 SF4 a 702 " - pdb=" SG CYS a 295 " pdb="FE3 SF4 a 702 " - pdb=" SG CYS a 486 " pdb=" SF4 a 703 " pdb="FE1 SF4 a 703 " - pdb=" SG CYS a 186 " pdb="FE2 SF4 a 703 " - pdb=" SG CYS a 189 " pdb="FE3 SF4 a 703 " - pdb=" SG CYS a 192 " pdb="FE4 SF4 a 703 " - pdb=" SG CYS a 153 " pdb=" SF4 a 704 " pdb="FE4 SF4 a 704 " - pdb=" SG CYS a 143 " pdb="FE1 SF4 a 704 " - pdb=" SG CYS a 149 " pdb="FE2 SF4 a 704 " - pdb=" SG CYS a 146 " pdb="FE3 SF4 a 704 " - pdb=" SG CYS a 196 " pdb=" SF4 a 705 " pdb="FE2 SF4 a 705 " - pdb=" NE2 HIS a 92 " pdb="FE1 SF4 a 705 " - pdb=" SG CYS a 99 " pdb="FE4 SF4 a 705 " - pdb=" SG CYS a 96 " pdb="FE3 SF4 a 705 " - pdb=" SG CYS a 105 " pdb=" SF4 b 701 " pdb="FE1 SF4 b 701 " - pdb=" SG CYS b 485 " pdb="FE3 SF4 b 701 " - pdb=" SG CYS b 531 " pdb="FE4 SF4 b 701 " - pdb=" SG CYS b 488 " pdb="FE2 SF4 b 701 " - pdb=" SG CYS b 491 " Number of angles added : 180 Zn2+ tetrahedral coordination pdb=" ZN B 706 " pdb="ZN ZN B 706 " - pdb=" NE2 HIS B 555 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 468 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 560 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 565 " pdb=" ZN b 704 " pdb="ZN ZN b 704 " - pdb=" NE2 HIS b 555 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 560 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 565 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 468 " Number of angles added : 6 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 21 sheets defined 51.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'a' and resid 18 through 27 Processing helix chain 'a' and resid 60 through 62 No H-bonds generated for 'chain 'a' and resid 60 through 62' Processing helix chain 'a' and resid 74 through 91 removed outlier: 3.971A pdb=" N THR a 91 " --> pdb=" O LEU a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 114 Processing helix chain 'a' and resid 141 through 143 No H-bonds generated for 'chain 'a' and resid 141 through 143' Processing helix chain 'a' and resid 147 through 156 Processing helix chain 'a' and resid 167 through 171 removed outlier: 3.553A pdb=" N GLU a 170 " --> pdb=" O ARG a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'a' and resid 180 through 184 Processing helix chain 'a' and resid 190 through 196 Processing helix chain 'a' and resid 206 through 216 Processing helix chain 'a' and resid 231 through 237 removed outlier: 3.549A pdb=" N PHE a 236 " --> pdb=" O GLN a 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 255 Processing helix chain 'a' and resid 263 through 285 Processing helix chain 'a' and resid 295 through 306 Processing helix chain 'a' and resid 307 through 310 removed outlier: 3.578A pdb=" N LEU a 310 " --> pdb=" O PRO a 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 307 through 310' Processing helix chain 'a' and resid 318 through 336 removed outlier: 4.547A pdb=" N ALA a 332 " --> pdb=" O LYS a 328 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG a 333 " --> pdb=" O LYS a 329 " (cutoff:3.500A) Processing helix chain 'a' and resid 338 through 340 No H-bonds generated for 'chain 'a' and resid 338 through 340' Processing helix chain 'a' and resid 351 through 358 removed outlier: 3.870A pdb=" N PHE a 355 " --> pdb=" O THR a 351 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 383 removed outlier: 3.591A pdb=" N SER a 382 " --> pdb=" O LEU a 378 " (cutoff:3.500A) Processing helix chain 'a' and resid 402 through 407 Processing helix chain 'a' and resid 408 through 410 No H-bonds generated for 'chain 'a' and resid 408 through 410' Processing helix chain 'a' and resid 412 through 426 Processing helix chain 'a' and resid 463 through 471 removed outlier: 3.612A pdb=" N PHE a 467 " --> pdb=" O LYS a 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 484 through 489 removed outlier: 4.214A pdb=" N VAL a 487 " --> pdb=" O TYR a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 497 through 514 removed outlier: 3.729A pdb=" N ILE a 514 " --> pdb=" O ASP a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 519 through 522 Processing helix chain 'a' and resid 523 through 533 Processing helix chain 'a' and resid 536 through 545 Processing helix chain 'a' and resid 577 through 582 Processing helix chain 'a' and resid 584 through 599 Processing helix chain 'a' and resid 633 through 642 Processing helix chain 'b' and resid 4 through 25 removed outlier: 3.751A pdb=" N PHE b 8 " --> pdb=" O ASN b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 40 Processing helix chain 'b' and resid 40 through 55 Processing helix chain 'b' and resid 101 through 103 No H-bonds generated for 'chain 'b' and resid 101 through 103' Processing helix chain 'b' and resid 104 through 112 Processing helix chain 'b' and resid 119 through 123 Processing helix chain 'b' and resid 139 through 145 Processing helix chain 'b' and resid 160 through 167 Processing helix chain 'b' and resid 170 through 179 Processing helix chain 'b' and resid 181 through 193 removed outlier: 3.565A pdb=" N GLY b 193 " --> pdb=" O VAL b 189 " (cutoff:3.500A) Processing helix chain 'b' and resid 203 through 214 Processing helix chain 'b' and resid 233 through 242 Processing helix chain 'b' and resid 242 through 258 removed outlier: 3.615A pdb=" N VAL b 246 " --> pdb=" O ASP b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 270 through 287 Processing helix chain 'b' and resid 311 through 315 Processing helix chain 'b' and resid 316 through 325 Processing helix chain 'b' and resid 342 through 346 Processing helix chain 'b' and resid 353 through 365 Proline residue: b 360 - end of helix Processing helix chain 'b' and resid 366 through 372 Processing helix chain 'b' and resid 403 through 409 Processing helix chain 'b' and resid 427 through 431 removed outlier: 3.809A pdb=" N SER b 430 " --> pdb=" O GLY b 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 435 through 439 Processing helix chain 'b' and resid 468 through 484 Processing helix chain 'b' and resid 488 through 507 removed outlier: 4.128A pdb=" N MET b 496 " --> pdb=" O ARG b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 511 through 529 removed outlier: 3.669A pdb=" N LYS b 523 " --> pdb=" O GLU b 519 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR b 524 " --> pdb=" O HIS b 520 " (cutoff:3.500A) Processing helix chain 'b' and resid 531 through 536 Processing helix chain 'b' and resid 538 through 548 Processing helix chain 'b' and resid 548 through 557 removed outlier: 3.552A pdb=" N TYR b 552 " --> pdb=" O PHE b 548 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 15 Processing helix chain 'c' and resid 18 through 20 No H-bonds generated for 'chain 'c' and resid 18 through 20' Processing helix chain 'c' and resid 21 through 34 Processing helix chain 'c' and resid 37 through 49 Processing helix chain 'c' and resid 51 through 60 removed outlier: 3.593A pdb=" N ILE c 55 " --> pdb=" O PRO c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 87 Processing helix chain 'c' and resid 87 through 100 Processing helix chain 'c' and resid 122 through 126 Processing helix chain 'c' and resid 140 through 158 removed outlier: 4.031A pdb=" N SER c 158 " --> pdb=" O LYS c 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 74 through 92 removed outlier: 4.003A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 263 through 285 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.714A pdb=" N LEU A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 311 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.724A pdb=" N PHE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 462 through 471 removed outlier: 4.479A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 4.439A pdb=" N VAL A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.728A pdb=" N ILE A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.932A pdb=" N PHE B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 56 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.767A pdb=" N TYR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.583A pdb=" N GLY B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 242 through 258 removed outlier: 4.033A pdb=" N VAL B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 288 Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 353 through 365 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.409A pdb=" N ASP B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 468 through 484 Processing helix chain 'B' and resid 488 through 507 removed outlier: 4.020A pdb=" N MET B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 529 Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 538 through 557 removed outlier: 7.145A pdb=" N GLU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 4.103A pdb=" N PHE B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.620A pdb=" N CYS B 578 " --> pdb=" O PRO B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.529A pdb=" N LYS B 607 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS B 608 " --> pdb=" O GLN B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 608' Processing helix chain 'B' and resid 612 through 617 removed outlier: 3.666A pdb=" N SER B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 617' Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.583A pdb=" N ILE C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 140 through 158 removed outlier: 3.984A pdb=" N SER C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 11 removed outlier: 9.134A pdb=" N VAL a 70 " --> pdb=" O LYS a 2 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR a 4 " --> pdb=" O VAL a 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'a' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'a' and resid 259 through 262 removed outlier: 6.692A pdb=" N VAL a 220 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N PHE a 261 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY a 222 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE a 219 " --> pdb=" O PHE a 343 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL a 345 " --> pdb=" O ILE a 219 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE a 221 " --> pdb=" O VAL a 345 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE a 347 " --> pdb=" O ILE a 221 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET a 223 " --> pdb=" O PHE a 347 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ILE a 368 " --> pdb=" O ILE a 342 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU a 344 " --> pdb=" O ILE a 368 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU a 370 " --> pdb=" O LEU a 344 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER a 346 " --> pdb=" O LEU a 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 290 through 291 removed outlier: 6.364A pdb=" N GLN a 290 " --> pdb=" O ILE a 477 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL a 479 " --> pdb=" O GLN a 290 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE a 476 " --> pdb=" O LYS a 454 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE a 440 " --> pdb=" O PRO a 436 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS a 430 " --> pdb=" O THR a 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 607 through 610 removed outlier: 6.175A pdb=" N VAL a 572 " --> pdb=" O LEU a 608 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR a 610 " --> pdb=" O VAL a 572 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL a 574 " --> pdb=" O THR a 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 72 through 76 Processing sheet with id=AA8, first strand: chain 'b' and resid 124 through 125 removed outlier: 4.138A pdb=" N LEU b 124 " --> pdb=" O VAL b 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 303 through 308 removed outlier: 6.593A pdb=" N GLY b 262 " --> pdb=" O GLU b 304 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LYS b 306 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA b 264 " --> pdb=" O LYS b 306 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY b 308 " --> pdb=" O ALA b 264 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE b 266 " --> pdb=" O GLY b 308 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL b 221 " --> pdb=" O TYR b 263 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR b 265 " --> pdb=" O VAL b 221 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS b 223 " --> pdb=" O TYR b 265 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ARG b 267 " --> pdb=" O CYS b 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 394 through 399 removed outlier: 7.918A pdb=" N ILE b 460 " --> pdb=" O MET b 383 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER b 385 " --> pdb=" O ILE b 460 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL b 462 " --> pdb=" O SER b 385 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA b 387 " --> pdb=" O VAL b 462 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N THR b 464 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 112 through 117 Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 11 removed outlier: 9.098A pdb=" N VAL A 70 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR A 4 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB5, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.689A pdb=" N LYS A 259 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 219 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 345 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 221 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 347 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET A 223 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILE A 368 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 370 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 346 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.322A pdb=" N GLN A 290 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL A 479 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 440 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER A 435 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 442 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 433 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A 444 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 431 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 446 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.561A pdb=" N VAL B 30 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 87 " --> pdb=" O CYS B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.929A pdb=" N LEU B 124 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 302 through 308 removed outlier: 6.680A pdb=" N GLY B 262 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS B 306 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA B 264 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 308 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 266 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 221 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR B 265 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS B 223 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ARG B 267 " --> pdb=" O CYS B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 395 through 399 removed outlier: 7.822A pdb=" N ILE B 460 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER B 385 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 462 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 387 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 105 through 106 removed outlier: 3.565A pdb=" N ASN C 105 " --> pdb=" O LEU C 114 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 8525 1.42 - 1.63: 12575 1.63 - 1.85: 218 1.85 - 2.07: 0 2.07 - 2.28: 172 Bond restraints: 21490 Sorted by residual: bond pdb=" CA THR C 102 " pdb=" C THR C 102 " ideal model delta sigma weight residual 1.524 1.581 -0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" C THR C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 1.332 1.375 -0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 1.526 1.491 0.035 1.29e-02 6.01e+03 7.28e+00 bond pdb=" C ASN C 138 " pdb=" O ASN C 138 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.30e-02 5.92e+03 5.95e+00 bond pdb=" C LYS A 209 " pdb=" O LYS A 209 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.15e-02 7.56e+03 4.40e+00 ... (remaining 21485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 28544 1.58 - 3.15: 408 3.15 - 4.73: 87 4.73 - 6.30: 11 6.30 - 7.88: 2 Bond angle restraints: 29052 Sorted by residual: angle pdb=" N MET b 91 " pdb=" CA MET b 91 " pdb=" C MET b 91 " ideal model delta sigma weight residual 109.81 115.65 -5.84 2.21e+00 2.05e-01 6.98e+00 angle pdb=" CB LYS A 506 " pdb=" CG LYS A 506 " pdb=" CD LYS A 506 " ideal model delta sigma weight residual 111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00 angle pdb=" O LEU C 101 " pdb=" C LEU C 101 " pdb=" N THR C 102 " ideal model delta sigma weight residual 123.19 126.38 -3.19 1.30e+00 5.92e-01 6.01e+00 angle pdb=" CA ASN C 138 " pdb=" C ASN C 138 " pdb=" O ASN C 138 " ideal model delta sigma weight residual 121.54 118.76 2.78 1.16e+00 7.43e-01 5.75e+00 angle pdb=" N GLN B 10 " pdb=" CA GLN B 10 " pdb=" CB GLN B 10 " ideal model delta sigma weight residual 110.12 113.55 -3.43 1.47e+00 4.63e-01 5.44e+00 ... (remaining 29047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12795 35.65 - 71.31: 228 71.31 - 106.96: 24 106.96 - 142.62: 0 142.62 - 178.27: 2 Dihedral angle restraints: 13049 sinusoidal: 5372 harmonic: 7677 Sorted by residual: dihedral pdb=" C10 FMN b 702 " pdb=" C1' FMN b 702 " pdb=" N10 FMN b 702 " pdb=" C2' FMN b 702 " ideal model delta sinusoidal sigma weight residual 257.59 79.32 178.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN B 704 " pdb=" C1' FMN B 704 " pdb=" N10 FMN B 704 " pdb=" C2' FMN B 704 " ideal model delta sinusoidal sigma weight residual 257.59 96.05 161.54 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" CA LYS B 334 " pdb=" C LYS B 334 " pdb=" N PRO B 335 " pdb=" CA PRO B 335 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 13046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2645 0.048 - 0.096: 453 0.096 - 0.143: 166 0.143 - 0.191: 3 0.191 - 0.239: 1 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CA ASN C 138 " pdb=" N ASN C 138 " pdb=" C ASN C 138 " pdb=" CB ASN C 138 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA THR C 102 " pdb=" N THR C 102 " pdb=" C THR C 102 " pdb=" CB THR C 102 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU a 526 " pdb=" CB LEU a 526 " pdb=" CD1 LEU a 526 " pdb=" CD2 LEU a 526 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 3265 not shown) Planarity restraints: 3693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 138 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ASN C 138 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN C 138 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 139 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 121 " -0.228 9.50e-02 1.11e+02 1.02e-01 6.98e+00 pdb=" NE ARG b 121 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG b 121 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG b 121 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG b 121 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 101 " 0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 102 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " 0.034 5.00e-02 4.00e+02 ... (remaining 3690 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 327 2.63 - 3.20: 19883 3.20 - 3.76: 34396 3.76 - 4.33: 50438 4.33 - 4.90: 80317 Nonbonded interactions: 185361 Sorted by model distance: nonbonded pdb=" O GLY b 486 " pdb=" O HOH b 801 " model vdw 2.062 3.040 nonbonded pdb=" O PHE A 394 " pdb=" O HOH A 801 " model vdw 2.068 3.040 nonbonded pdb=" O HOH A 825 " pdb=" O HOH A 870 " model vdw 2.077 3.040 nonbonded pdb=" O HOH A 877 " pdb=" O HOH A 890 " model vdw 2.094 3.040 nonbonded pdb=" O CYS a 143 " pdb=" O HOH a 801 " model vdw 2.098 3.040 ... (remaining 185356 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 129 or resid 131 through 705)) selection = (chain 'a' and (resid 1 through 129 or resid 131 through 554 or resid 702 throug \ h 706)) } ncs_group { reference = (chain 'B' and (resid 1 through 235 or resid 237 through 571 or resid 703 throug \ h 706)) selection = (chain 'b' and (resid 1 through 235 or resid 237 through 704)) } ncs_group { reference = chain 'C' selection = chain 'c' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.790 Find NCS groups from input model: 0.530 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.003 0.057 21574 Z= 0.126 Angle : 0.763 27.016 29238 Z= 0.279 Chirality : 0.041 0.239 3268 Planarity : 0.004 0.102 3693 Dihedral : 14.728 178.274 8149 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.13 % Allowed : 0.31 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2669 helix: 1.33 (0.15), residues: 1180 sheet: -0.59 (0.30), residues: 318 loop : -0.68 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG b 121 TYR 0.021 0.001 TYR B 97 PHE 0.033 0.001 PHE B 96 TRP 0.005 0.001 TRP b 344 HIS 0.006 0.001 HIS a 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (21490) covalent geometry : angle 0.51665 / 0.28 (29052) hydrogen bonds : bond 0.16675 / 11.05 ( 959) hydrogen bonds : angle 6.33704 / 4.51 ( 2692) metal coordination : bond 0.00931 / 0.63 ( 84) metal coordination : angle 7.05120 / 4.73 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 393 time to evaluate : 0.563 Fit side-chains REVERT: b 340 GLN cc_start: 0.7473 (mp10) cc_final: 0.7249 (mm-40) REVERT: b 513 GLU cc_start: 0.6874 (mp0) cc_final: 0.6661 (mp0) REVERT: c 34 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7639 (mtp85) REVERT: c 38 GLU cc_start: 0.6973 (tt0) cc_final: 0.6746 (tm-30) REVERT: A 35 TYR cc_start: 0.7432 (t80) cc_final: 0.7231 (t80) REVERT: B 238 LEU cc_start: 0.8647 (tt) cc_final: 0.8406 (tt) REVERT: B 493 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 570 LYS cc_start: 0.5458 (ttmm) cc_final: 0.5159 (tptp) REVERT: B 623 ILE cc_start: 0.6521 (mm) cc_final: 0.6313 (mm) outliers start: 3 outliers final: 0 residues processed: 393 average time/residue: 0.7168 time to fit residues: 315.5127 Evaluate side-chains 319 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 507 HIS A 53 ASN A 483 ASN B 520 HIS C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.155640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126238 restraints weight = 32720.948| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.73 r_work: 0.2900 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21574 Z= 0.135 Angle : 0.820 29.304 29238 Z= 0.302 Chirality : 0.045 0.171 3268 Planarity : 0.005 0.060 3693 Dihedral : 6.324 178.569 2954 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.28 % Allowed : 9.06 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2669 helix: 1.34 (0.15), residues: 1185 sheet: -0.49 (0.30), residues: 312 loop : -0.51 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.015 0.001 TYR B 97 PHE 0.036 0.001 PHE B 96 TRP 0.011 0.001 TRP B 208 HIS 0.004 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21490) covalent geometry : angle 0.57372 / 0.30 (29052) hydrogen bonds : bond 0.04550 / 3.04 ( 959) hydrogen bonds : angle 5.09007 / 3.62 ( 2692) metal coordination : bond 0.01023 / 0.64 ( 84) metal coordination : angle 7.36627 / 5.00 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 0.915 Fit side-chains REVERT: a 120 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7163 (mtm180) REVERT: a 170 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: a 532 GLU cc_start: 0.6345 (mm-30) cc_final: 0.6066 (pt0) REVERT: b 340 GLN cc_start: 0.7710 (mp10) cc_final: 0.7473 (mm-40) REVERT: c 38 GLU cc_start: 0.7595 (tt0) cc_final: 0.7180 (tm-30) REVERT: A 35 TYR cc_start: 0.8218 (t80) cc_final: 0.7646 (t80) REVERT: B 91 MET cc_start: 0.5205 (mmp) cc_final: 0.4400 (mmp) REVERT: B 242 ASP cc_start: 0.7776 (m-30) cc_final: 0.7020 (t0) REVERT: B 292 GLU cc_start: 0.5688 (tt0) cc_final: 0.5363 (pm20) REVERT: B 364 ARG cc_start: 0.6837 (tmm160) cc_final: 0.6446 (tmm-80) REVERT: B 405 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6711 (ttt90) REVERT: B 570 LYS cc_start: 0.5534 (ttmm) cc_final: 0.4968 (tptp) REVERT: B 603 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5922 (tt) REVERT: C 28 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6906 (mm-30) REVERT: C 76 MET cc_start: 0.7817 (mtt) cc_final: 0.7387 (ptp) outliers start: 29 outliers final: 10 residues processed: 353 average time/residue: 0.7038 time to fit residues: 279.6091 Evaluate side-chains 320 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 174 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 138 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 185 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.155675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.130421 restraints weight = 42848.925| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.97 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21574 Z= 0.113 Angle : 0.785 31.225 29238 Z= 0.277 Chirality : 0.043 0.147 3268 Planarity : 0.004 0.062 3693 Dihedral : 6.319 178.992 2954 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.67 % Allowed : 10.91 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2669 helix: 1.46 (0.15), residues: 1185 sheet: -0.43 (0.29), residues: 311 loop : -0.46 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 333 TYR 0.014 0.001 TYR b 11 PHE 0.014 0.001 PHE b 202 TRP 0.008 0.001 TRP B 208 HIS 0.006 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (21490) covalent geometry : angle 0.53334 / 0.27 (29052) hydrogen bonds : bond 0.03869 / 2.57 ( 959) hydrogen bonds : angle 4.75753 / 3.38 ( 2692) metal coordination : bond 0.00908 / 0.55 ( 84) metal coordination : angle 7.24553 / 4.90 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 335 time to evaluate : 0.878 Fit side-chains REVERT: a 120 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6857 (mtm180) REVERT: a 170 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: a 533 ASP cc_start: 0.7239 (m-30) cc_final: 0.6908 (m-30) REVERT: b 95 PHE cc_start: 0.7207 (m-10) cc_final: 0.6944 (m-80) REVERT: b 316 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: b 340 GLN cc_start: 0.7511 (mp10) cc_final: 0.7246 (mm-40) REVERT: b 436 GLU cc_start: 0.5217 (pm20) cc_final: 0.5003 (pm20) REVERT: b 439 ILE cc_start: 0.6875 (mm) cc_final: 0.6188 (tt) REVERT: c 31 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: c 38 GLU cc_start: 0.7132 (tt0) cc_final: 0.6727 (tm-30) REVERT: A 35 TYR cc_start: 0.7450 (t80) cc_final: 0.7162 (t80) REVERT: A 163 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: A 469 GLU cc_start: 0.6128 (tt0) cc_final: 0.5915 (pt0) REVERT: B 96 PHE cc_start: 0.6109 (t80) cc_final: 0.5586 (t80) REVERT: B 237 THR cc_start: 0.8432 (m) cc_final: 0.8224 (t) REVERT: B 242 ASP cc_start: 0.7312 (m-30) cc_final: 0.6540 (t0) REVERT: B 365 ASP cc_start: 0.6012 (m-30) cc_final: 0.5775 (m-30) REVERT: B 405 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6603 (ttt90) REVERT: B 493 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 570 LYS cc_start: 0.5308 (ttmm) cc_final: 0.5013 (tptp) REVERT: B 603 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6411 (tt) REVERT: C 28 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6335 (mm-30) REVERT: C 136 TYR cc_start: 0.7581 (m-80) cc_final: 0.7191 (m-80) outliers start: 38 outliers final: 14 residues processed: 356 average time/residue: 0.7071 time to fit residues: 284.2505 Evaluate side-chains 335 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130033 restraints weight = 41522.466| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.90 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21574 Z= 0.124 Angle : 0.794 32.878 29238 Z= 0.280 Chirality : 0.043 0.157 3268 Planarity : 0.005 0.065 3693 Dihedral : 6.357 179.317 2954 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.29 % Allowed : 12.14 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2669 helix: 1.47 (0.15), residues: 1185 sheet: -0.41 (0.29), residues: 311 loop : -0.47 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 333 TYR 0.015 0.001 TYR a 459 PHE 0.015 0.001 PHE C 112 TRP 0.006 0.001 TRP b 344 HIS 0.005 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (21490) covalent geometry : angle 0.53822 / 0.28 (29052) hydrogen bonds : bond 0.03885 / 2.57 ( 959) hydrogen bonds : angle 4.67697 / 3.32 ( 2692) metal coordination : bond 0.01023 / 0.61 ( 84) metal coordination : angle 7.34395 / 4.94 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 0.784 Fit side-chains REVERT: a 170 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: a 533 ASP cc_start: 0.7219 (m-30) cc_final: 0.6944 (m-30) REVERT: b 95 PHE cc_start: 0.7178 (m-10) cc_final: 0.6769 (m-10) REVERT: b 316 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: b 340 GLN cc_start: 0.7524 (mp10) cc_final: 0.7254 (mm-40) REVERT: b 433 CYS cc_start: 0.7764 (t) cc_final: 0.6151 (p) REVERT: b 436 GLU cc_start: 0.5168 (pm20) cc_final: 0.4956 (pm20) REVERT: b 439 ILE cc_start: 0.6897 (mm) cc_final: 0.6212 (tt) REVERT: c 31 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: c 38 GLU cc_start: 0.7187 (tt0) cc_final: 0.6745 (tm-30) REVERT: A 35 TYR cc_start: 0.7468 (t80) cc_final: 0.6955 (t80) REVERT: A 163 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: A 403 GLN cc_start: 0.6815 (mt0) cc_final: 0.6601 (mt0) REVERT: A 469 GLU cc_start: 0.6152 (tt0) cc_final: 0.5918 (pt0) REVERT: B 50 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: B 96 PHE cc_start: 0.6139 (t80) cc_final: 0.5694 (t80) REVERT: B 237 THR cc_start: 0.8462 (m) cc_final: 0.8241 (t) REVERT: B 242 ASP cc_start: 0.7364 (m-30) cc_final: 0.6618 (t70) REVERT: B 405 ARG cc_start: 0.6965 (ttm-80) cc_final: 0.6525 (ttt180) REVERT: B 493 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7646 (mp0) REVERT: B 570 LYS cc_start: 0.5363 (ttmm) cc_final: 0.5058 (tptp) REVERT: B 603 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6414 (tt) REVERT: C 28 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: C 136 TYR cc_start: 0.7570 (m-80) cc_final: 0.7079 (m-80) outliers start: 52 outliers final: 23 residues processed: 361 average time/residue: 0.6522 time to fit residues: 265.4214 Evaluate side-chains 344 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 406 LEU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 506 THR Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 184 optimal weight: 0.0050 chunk 91 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.153309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127870 restraints weight = 40387.711| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.84 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21574 Z= 0.164 Angle : 0.848 36.897 29238 Z= 0.306 Chirality : 0.045 0.153 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.529 179.727 2954 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 12.80 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2669 helix: 1.34 (0.15), residues: 1191 sheet: -0.44 (0.29), residues: 311 loop : -0.62 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 333 TYR 0.020 0.002 TYR a 459 PHE 0.012 0.002 PHE a 236 TRP 0.006 0.001 TRP b 344 HIS 0.004 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (21490) covalent geometry : angle 0.58990 / 0.30 (29052) hydrogen bonds : bond 0.04389 / 2.89 ( 959) hydrogen bonds : angle 4.80909 / 3.42 ( 2692) metal coordination : bond 0.01298 / 0.77 ( 84) metal coordination : angle 7.65419 / 5.11 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6529 (tpp) REVERT: a 170 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: a 215 GLU cc_start: 0.7529 (tt0) cc_final: 0.7260 (tt0) REVERT: a 533 ASP cc_start: 0.7210 (m-30) cc_final: 0.6876 (m-30) REVERT: b 95 PHE cc_start: 0.7188 (m-10) cc_final: 0.6891 (m-80) REVERT: b 316 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: b 340 GLN cc_start: 0.7569 (mp10) cc_final: 0.7282 (mm-40) REVERT: b 433 CYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6487 (p) REVERT: c 31 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: c 38 GLU cc_start: 0.7238 (tt0) cc_final: 0.6802 (tm-30) REVERT: A 35 TYR cc_start: 0.7424 (t80) cc_final: 0.7107 (t80) REVERT: A 163 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: B 50 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: B 242 ASP cc_start: 0.7426 (m-30) cc_final: 0.6705 (t70) REVERT: B 493 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7462 (mt-10) REVERT: B 570 LYS cc_start: 0.5474 (ttmm) cc_final: 0.5178 (tptp) REVERT: B 603 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6579 (tt) REVERT: C 28 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: C 136 TYR cc_start: 0.7651 (m-80) cc_final: 0.7170 (m-80) outliers start: 59 outliers final: 28 residues processed: 345 average time/residue: 0.6486 time to fit residues: 252.2339 Evaluate side-chains 341 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 406 LEU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 582 THR Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 506 THR Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 116 GLN Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN A 403 GLN C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.152363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120573 restraints weight = 27559.536| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.47 r_work: 0.2859 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21574 Z= 0.219 Angle : 0.909 40.307 29238 Z= 0.341 Chirality : 0.047 0.161 3268 Planarity : 0.006 0.068 3693 Dihedral : 6.732 179.953 2954 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 2.59 % Allowed : 13.63 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2669 helix: 1.05 (0.15), residues: 1191 sheet: -0.57 (0.29), residues: 313 loop : -0.75 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 333 TYR 0.022 0.002 TYR a 459 PHE 0.019 0.002 PHE b 8 TRP 0.007 0.002 TRP b 344 HIS 0.004 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (21490) covalent geometry : angle 0.65336 / 0.34 (29052) hydrogen bonds : bond 0.04948 / 3.25 ( 959) hydrogen bonds : angle 4.99663 / 3.55 ( 2692) metal coordination : bond 0.01645 / 0.98 ( 84) metal coordination : angle 7.95824 / 5.30 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: a 170 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: a 533 ASP cc_start: 0.7456 (m-30) cc_final: 0.7082 (m-30) REVERT: a 560 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5936 (mm-30) REVERT: a 602 GLU cc_start: 0.5691 (mp0) cc_final: 0.5026 (mp0) REVERT: b 95 PHE cc_start: 0.7069 (m-10) cc_final: 0.6829 (m-80) REVERT: b 316 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: b 340 GLN cc_start: 0.7704 (mp10) cc_final: 0.7441 (mm-40) REVERT: b 433 CYS cc_start: 0.8119 (OUTLIER) cc_final: 0.6708 (p) REVERT: c 31 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: c 38 GLU cc_start: 0.7725 (tt0) cc_final: 0.7255 (tm-30) REVERT: A 35 TYR cc_start: 0.8176 (t80) cc_final: 0.7838 (t80) REVERT: A 163 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 50 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: B 148 TYR cc_start: 0.7878 (t80) cc_final: 0.7589 (t80) REVERT: B 441 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5579 (ttt) REVERT: B 493 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8091 (mt-10) REVERT: B 570 LYS cc_start: 0.5596 (ttmm) cc_final: 0.5009 (tptp) REVERT: C 28 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: C 90 GLU cc_start: 0.6769 (pt0) cc_final: 0.6569 (pt0) REVERT: C 136 TYR cc_start: 0.7760 (m-80) cc_final: 0.7223 (m-80) outliers start: 59 outliers final: 37 residues processed: 341 average time/residue: 0.6817 time to fit residues: 262.2452 Evaluate side-chains 340 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 406 LEU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 517 LEU Chi-restraints excluded: chain a residue 519 THR Chi-restraints excluded: chain a residue 582 THR Chi-restraints excluded: chain a residue 592 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 294 ILE Chi-restraints excluded: chain b residue 302 ASP Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 506 THR Chi-restraints excluded: chain b residue 516 LYS Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 116 GLN Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 177 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN A 403 GLN B 340 GLN C 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124476 restraints weight = 34930.583| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.90 r_work: 0.2827 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21574 Z= 0.126 Angle : 0.809 33.224 29238 Z= 0.288 Chirality : 0.043 0.148 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.528 179.731 2954 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.73 % Allowed : 14.56 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2669 helix: 1.32 (0.15), residues: 1186 sheet: -0.44 (0.29), residues: 309 loop : -0.68 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 333 TYR 0.015 0.001 TYR b 11 PHE 0.015 0.001 PHE b 8 TRP 0.008 0.001 TRP b 344 HIS 0.003 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21490) covalent geometry : angle 0.55336 / 0.28 (29052) hydrogen bonds : bond 0.03950 / 2.61 ( 959) hydrogen bonds : angle 4.73815 / 3.36 ( 2692) metal coordination : bond 0.01042 / 0.61 ( 84) metal coordination : angle 7.41999 / 4.98 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: a 170 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: a 506 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (ttpp) REVERT: a 532 GLU cc_start: 0.6966 (pt0) cc_final: 0.6760 (pt0) REVERT: a 533 ASP cc_start: 0.7445 (m-30) cc_final: 0.7089 (m-30) REVERT: a 602 GLU cc_start: 0.5690 (mp0) cc_final: 0.5033 (mp0) REVERT: b 95 PHE cc_start: 0.7016 (m-10) cc_final: 0.6779 (m-80) REVERT: b 340 GLN cc_start: 0.7721 (mp10) cc_final: 0.7486 (mm-40) REVERT: b 433 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.6746 (p) REVERT: b 436 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: c 31 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: c 38 GLU cc_start: 0.7759 (tt0) cc_final: 0.7323 (tm-30) REVERT: A 35 TYR cc_start: 0.8275 (t80) cc_final: 0.7641 (t80) REVERT: A 55 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7505 (mm110) REVERT: A 163 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: B 17 THR cc_start: 0.5889 (t) cc_final: 0.5632 (p) REVERT: B 18 LEU cc_start: 0.5929 (tm) cc_final: 0.5469 (mt) REVERT: B 50 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: B 148 TYR cc_start: 0.7816 (t80) cc_final: 0.7536 (t80) REVERT: B 405 ARG cc_start: 0.7168 (ttm-80) cc_final: 0.6761 (ttt180) REVERT: B 493 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8144 (mt-10) REVERT: B 570 LYS cc_start: 0.5540 (ttmm) cc_final: 0.5000 (tptp) REVERT: C 28 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: C 136 TYR cc_start: 0.7738 (m-80) cc_final: 0.7364 (m-80) outliers start: 62 outliers final: 33 residues processed: 346 average time/residue: 0.6399 time to fit residues: 249.3815 Evaluate side-chains 346 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 506 LYS Chi-restraints excluded: chain a residue 519 THR Chi-restraints excluded: chain a residue 592 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 436 GLU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 516 LYS Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 46 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 218 optimal weight: 0.0050 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.153742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122910 restraints weight = 34023.012| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.92 r_work: 0.2832 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21574 Z= 0.136 Angle : 0.816 32.579 29238 Z= 0.293 Chirality : 0.043 0.160 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.523 179.814 2954 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.46 % Allowed : 15.04 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2669 helix: 1.32 (0.15), residues: 1188 sheet: -0.43 (0.29), residues: 307 loop : -0.67 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 333 TYR 0.016 0.001 TYR a 459 PHE 0.012 0.001 PHE b 8 TRP 0.007 0.001 TRP b 344 HIS 0.004 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21490) covalent geometry : angle 0.56693 / 0.29 (29052) hydrogen bonds : bond 0.04047 / 2.66 ( 959) hydrogen bonds : angle 4.72210 / 3.35 ( 2692) metal coordination : bond 0.01133 / 0.67 ( 84) metal coordination : angle 7.37378 / 4.95 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 310 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: a 170 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: a 506 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (ttpp) REVERT: a 533 ASP cc_start: 0.7437 (m-30) cc_final: 0.7066 (m-30) REVERT: a 602 GLU cc_start: 0.5763 (mp0) cc_final: 0.5101 (mp0) REVERT: b 95 PHE cc_start: 0.7034 (m-10) cc_final: 0.6831 (m-80) REVERT: b 340 GLN cc_start: 0.7718 (mp10) cc_final: 0.7478 (mm-40) REVERT: b 420 GLU cc_start: 0.6987 (mp0) cc_final: 0.6768 (mp0) REVERT: b 433 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.6908 (p) REVERT: c 31 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: c 38 GLU cc_start: 0.7751 (tt0) cc_final: 0.7301 (tm-30) REVERT: A 35 TYR cc_start: 0.8275 (t80) cc_final: 0.7640 (t80) REVERT: A 163 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: A 506 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7753 (tmmt) REVERT: B 18 LEU cc_start: 0.5884 (tm) cc_final: 0.5480 (mt) REVERT: B 50 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: B 148 TYR cc_start: 0.7847 (t80) cc_final: 0.7570 (t80) REVERT: B 405 ARG cc_start: 0.7210 (ttm-80) cc_final: 0.6833 (ttt90) REVERT: B 493 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8152 (mt-10) REVERT: B 570 LYS cc_start: 0.5545 (ttmm) cc_final: 0.4981 (tptp) REVERT: C 28 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: C 136 TYR cc_start: 0.7740 (m-80) cc_final: 0.7318 (m-80) outliers start: 56 outliers final: 37 residues processed: 341 average time/residue: 0.6855 time to fit residues: 263.0780 Evaluate side-chains 344 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 506 LYS Chi-restraints excluded: chain a residue 519 THR Chi-restraints excluded: chain a residue 588 ILE Chi-restraints excluded: chain a residue 592 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 516 LYS Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 116 GLN Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 220 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122887 restraints weight = 27040.149| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.53 r_work: 0.2865 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21574 Z= 0.138 Angle : 0.816 32.204 29238 Z= 0.294 Chirality : 0.044 0.170 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.529 179.883 2954 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.29 % Allowed : 15.48 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2669 helix: 1.31 (0.15), residues: 1188 sheet: -0.42 (0.29), residues: 307 loop : -0.66 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 333 TYR 0.018 0.001 TYR b 11 PHE 0.018 0.001 PHE b 8 TRP 0.007 0.001 TRP b 344 HIS 0.003 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21490) covalent geometry : angle 0.56903 / 0.29 (29052) hydrogen bonds : bond 0.04028 / 2.65 ( 959) hydrogen bonds : angle 4.71874 / 3.35 ( 2692) metal coordination : bond 0.01138 / 0.67 ( 84) metal coordination : angle 7.35123 / 4.94 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 170 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8007 (mm-30) REVERT: a 506 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8155 (ttpp) REVERT: a 533 ASP cc_start: 0.7360 (m-30) cc_final: 0.6994 (m-30) REVERT: a 602 GLU cc_start: 0.5708 (mp0) cc_final: 0.5059 (mp0) REVERT: b 52 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5463 (mt) REVERT: b 91 MET cc_start: 0.5768 (mmm) cc_final: 0.5555 (mmm) REVERT: b 287 LEU cc_start: 0.7923 (mt) cc_final: 0.7539 (tp) REVERT: b 340 GLN cc_start: 0.7668 (mp10) cc_final: 0.7410 (mm-40) REVERT: b 420 GLU cc_start: 0.6954 (mp0) cc_final: 0.6734 (mp0) REVERT: b 433 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.6886 (p) REVERT: b 568 PHE cc_start: 0.2610 (OUTLIER) cc_final: 0.1702 (p90) REVERT: c 31 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: c 38 GLU cc_start: 0.7652 (tt0) cc_final: 0.7192 (tm-30) REVERT: A 35 TYR cc_start: 0.8212 (t80) cc_final: 0.7580 (t80) REVERT: A 163 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: A 506 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7636 (tmmt) REVERT: B 18 LEU cc_start: 0.5889 (tm) cc_final: 0.5497 (mt) REVERT: B 50 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6321 (tm-30) REVERT: B 148 TYR cc_start: 0.7778 (t80) cc_final: 0.7502 (t80) REVERT: B 405 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6730 (ttt90) REVERT: B 493 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8037 (mt-10) REVERT: B 570 LYS cc_start: 0.5462 (ttmm) cc_final: 0.4837 (tptp) REVERT: C 28 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: C 136 TYR cc_start: 0.7711 (m-80) cc_final: 0.7285 (m-80) outliers start: 52 outliers final: 36 residues processed: 332 average time/residue: 0.6934 time to fit residues: 259.6096 Evaluate side-chains 340 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 406 LEU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 506 LYS Chi-restraints excluded: chain a residue 519 THR Chi-restraints excluded: chain a residue 592 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 516 LYS Chi-restraints excluded: chain b residue 568 PHE Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 260 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 159 optimal weight: 0.0020 chunk 255 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 621 ASN b 99 ASN b 352 ASN b 507 HIS A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.155828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130187 restraints weight = 39143.708| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.71 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21574 Z= 0.124 Angle : 0.800 30.067 29238 Z= 0.288 Chirality : 0.043 0.169 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.486 179.839 2954 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.07 % Allowed : 15.92 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 2669 helix: 1.38 (0.15), residues: 1186 sheet: -0.54 (0.29), residues: 297 loop : -0.59 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 333 TYR 0.020 0.001 TYR b 11 PHE 0.014 0.001 PHE b 95 TRP 0.007 0.001 TRP b 344 HIS 0.003 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (21490) covalent geometry : angle 0.55857 / 0.28 (29052) hydrogen bonds : bond 0.03840 / 2.53 ( 959) hydrogen bonds : angle 4.66174 / 3.30 ( 2692) metal coordination : bond 0.01032 / 0.60 ( 84) metal coordination : angle 7.19845 / 4.86 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 120 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6553 (mtm110) REVERT: a 170 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: a 506 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (ttpp) REVERT: a 533 ASP cc_start: 0.7170 (m-30) cc_final: 0.6891 (m-30) REVERT: a 602 GLU cc_start: 0.5751 (mp0) cc_final: 0.5362 (mp0) REVERT: b 52 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5884 (mt) REVERT: b 340 GLN cc_start: 0.7522 (mp10) cc_final: 0.7249 (mm-40) REVERT: b 433 CYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6687 (p) REVERT: b 568 PHE cc_start: 0.2488 (OUTLIER) cc_final: 0.1919 (p90) REVERT: c 31 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: c 38 GLU cc_start: 0.7161 (tt0) cc_final: 0.6732 (tm-30) REVERT: c 115 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6505 (t0) REVERT: A 35 TYR cc_start: 0.7526 (t80) cc_final: 0.6985 (t80) REVERT: A 163 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: B 18 LEU cc_start: 0.5869 (tm) cc_final: 0.5329 (mt) REVERT: B 50 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: B 405 ARG cc_start: 0.6963 (ttm-80) cc_final: 0.6543 (ttt180) REVERT: B 493 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7461 (mt-10) REVERT: B 570 LYS cc_start: 0.5366 (ttmm) cc_final: 0.5051 (tptp) REVERT: C 28 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6493 (mm-30) REVERT: C 136 TYR cc_start: 0.7567 (m-80) cc_final: 0.7239 (m-80) outliers start: 47 outliers final: 32 residues processed: 328 average time/residue: 0.7061 time to fit residues: 261.6755 Evaluate side-chains 335 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 170 GLU Chi-restraints excluded: chain a residue 434 LYS Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 506 LYS Chi-restraints excluded: chain a residue 519 THR Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 181 THR Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 516 LYS Chi-restraints excluded: chain b residue 568 PHE Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 51 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 246 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 99 ASN b 352 ASN b 507 HIS ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 503 HIS B 13 ASN C 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125345 restraints weight = 35564.506| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.87 r_work: 0.2852 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21574 Z= 0.126 Angle : 0.801 31.173 29238 Z= 0.288 Chirality : 0.043 0.173 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.489 179.874 2954 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.07 % Allowed : 16.23 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2669 helix: 1.39 (0.15), residues: 1186 sheet: -0.57 (0.29), residues: 297 loop : -0.57 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 333 TYR 0.015 0.001 TYR a 459 PHE 0.016 0.001 PHE b 8 TRP 0.007 0.001 TRP b 344 HIS 0.003 0.001 HIS a 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21490) covalent geometry : angle 0.55903 / 0.28 (29052) hydrogen bonds : bond 0.03874 / 2.56 ( 959) hydrogen bonds : angle 4.67433 / 3.31 ( 2692) metal coordination : bond 0.01053 / 0.62 ( 84) metal coordination : angle 7.21447 / 4.88 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7240.88 seconds wall clock time: 124 minutes 21.94 seconds (7461.94 seconds total)