Starting phenix.real_space_refine on Thu Feb 5 23:43:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.map" model { file = "/net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p8n_13254/02_2026/7p8n_13254.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 4315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21429 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} 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 612 124.885 39.782 33.770 1.00 25.96 S ATOM 4848 SG CYS a 616 127.544 39.845 31.247 1.00 37.67 S ATOM 4528 SG CYS a 575 121.419 41.034 29.776 1.00 27.90 S ATOM 4559 SG CYS a 580 123.549 40.460 27.152 1.00 29.31 S ATOM 2305 SG CYS a 295 106.089 36.726 69.357 1.00 15.91 S ATOM 2747 SG CYS a 350 100.499 39.217 67.852 1.00 7.29 S ATOM 3765 SG CYS a 482 104.648 42.743 70.351 1.00 10.99 S ATOM 3795 SG CYS a 486 101.706 37.870 74.055 1.00 15.91 S ATOM 1504 SG CYS a 192 104.341 49.015 62.054 1.00 15.91 S ATOM 1485 SG CYS a 189 106.700 44.391 65.368 1.00 15.91 S ATOM 1211 SG CYS a 153 110.474 47.389 61.088 1.00 15.91 S ATOM 1464 SG CYS a 186 105.555 43.525 59.016 1.00 15.91 S ATOM 1180 SG CYS a 149 107.130 54.546 60.283 1.00 15.91 S ATOM 1162 SG CYS a 146 106.254 59.955 63.359 1.00 15.91 S ATOM 1534 SG CYS a 196 101.403 56.033 62.322 1.00 15.91 S ATOM 1140 SG CYS a 143 104.370 59.202 57.129 1.00 15.91 S ATOM 782 SG CYS a 99 93.051 58.411 61.202 1.00 15.91 S ATOM 825 SG CYS a 105 95.818 62.943 64.526 1.00 15.91 S ATOM 762 SG CYS a 96 90.205 64.074 60.976 1.00 15.91 S ATOM 377 SG CYS a 48 110.919 73.607 68.865 1.00 8.03 S ATOM 464 SG CYS a 60 113.445 71.097 68.675 1.00 9.64 S ATOM 271 SG CYS a 34 109.782 67.568 66.073 1.00 10.65 S ATOM 352 SG CYS a 45 107.711 70.555 65.817 1.00 9.05 S ATOM 8710 SG CYS b 488 112.865 71.615 57.421 1.00 15.91 S ATOM 9049 SG CYS b 531 119.226 72.360 55.094 1.00 8.60 S ATOM 8730 SG CYS b 491 113.426 72.513 52.140 1.00 7.95 S ATOM 8691 SG CYS b 485 116.282 66.955 54.254 1.00 10.90 S ATOM 5293 SG CYS b 31 140.977 74.631 28.418 1.00 25.45 S ATOM 5321 SG CYS b 36 138.256 75.197 26.117 1.00 22.66 S ATOM 5564 SG CYS b 78 138.559 77.537 32.284 1.00 26.39 S ATOM 5591 SG CYS b 82 135.688 78.140 30.361 1.00 25.23 S ATOM 8547 SG CYS b 468 107.950 86.811 33.734 1.00 24.14 S ATOM 9273 SG CYS b 560 105.738 88.138 30.755 1.00 29.92 S ATOM 9304 SG CYS b 565 105.244 84.568 31.827 1.00 35.14 S ATOM 10272 SG CYS c 119 127.342 74.915 34.187 1.00 16.80 S ATOM 10295 SG CYS c 123 127.438 77.757 32.315 1.00 17.53 S ATOM 9978 SG CYS c 78 122.814 72.832 32.136 1.00 16.06 S ATOM 10008 SG CYS c 83 122.747 75.263 29.544 1.00 14.34 S ATOM 13333 SG CYS A 350 75.529 89.170 68.625 1.00 9.05 S ATOM 12891 SG CYS A 295 70.013 91.657 70.143 1.00 15.91 S ATOM 14381 SG CYS A 486 74.424 90.398 74.911 1.00 15.91 S ATOM 14351 SG CYS A 482 71.392 85.679 71.110 1.00 8.10 S ATOM 12071 SG CYS A 189 69.413 84.306 65.952 1.00 15.91 S ATOM 11797 SG CYS A 153 65.547 81.240 61.726 1.00 15.91 S ATOM 12090 SG CYS A 192 71.678 79.566 62.624 1.00 15.91 S ATOM 12050 SG CYS A 186 70.507 85.185 59.759 1.00 8.39 S ATOM 11766 SG CYS A 149 68.824 73.959 60.679 1.00 15.91 S ATOM 11748 SG CYS A 146 69.818 68.467 63.572 1.00 15.91 S ATOM 12120 SG CYS A 196 74.642 72.498 62.624 1.00 15.91 S ATOM 11726 SG CYS A 143 71.666 69.405 57.433 1.00 15.91 S ATOM 11357 SG CYS A 99 82.982 70.203 61.560 1.00 15.91 S ATOM 11400 SG CYS A 105 80.135 65.556 64.661 1.00 9.57 S ATOM 11337 SG CYS A 96 85.770 64.538 61.159 1.00 15.91 S ATOM 10952 SG CYS A 48 65.178 54.864 68.765 1.00 7.18 S ATOM 11039 SG CYS A 60 62.624 57.298 68.539 1.00 9.62 S ATOM 10846 SG CYS A 34 66.127 60.972 66.048 1.00 8.57 S ATOM 10927 SG CYS A 45 68.323 57.972 65.757 1.00 15.91 S ATOM 19574 SG CYS B 611 80.518 38.128 22.983 1.00 41.48 S ATOM 19592 SG CYS B 614 84.972 41.775 23.914 1.00 42.78 S ATOM 19552 SG CYS B 608 79.973 44.499 20.481 1.00 46.78 S ATOM 19396 SG CYS B 588 84.882 40.121 19.035 1.00 46.86 S ATOM 19331 SG CYS B 578 92.846 48.457 26.763 1.00 39.30 S ATOM 19368 SG CYS B 584 89.907 42.854 24.733 1.00 41.80 S ATOM 19618 SG CYS B 618 89.860 43.884 30.427 1.00 37.33 S ATOM 19350 SG CYS B 581 95.477 42.512 27.882 1.00 36.75 S ATOM 18632 SG CYS B 488 63.100 56.999 57.364 1.00 15.91 S ATOM 18971 SG CYS B 531 56.736 56.421 55.254 1.00 11.57 S ATOM 18652 SG CYS B 491 62.526 56.300 52.200 1.00 8.03 S ATOM 18613 SG CYS B 485 59.630 61.860 54.383 1.00 12.35 S ATOM 15207 SG CYS B 31 35.147 55.260 28.390 1.00 29.62 S ATOM 15235 SG CYS B 36 37.663 54.106 26.007 1.00 25.86 S ATOM 15478 SG CYS B 78 37.125 51.767 32.347 1.00 29.61 S ATOM 15505 SG CYS B 82 39.966 51.461 30.263 1.00 28.73 S ATOM 18469 SG CYS B 468 67.496 42.585 33.975 1.00 19.59 S ATOM 19195 SG CYS B 560 69.184 41.481 30.661 1.00 26.65 S ATOM 19226 SG CYS B 565 69.823 45.010 32.129 1.00 28.40 S ATOM 20582 SG CYS C 119 48.819 54.385 34.257 1.00 18.54 S ATOM 20605 SG CYS C 123 48.689 51.768 32.080 1.00 21.69 S ATOM 20288 SG CYS C 78 53.022 56.794 31.810 1.00 18.80 S ATOM 20318 SG CYS C 83 53.401 54.446 29.318 1.00 17.27 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: 6.91, per 1000 atoms: 0.32 Number of scatterers: 21429 At special positions: 0 Unit cell: (177.984, 129.368, 103.824, 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 4315 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.3 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 82 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 36 " pdb="FE2 FES B 705 " - pdb=" SG CYS B 78 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 31 " pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " 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="FE2 FES a 706 " - pdb=" SG CYS a 34 " pdb="FE1 FES a 706 " - pdb=" SG CYS a 60 " pdb=" FES b 703 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 78 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 82 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 36 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 31 " pdb=" FES c 201 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 83 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 78 " 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="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 189 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 153 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 192 " pdb=" SF4 A 703 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 149 " 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="FE2 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 105 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 99 " pdb=" SF4 B 701 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 614 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 611 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 588 " 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="FE4 SF4 B 703 " - pdb=" SG CYS B 485 " pdb="FE1 SF4 B 703 " - pdb=" SG CYS B 488 " pdb="FE2 SF4 B 703 " - pdb=" SG CYS B 531 " pdb="FE3 SF4 B 703 " - pdb=" SG CYS B 491 " pdb=" SF4 a 702 " pdb="FE2 SF4 a 702 " - pdb=" SG CYS a 350 " pdb="FE3 SF4 a 702 " - pdb=" SG CYS a 482 " pdb="FE1 SF4 a 702 " - pdb=" SG CYS a 295 " pdb="FE4 SF4 a 702 " - pdb=" SG CYS a 486 " pdb=" SF4 a 703 " pdb="FE4 SF4 a 703 " - pdb=" SG CYS a 186 " pdb="FE2 SF4 a 703 " - pdb=" SG CYS a 189 " pdb="FE1 SF4 a 703 " - pdb=" SG CYS a 192 " pdb="FE3 SF4 a 703 " - pdb=" SG CYS a 153 " pdb=" SF4 a 704 " pdb="FE1 SF4 a 704 " - pdb=" SG CYS a 149 " pdb="FE4 SF4 a 704 " - pdb=" SG CYS a 143 " 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="FE4 SF4 b 701 " - pdb=" SG CYS b 485 " pdb="FE1 SF4 b 701 " - pdb=" SG CYS b 488 " pdb="FE2 SF4 b 701 " - pdb=" SG CYS b 531 " pdb="FE3 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 565 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 560 " 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: 138 helices and 21 sheets defined 51.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'a' and resid 18 through 27 Processing helix chain 'a' and resid 74 through 91 removed outlier: 3.965A 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 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 removed outlier: 3.572A pdb=" N LEU a 210 " --> pdb=" O ASP a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 235 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: 3.556A 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: 4.464A pdb=" N ALA a 332 " --> pdb=" O LYS a 328 " (cutoff:3.500A) removed outlier: 4.777A 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: 3.716A pdb=" N PHE a 355 " --> pdb=" O THR a 351 " (cutoff:3.500A) Processing helix chain 'a' and resid 359 through 363 Processing helix chain 'a' and resid 372 through 383 removed outlier: 3.564A pdb=" N SER a 382 " --> pdb=" O LEU a 378 " (cutoff:3.500A) 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 463 through 471 removed outlier: 3.500A pdb=" N PHE a 467 " --> pdb=" O LYS a 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 484 through 489 removed outlier: 4.220A pdb=" N VAL a 487 " --> pdb=" O TYR a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 497 through 514 removed outlier: 3.719A 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 removed outlier: 3.686A pdb=" N GLU a 640 " --> pdb=" O LYS a 636 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 25 removed outlier: 4.075A pdb=" N PHE b 8 " --> pdb=" O ASN b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 55 Processing helix chain 'b' and resid 104 through 112 Processing helix chain 'b' and resid 119 through 123 Processing helix chain 'b' and resid 135 through 138 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: 3.641A 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 removed outlier: 3.559A pdb=" N THR b 237 " --> pdb=" O PHE b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 257 removed outlier: 3.681A 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 367 through 372 Processing helix chain 'b' and resid 403 through 410 Processing helix chain 'b' and resid 427 through 431 removed outlier: 3.805A 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: 3.708A pdb=" N LYS b 523 " --> pdb=" O GLU b 519 " (cutoff:3.500A) removed outlier: 3.537A 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: 3.551A 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: 3.614A 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: 3.975A 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: 4.005A 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 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 236 removed outlier: 4.260A pdb=" N GLU A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' 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: 3.701A 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 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 removed outlier: 3.586A pdb=" N SER A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) 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: 4.327A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 4.262A pdb=" N VAL A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.726A 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 'B' and resid 4 through 25 removed outlier: 3.797A 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 139 through 145 removed outlier: 3.772A pdb=" N GLN B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.743A pdb=" N TYR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.544A pdb=" N SER B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 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: 3.748A 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 444 through 450 removed outlier: 3.639A pdb=" N LYS B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 484 Processing helix chain 'B' and resid 488 through 506 removed outlier: 3.984A 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: 7.097A pdb=" N GLU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 4.086A pdb=" N PHE B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.855A pdb=" N LYS B 607 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.816A 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: 3.529A pdb=" N SER B 616 " --> pdb=" O GLY B 612 " (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 62 removed outlier: 3.560A pdb=" N ILE C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.569A 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: 4.063A 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: 9.021A pdb=" N VAL a 70 " --> pdb=" O LYS a 2 " (cutoff:3.500A) removed outlier: 6.214A 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: 6.639A pdb=" N VAL a 220 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE a 261 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY a 222 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE a 219 " --> pdb=" O PHE a 343 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL a 345 " --> pdb=" O ILE a 219 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE a 221 " --> pdb=" O VAL a 345 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE a 347 " --> pdb=" O ILE a 221 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET a 223 " --> pdb=" O PHE a 347 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ILE a 368 " --> pdb=" O ILE a 342 " (cutoff:3.500A) removed outlier: 6.617A 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: 6.163A 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: 6.365A pdb=" N GLN a 290 " --> pdb=" O ILE a 477 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL a 479 " --> pdb=" O GLN a 290 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS a 430 " --> pdb=" O THR a 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 559 through 562 removed outlier: 3.652A pdb=" N ILE a 561 " --> pdb=" O VAL a 607 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL a 607 " --> pdb=" O ILE a 561 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL a 572 " --> pdb=" O LEU a 608 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR a 610 " --> pdb=" O VAL a 572 " (cutoff:3.500A) removed outlier: 5.680A 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 removed outlier: 6.112A pdb=" N ILE b 28 " --> pdb=" O ASN b 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR b 76 " --> pdb=" O ILE b 28 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL b 30 " --> pdb=" O THR b 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 124 through 126 removed outlier: 4.082A pdb=" N LEU b 124 " --> pdb=" O VAL b 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU b 131 " --> pdb=" O ASP b 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 302 through 308 removed outlier: 6.503A pdb=" N GLY b 262 " --> pdb=" O GLU b 304 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS b 306 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA b 264 " --> pdb=" O LYS b 306 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY b 308 " --> pdb=" O ALA b 264 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE b 266 " --> pdb=" O GLY b 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 394 through 399 removed outlier: 7.845A pdb=" N ILE b 460 " --> pdb=" O MET b 383 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER b 385 " --> pdb=" O ILE b 460 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL b 462 " --> pdb=" O SER b 385 " (cutoff:3.500A) removed outlier: 7.168A 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 removed outlier: 3.577A pdb=" N SER c 113 " --> pdb=" O TYR c 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 11 removed outlier: 9.067A pdb=" N VAL A 70 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.548A 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 163 through 165 Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.857A pdb=" N VAL A 220 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N PHE A 261 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 222 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 219 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 345 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 221 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE A 347 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET A 223 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE A 368 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU A 370 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 346 " --> pdb=" O LEU A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.287A pdb=" N GLN A 290 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 479 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 440 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER A 435 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 442 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 433 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU A 444 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 431 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 446 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 76 removed outlier: 6.520A pdb=" N VAL B 26 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASN B 74 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE B 28 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 76 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 30 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 124 through 126 removed outlier: 4.340A pdb=" N LEU B 124 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 133 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 294 removed outlier: 4.921A pdb=" N ASN B 293 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE B 299 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 262 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS B 306 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA B 264 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 308 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 266 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 221 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR B 265 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 223 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 8.260A 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 Processing sheet with id=AC3, first strand: chain 'C' and resid 105 through 106 removed outlier: 3.555A pdb=" N ASN C 105 " --> pdb=" O LEU C 114 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2644 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: 4.44 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8687 1.43 - 1.65: 12413 1.65 - 1.86: 218 1.86 - 2.07: 0 2.07 - 2.28: 172 Bond restraints: 21490 Sorted by residual: bond pdb=" C4 FMN B 704 " pdb=" C4A FMN B 704 " ideal model delta sigma weight residual 1.485 1.385 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C4 FMN b 702 " pdb=" C4A FMN b 702 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C4A FMN b 702 " pdb=" N5 FMN b 702 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C4A FMN B 704 " pdb=" N5 FMN B 704 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5' FMN B 704 " pdb=" P FMN B 704 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 21485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 28490 1.56 - 3.12: 434 3.12 - 4.68: 106 4.68 - 6.24: 14 6.24 - 7.80: 8 Bond angle restraints: 29052 Sorted by residual: angle pdb=" O3P FMN b 702 " pdb=" P FMN b 702 " pdb=" O5' FMN b 702 " ideal model delta sigma weight residual 102.33 110.13 -7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" N MET b 91 " pdb=" CA MET b 91 " pdb=" C MET b 91 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.04e+00 angle pdb=" N GLY a 584 " pdb=" CA GLY a 584 " pdb=" C GLY a 584 " ideal model delta sigma weight residual 113.18 118.82 -5.64 2.37e+00 1.78e-01 5.67e+00 angle pdb=" C2 FMN B 704 " pdb=" N3 FMN B 704 " pdb=" C4 FMN B 704 " ideal model delta sigma weight residual 126.69 119.68 7.01 3.00e+00 1.11e-01 5.47e+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 - 17.99: 11751 17.99 - 35.99: 1079 35.99 - 53.98: 160 53.98 - 71.98: 46 71.98 - 89.97: 17 Dihedral angle restraints: 13053 sinusoidal: 5376 harmonic: 7677 Sorted by residual: 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 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP a 367 " pdb=" CB ASP a 367 " pdb=" CG ASP a 367 " pdb=" OD1 ASP a 367 " ideal model delta sinusoidal sigma weight residual -30.00 -89.57 59.57 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU A 437 " pdb=" CG GLU A 437 " pdb=" CD GLU A 437 " pdb=" OE1 GLU A 437 " ideal model delta sinusoidal sigma weight residual 0.00 89.97 -89.97 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 13050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2123 0.031 - 0.062: 734 0.062 - 0.094: 228 0.094 - 0.125: 161 0.125 - 0.156: 22 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE B 623 " pdb=" N ILE B 623 " pdb=" C ILE B 623 " pdb=" CB ILE B 623 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE a 30 " pdb=" N ILE a 30 " pdb=" C ILE a 30 " pdb=" CB ILE a 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 3265 not shown) Planarity restraints: 3695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU b 117 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO b 118 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO b 118 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO b 118 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 105 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO B 106 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 334 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 335 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.028 5.00e-02 4.00e+02 ... (remaining 3692 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 161 2.53 - 3.12: 16684 3.12 - 3.71: 34618 3.71 - 4.31: 51161 4.31 - 4.90: 82708 Nonbonded interactions: 185332 Sorted by model distance: nonbonded pdb=" OG SER c 45 " pdb=" O ILE c 50 " model vdw 1.936 3.040 nonbonded pdb=" O HOH a 883 " pdb=" O HOH a 919 " model vdw 1.975 3.040 nonbonded pdb=" O HOH B 812 " pdb=" O HOH B 820 " model vdw 2.017 3.040 nonbonded pdb=" O HOH b 827 " pdb=" O HOH b 833 " model vdw 2.024 3.040 nonbonded pdb=" O HOH a 852 " pdb=" O HOH a 915 " model vdw 2.063 3.040 ... (remaining 185327 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 28.440 Find NCS groups from input model: 0.600 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:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.007 0.878 21575 Z= 0.615 Angle : 0.799 29.877 29238 Z= 0.279 Chirality : 0.041 0.156 3268 Planarity : 0.004 0.074 3695 Dihedral : 14.215 89.972 8153 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.45 (0.17), residues: 2669 helix: 1.47 (0.15), residues: 1170 sheet: -0.38 (0.31), residues: 296 loop : -0.67 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 332 TYR 0.018 0.001 TYR A 530 PHE 0.019 0.001 PHE B 123 TRP 0.005 0.001 TRP b 344 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00313 (21490) covalent geometry : angle 0.53495 (29052) hydrogen bonds : bond 0.16525 ( 949) hydrogen bonds : angle 6.09715 ( 2644) metal coordination : bond 0.00755 ( 84) metal coordination : angle 7.45389 ( 186) Misc. bond : bond 0.87838 ( 1) *********************** 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 402 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: a 424 GLU cc_start: 0.6699 (tp30) cc_final: 0.6494 (mm-30) REVERT: a 506 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7958 (ttpp) REVERT: b 132 LYS cc_start: 0.5447 (mtpp) cc_final: 0.5205 (mmtm) REVERT: b 150 MET cc_start: 0.6829 (mtm) cc_final: 0.6402 (mtp) REVERT: c 72 LYS cc_start: 0.7769 (tttp) cc_final: 0.7154 (tmtm) REVERT: A 1 MET cc_start: 0.6304 (tpp) cc_final: 0.6092 (tpt) REVERT: A 385 ASP cc_start: 0.6750 (t0) cc_final: 0.6315 (t70) REVERT: B 405 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6759 (ttt90) outliers start: 0 outliers final: 1 residues processed: 402 average time/residue: 0.7713 time to fit residues: 344.7207 Evaluate side-chains 312 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 403 GLN B 500 ASN C 42 ASN C 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123686 restraints weight = 32417.632| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.82 r_work: 0.2873 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 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 = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21575 Z= 0.148 Angle : 0.850 31.592 29238 Z= 0.306 Chirality : 0.045 0.223 3268 Planarity : 0.005 0.074 3695 Dihedral : 4.331 57.273 2960 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 1.76 % Allowed : 8.71 % Favored : 89.53 % 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: 0.45 (0.16), residues: 2669 helix: 1.33 (0.15), residues: 1173 sheet: -0.28 (0.30), residues: 296 loop : -0.54 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 130 TYR 0.014 0.001 TYR A 530 PHE 0.011 0.002 PHE b 142 TRP 0.010 0.002 TRP b 344 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00344 (21490) covalent geometry : angle 0.57753 (29052) hydrogen bonds : bond 0.04734 ( 949) hydrogen bonds : angle 5.12826 ( 2644) metal coordination : bond 0.01080 ( 84) metal coordination : angle 7.83302 ( 186) Misc. bond : bond 0.00202 ( 1) *********************** 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 361 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7117 (tp30) cc_final: 0.6825 (mm-30) REVERT: a 444 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: a 588 ILE cc_start: 0.7643 (mt) cc_final: 0.7441 (mm) REVERT: a 601 MET cc_start: 0.3939 (OUTLIER) cc_final: 0.2832 (ttp) REVERT: a 615 ASN cc_start: 0.7173 (t0) cc_final: 0.6754 (t0) REVERT: b 132 LYS cc_start: 0.5394 (mtpp) cc_final: 0.4860 (mmtm) REVERT: b 150 MET cc_start: 0.7518 (mtm) cc_final: 0.6965 (mtp) REVERT: b 226 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.5750 (m-30) REVERT: b 316 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: b 471 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7684 (tm-30) REVERT: c 72 LYS cc_start: 0.8078 (tttp) cc_final: 0.7167 (tmtm) REVERT: A 1 MET cc_start: 0.6829 (tpp) cc_final: 0.6185 (ttt) REVERT: A 163 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: B 120 GLU cc_start: 0.4954 (tm-30) cc_final: 0.4729 (tp30) REVERT: B 449 LYS cc_start: 0.6138 (mtmm) cc_final: 0.5872 (mtmm) REVERT: B 454 MET cc_start: 0.6781 (pmm) cc_final: 0.6513 (pmm) REVERT: B 493 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8072 (mp0) REVERT: C 34 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7605 (mtp180) REVERT: C 132 ASN cc_start: 0.7798 (m-40) cc_final: 0.7557 (m110) REVERT: C 136 TYR cc_start: 0.7932 (m-80) cc_final: 0.7439 (m-80) outliers start: 40 outliers final: 18 residues processed: 342 average time/residue: 0.7734 time to fit residues: 296.4727 Evaluate side-chains 318 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 444 GLU Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 228 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 42 ASN c 116 GLN A 403 GLN A 483 ASN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.127496 restraints weight = 42233.276| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.98 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21575 Z= 0.176 Angle : 0.873 34.984 29238 Z= 0.317 Chirality : 0.046 0.211 3268 Planarity : 0.005 0.064 3695 Dihedral : 4.480 49.251 2958 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 2.59 % Allowed : 11.08 % Favored : 86.32 % 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: 0.25 (0.16), residues: 2669 helix: 1.11 (0.15), residues: 1178 sheet: -0.30 (0.30), residues: 297 loop : -0.60 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 130 TYR 0.018 0.002 TYR A 459 PHE 0.015 0.002 PHE b 95 TRP 0.010 0.002 TRP b 344 HIS 0.004 0.001 HIS a 503 Details of bonding type rmsd covalent geometry : bond 0.00422 (21490) covalent geometry : angle 0.60271 (29052) hydrogen bonds : bond 0.04751 ( 949) hydrogen bonds : angle 5.05809 ( 2644) metal coordination : bond 0.01250 ( 84) metal coordination : angle 7.94176 ( 186) Misc. bond : bond 0.00183 ( 1) *********************** 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 367 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: a 424 GLU cc_start: 0.6760 (tp30) cc_final: 0.6535 (mm-30) REVERT: a 444 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: a 588 ILE cc_start: 0.7877 (mt) cc_final: 0.7676 (mm) REVERT: a 615 ASN cc_start: 0.7139 (t0) cc_final: 0.6766 (t0) REVERT: b 150 MET cc_start: 0.7048 (mtm) cc_final: 0.6440 (mtp) REVERT: b 226 ASP cc_start: 0.6096 (OUTLIER) cc_final: 0.5549 (m-30) REVERT: b 316 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6409 (tp30) REVERT: c 72 LYS cc_start: 0.7936 (tttp) cc_final: 0.7205 (tmtm) REVERT: A 1 MET cc_start: 0.6392 (tpp) cc_final: 0.5996 (ttt) REVERT: A 163 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: B 55 ARG cc_start: 0.5714 (OUTLIER) cc_final: 0.4605 (mmt90) REVERT: B 493 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7182 (mt-10) REVERT: C 111 MET cc_start: 0.6180 (tpp) cc_final: 0.5853 (tpp) REVERT: C 132 ASN cc_start: 0.7590 (m-40) cc_final: 0.7348 (m110) REVERT: C 136 TYR cc_start: 0.7806 (m-80) cc_final: 0.7262 (m-80) outliers start: 59 outliers final: 28 residues processed: 343 average time/residue: 0.7284 time to fit residues: 280.1851 Evaluate side-chains 323 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 444 GLU Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 276 MET Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 47 optimal weight: 0.9980 chunk 245 optimal weight: 0.0870 chunk 202 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN c 42 ASN A 403 GLN C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125212 restraints weight = 31924.681| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.76 r_work: 0.2876 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21575 Z= 0.111 Angle : 0.788 28.424 29238 Z= 0.276 Chirality : 0.043 0.153 3268 Planarity : 0.004 0.067 3695 Dihedral : 4.209 44.500 2958 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 12.88 % Favored : 85.09 % 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: 0.48 (0.16), residues: 2669 helix: 1.33 (0.15), residues: 1174 sheet: -0.32 (0.30), residues: 297 loop : -0.47 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 549 TYR 0.011 0.001 TYR A 459 PHE 0.020 0.001 PHE B 8 TRP 0.008 0.001 TRP b 344 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00252 (21490) covalent geometry : angle 0.52251 (29052) hydrogen bonds : bond 0.03793 ( 949) hydrogen bonds : angle 4.82084 ( 2644) metal coordination : bond 0.00860 ( 84) metal coordination : angle 7.42175 ( 186) Misc. bond : bond 0.00081 ( 1) *********************** 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 359 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7142 (tp30) cc_final: 0.6857 (mm-30) REVERT: a 441 ARG cc_start: 0.8223 (mtp180) cc_final: 0.8021 (mtp180) REVERT: a 444 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: a 528 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7776 (ptpt) REVERT: a 549 ARG cc_start: 0.8099 (ppt-90) cc_final: 0.7833 (ppt170) REVERT: a 588 ILE cc_start: 0.7680 (mt) cc_final: 0.7449 (mm) REVERT: a 615 ASN cc_start: 0.7204 (t0) cc_final: 0.6461 (t0) REVERT: b 150 MET cc_start: 0.7504 (mtm) cc_final: 0.6851 (mtp) REVERT: b 285 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7312 (mtt180) REVERT: c 72 LYS cc_start: 0.7979 (tttp) cc_final: 0.7099 (tmtm) REVERT: A 1 MET cc_start: 0.6740 (tpp) cc_final: 0.6261 (ttt) REVERT: A 163 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: B 454 MET cc_start: 0.6833 (pmm) cc_final: 0.6564 (pmm) REVERT: B 493 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8075 (mp0) REVERT: B 607 LYS cc_start: 0.5740 (ptpt) cc_final: 0.5440 (ptpp) REVERT: C 132 ASN cc_start: 0.7798 (m-40) cc_final: 0.7518 (m110) REVERT: C 136 TYR cc_start: 0.7907 (m-80) cc_final: 0.7389 (m-80) REVERT: C 146 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5914 (mm-30) outliers start: 46 outliers final: 21 residues processed: 339 average time/residue: 0.7113 time to fit residues: 270.3085 Evaluate side-chains 312 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 223 MET Chi-restraints excluded: chain a residue 444 GLU Chi-restraints excluded: chain a residue 528 LYS Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 199 optimal weight: 0.0170 chunk 36 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 483 ASN c 116 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.152267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.120103 restraints weight = 30394.056| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.78 r_work: 0.2844 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21575 Z= 0.236 Angle : 0.927 38.422 29238 Z= 0.348 Chirality : 0.049 0.200 3268 Planarity : 0.006 0.073 3695 Dihedral : 4.710 37.114 2958 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.95 % Allowed : 13.15 % Favored : 83.91 % 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: 0.00 (0.16), residues: 2669 helix: 0.90 (0.15), residues: 1178 sheet: -0.53 (0.29), residues: 309 loop : -0.69 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 549 TYR 0.023 0.002 TYR A 459 PHE 0.022 0.002 PHE B 123 TRP 0.009 0.002 TRP b 344 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00568 (21490) covalent geometry : angle 0.66220 (29052) hydrogen bonds : bond 0.05097 ( 949) hydrogen bonds : angle 5.11094 ( 2644) metal coordination : bond 0.01574 ( 84) metal coordination : angle 8.15227 ( 186) Misc. bond : bond 0.00126 ( 1) *********************** 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 364 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 334 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7150 (mttp) REVERT: a 424 GLU cc_start: 0.7223 (tp30) cc_final: 0.6936 (mm-30) REVERT: a 444 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: a 588 ILE cc_start: 0.7663 (mt) cc_final: 0.7445 (mm) REVERT: a 601 MET cc_start: 0.4138 (OUTLIER) cc_final: 0.2993 (mpp) REVERT: a 615 ASN cc_start: 0.7307 (t0) cc_final: 0.6637 (t0) REVERT: b 56 ASN cc_start: 0.4904 (t0) cc_final: 0.4687 (p0) REVERT: b 150 MET cc_start: 0.7583 (mtm) cc_final: 0.6906 (mtp) REVERT: b 226 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5871 (m-30) REVERT: b 316 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: b 404 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6967 (mt) REVERT: c 72 LYS cc_start: 0.8141 (tttp) cc_final: 0.7309 (tmtm) REVERT: c 111 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7990 (ttm) REVERT: A 1 MET cc_start: 0.6836 (tpp) cc_final: 0.6251 (ttt) REVERT: A 14 ASP cc_start: 0.6937 (m-30) cc_final: 0.6714 (m-30) REVERT: A 51 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: A 55 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: A 163 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 498 SER cc_start: 0.8047 (p) cc_final: 0.7729 (m) REVERT: B 55 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.4936 (mmt90) REVERT: B 441 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5882 (mmm) REVERT: B 493 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7871 (mt-10) REVERT: C 111 MET cc_start: 0.6200 (tpp) cc_final: 0.5931 (tpp) REVERT: C 132 ASN cc_start: 0.7822 (m-40) cc_final: 0.7532 (m110) REVERT: C 136 TYR cc_start: 0.7984 (m-80) cc_final: 0.7424 (m-80) REVERT: C 146 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6125 (mp0) outliers start: 67 outliers final: 32 residues processed: 339 average time/residue: 0.7117 time to fit residues: 271.6290 Evaluate side-chains 332 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 444 GLU Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain a residue 610 THR Chi-restraints excluded: chain b residue 112 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 276 MET Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 20 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 264 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.155188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125254 restraints weight = 34321.882| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.93 r_work: 0.2850 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21575 Z= 0.114 Angle : 0.793 29.979 29238 Z= 0.278 Chirality : 0.043 0.151 3268 Planarity : 0.004 0.068 3695 Dihedral : 4.277 30.760 2958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 2.51 % Allowed : 14.25 % Favored : 83.25 % 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: 0.37 (0.16), residues: 2669 helix: 1.26 (0.15), residues: 1173 sheet: -0.45 (0.30), residues: 297 loop : -0.52 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 373 TYR 0.012 0.001 TYR A 459 PHE 0.017 0.001 PHE B 123 TRP 0.009 0.001 TRP b 344 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00260 (21490) covalent geometry : angle 0.52704 (29052) hydrogen bonds : bond 0.03827 ( 949) hydrogen bonds : angle 4.80836 ( 2644) metal coordination : bond 0.00902 ( 84) metal coordination : angle 7.45111 ( 186) Misc. bond : bond 0.00078 ( 1) *********************** 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 364 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 307 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7210 (tp30) cc_final: 0.6932 (mm-30) REVERT: a 444 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: a 528 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7766 (ptpt) REVERT: a 588 ILE cc_start: 0.7696 (mt) cc_final: 0.7471 (mm) REVERT: a 601 MET cc_start: 0.3880 (OUTLIER) cc_final: 0.2894 (ttp) REVERT: a 615 ASN cc_start: 0.7247 (t0) cc_final: 0.6481 (t0) REVERT: b 150 MET cc_start: 0.7562 (mtm) cc_final: 0.6851 (mtp) REVERT: b 226 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.6004 (m-30) REVERT: b 250 MET cc_start: 0.7996 (mtp) cc_final: 0.7659 (mtp) REVERT: b 285 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7277 (mtt180) REVERT: b 404 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6976 (mt) REVERT: b 507 HIS cc_start: 0.8028 (m170) cc_final: 0.7778 (m90) REVERT: b 513 GLU cc_start: 0.7203 (pt0) cc_final: 0.6575 (mp0) REVERT: c 72 LYS cc_start: 0.8083 (tttp) cc_final: 0.7181 (tmtm) REVERT: c 136 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: A 1 MET cc_start: 0.6744 (tpp) cc_final: 0.6295 (ttt) REVERT: A 55 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7321 (mm110) REVERT: A 82 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8322 (mtt-85) REVERT: A 163 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: A 286 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6818 (pt0) REVERT: B 55 ARG cc_start: 0.5853 (mmp80) cc_final: 0.4886 (mmm-85) REVERT: B 405 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6874 (ttt90) REVERT: B 441 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5876 (mmm) REVERT: B 493 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8119 (mp0) REVERT: C 111 MET cc_start: 0.6246 (tpp) cc_final: 0.5933 (tpp) REVERT: C 132 ASN cc_start: 0.7781 (m-40) cc_final: 0.7477 (m110) REVERT: C 136 TYR cc_start: 0.7926 (m-80) cc_final: 0.7389 (m-80) outliers start: 57 outliers final: 30 residues processed: 335 average time/residue: 0.6882 time to fit residues: 259.0223 Evaluate side-chains 329 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 444 GLU Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 528 LYS Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 276 MET Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 351 ASN Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 136 TYR Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 137 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 181 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 107 optimal weight: 0.0970 chunk 221 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 403 GLN c 116 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.156400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.124026 restraints weight = 30102.580| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.78 r_work: 0.2885 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21575 Z= 0.112 Angle : 0.777 28.304 29238 Z= 0.272 Chirality : 0.043 0.151 3268 Planarity : 0.004 0.065 3695 Dihedral : 4.144 25.830 2958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 2.33 % Allowed : 14.64 % Favored : 83.03 % 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: 0.50 (0.16), residues: 2669 helix: 1.38 (0.15), residues: 1172 sheet: -0.42 (0.30), residues: 297 loop : -0.46 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 405 TYR 0.013 0.001 TYR c 136 PHE 0.021 0.001 PHE b 421 TRP 0.007 0.001 TRP b 344 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00259 (21490) covalent geometry : angle 0.52269 (29052) hydrogen bonds : bond 0.03707 ( 949) hydrogen bonds : angle 4.71897 ( 2644) metal coordination : bond 0.00855 ( 84) metal coordination : angle 7.23241 ( 186) Misc. bond : bond 0.00075 ( 1) *********************** 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 357 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 276 HIS cc_start: 0.8139 (m90) cc_final: 0.7917 (m-70) REVERT: a 424 GLU cc_start: 0.7121 (tp30) cc_final: 0.6843 (mm-30) REVERT: a 441 ARG cc_start: 0.8258 (mtp180) cc_final: 0.8055 (mtp180) REVERT: a 588 ILE cc_start: 0.7637 (mt) cc_final: 0.7400 (mm) REVERT: a 601 MET cc_start: 0.3768 (OUTLIER) cc_final: 0.2796 (ttp) REVERT: a 615 ASN cc_start: 0.7150 (t0) cc_final: 0.6393 (t0) REVERT: b 56 ASN cc_start: 0.5081 (t0) cc_final: 0.4797 (p0) REVERT: b 150 MET cc_start: 0.7514 (mtm) cc_final: 0.6795 (mtp) REVERT: b 226 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6004 (m-30) REVERT: b 285 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7280 (mtt180) REVERT: b 404 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6910 (mt) REVERT: b 471 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7536 (tp30) REVERT: b 513 GLU cc_start: 0.7146 (pt0) cc_final: 0.6559 (mp0) REVERT: c 72 LYS cc_start: 0.8022 (tttp) cc_final: 0.7053 (tmtm) REVERT: c 136 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: A 1 MET cc_start: 0.6671 (tpp) cc_final: 0.6228 (ttt) REVERT: A 55 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7323 (mm110) REVERT: A 163 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: A 286 GLU cc_start: 0.7015 (pt0) cc_final: 0.6735 (pt0) REVERT: A 429 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: B 55 ARG cc_start: 0.5829 (mmp80) cc_final: 0.4871 (mmm-85) REVERT: B 157 GLU cc_start: 0.6077 (tp30) cc_final: 0.5602 (mm-30) REVERT: B 493 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8118 (mp0) REVERT: C 111 MET cc_start: 0.6215 (tpp) cc_final: 0.5929 (tpp) REVERT: C 136 TYR cc_start: 0.7896 (m-80) cc_final: 0.7363 (m-80) REVERT: C 146 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.5982 (mm-30) outliers start: 53 outliers final: 26 residues processed: 334 average time/residue: 0.7426 time to fit residues: 279.3250 Evaluate side-chains 329 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 276 MET Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 351 ASN Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 136 TYR Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 183 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 204 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 403 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125246 restraints weight = 32922.607| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.97 r_work: 0.2907 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21575 Z= 0.104 Angle : 0.766 31.377 29238 Z= 0.265 Chirality : 0.042 0.150 3268 Planarity : 0.004 0.063 3695 Dihedral : 4.057 25.842 2958 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 15.39 % Favored : 82.45 % 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: 1.48 (0.15), residues: 1165 sheet: -0.42 (0.30), residues: 297 loop : -0.45 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 373 TYR 0.013 0.001 TYR c 136 PHE 0.023 0.001 PHE b 421 TRP 0.006 0.001 TRP b 344 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00237 (21490) covalent geometry : angle 0.50768 (29052) hydrogen bonds : bond 0.03528 ( 949) hydrogen bonds : angle 4.64251 ( 2644) metal coordination : bond 0.00762 ( 84) metal coordination : angle 7.20665 ( 186) Misc. bond : bond 0.00068 ( 1) *********************** 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 355 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 306 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7102 (tp30) cc_final: 0.6810 (mm-30) REVERT: a 528 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7878 (ptpt) REVERT: a 588 ILE cc_start: 0.7660 (mt) cc_final: 0.7418 (mm) REVERT: a 601 MET cc_start: 0.3658 (OUTLIER) cc_final: 0.2689 (ttp) REVERT: a 615 ASN cc_start: 0.7160 (t0) cc_final: 0.6430 (t0) REVERT: b 150 MET cc_start: 0.7517 (mtm) cc_final: 0.6799 (mtp) REVERT: b 226 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: b 250 MET cc_start: 0.8008 (mtp) cc_final: 0.7626 (mtp) REVERT: b 285 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7261 (mtt180) REVERT: b 404 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6851 (mt) REVERT: b 471 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7567 (tp30) REVERT: b 513 GLU cc_start: 0.7115 (pt0) cc_final: 0.6540 (mp0) REVERT: c 72 LYS cc_start: 0.7977 (tttp) cc_final: 0.7054 (tmtm) REVERT: c 136 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: A 1 MET cc_start: 0.6634 (tpp) cc_final: 0.6247 (ttt) REVERT: A 55 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7313 (mm110) REVERT: A 82 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8350 (mtt180) REVERT: A 163 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: A 429 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: B 55 ARG cc_start: 0.5842 (mmp80) cc_final: 0.4882 (mmm-85) REVERT: B 157 GLU cc_start: 0.6006 (tp30) cc_final: 0.5546 (mm-30) REVERT: B 377 ASN cc_start: 0.6504 (m-40) cc_final: 0.5784 (p0) REVERT: B 493 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8143 (mp0) REVERT: C 136 TYR cc_start: 0.7880 (m-80) cc_final: 0.7353 (m-80) REVERT: C 146 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5913 (mm-30) outliers start: 49 outliers final: 31 residues processed: 335 average time/residue: 0.7421 time to fit residues: 278.9627 Evaluate side-chains 332 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 547 THR Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 151 GLU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 276 MET Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 351 ASN Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 136 TYR Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 175 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 218 optimal weight: 0.0470 chunk 216 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 403 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125348 restraints weight = 28536.655| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.53 r_work: 0.2942 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21575 Z= 0.105 Angle : 0.764 31.604 29238 Z= 0.264 Chirality : 0.042 0.148 3268 Planarity : 0.004 0.064 3695 Dihedral : 4.019 25.520 2958 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 2.24 % Allowed : 15.35 % Favored : 82.41 % 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: 0.60 (0.17), residues: 2669 helix: 1.49 (0.15), residues: 1172 sheet: -0.39 (0.30), residues: 297 loop : -0.43 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 549 TYR 0.013 0.001 TYR c 136 PHE 0.024 0.001 PHE b 421 TRP 0.006 0.001 TRP b 344 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00239 (21490) covalent geometry : angle 0.50849 (29052) hydrogen bonds : bond 0.03497 ( 949) hydrogen bonds : angle 4.61414 ( 2644) metal coordination : bond 0.00760 ( 84) metal coordination : angle 7.16753 ( 186) Misc. bond : bond 0.00069 ( 1) *********************** 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 358 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7041 (tp30) cc_final: 0.6749 (mm-30) REVERT: a 528 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7869 (ptpt) REVERT: a 588 ILE cc_start: 0.7656 (mt) cc_final: 0.7395 (mm) REVERT: a 601 MET cc_start: 0.3542 (OUTLIER) cc_final: 0.2600 (ttp) REVERT: a 615 ASN cc_start: 0.7171 (t0) cc_final: 0.6444 (t0) REVERT: b 150 MET cc_start: 0.7467 (mtm) cc_final: 0.6721 (mtp) REVERT: b 226 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6024 (m-30) REVERT: b 250 MET cc_start: 0.7996 (mtp) cc_final: 0.7605 (mtp) REVERT: b 285 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7246 (mtt180) REVERT: b 404 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6831 (mt) REVERT: b 438 PHE cc_start: 0.7107 (m-80) cc_final: 0.6885 (m-80) REVERT: b 471 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7551 (tp30) REVERT: b 513 GLU cc_start: 0.7067 (pt0) cc_final: 0.6525 (mp0) REVERT: c 72 LYS cc_start: 0.7938 (tttp) cc_final: 0.7010 (tmtm) REVERT: c 136 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: A 1 MET cc_start: 0.6622 (tpp) cc_final: 0.6283 (ttt) REVERT: A 55 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7299 (mm110) REVERT: A 163 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: A 429 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6720 (mt-10) REVERT: A 498 SER cc_start: 0.7914 (p) cc_final: 0.7610 (m) REVERT: B 55 ARG cc_start: 0.5832 (mmp80) cc_final: 0.4886 (mmm-85) REVERT: B 157 GLU cc_start: 0.5966 (tp30) cc_final: 0.5561 (mm-30) REVERT: B 377 ASN cc_start: 0.6489 (m-40) cc_final: 0.5753 (p0) REVERT: B 493 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8087 (mp0) REVERT: C 136 TYR cc_start: 0.7870 (m-80) cc_final: 0.7363 (m-80) outliers start: 51 outliers final: 30 residues processed: 335 average time/residue: 0.7125 time to fit residues: 268.8677 Evaluate side-chains 338 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 517 LEU Chi-restraints excluded: chain a residue 547 THR Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 351 ASN Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 136 TYR Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 0.0670 chunk 154 optimal weight: 0.6980 chunk 251 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 403 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.124064 restraints weight = 27970.833| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.55 r_work: 0.2900 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21575 Z= 0.118 Angle : 0.787 33.726 29238 Z= 0.275 Chirality : 0.043 0.150 3268 Planarity : 0.004 0.066 3695 Dihedral : 4.099 26.016 2958 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 1.89 % Allowed : 16.05 % Favored : 82.06 % 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: 0.56 (0.16), residues: 2669 helix: 1.46 (0.15), residues: 1171 sheet: -0.41 (0.30), residues: 297 loop : -0.46 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 130 TYR 0.014 0.001 TYR c 136 PHE 0.026 0.001 PHE b 421 TRP 0.006 0.001 TRP b 344 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00275 (21490) covalent geometry : angle 0.52749 (29052) hydrogen bonds : bond 0.03692 ( 949) hydrogen bonds : angle 4.64154 ( 2644) metal coordination : bond 0.00858 ( 84) metal coordination : angle 7.33588 ( 186) Misc. bond : bond 0.00078 ( 1) ********************** 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 341 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 424 GLU cc_start: 0.7094 (tp30) cc_final: 0.6812 (mm-30) REVERT: a 528 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7853 (ptpt) REVERT: a 588 ILE cc_start: 0.7567 (mt) cc_final: 0.7316 (mm) REVERT: a 601 MET cc_start: 0.3603 (OUTLIER) cc_final: 0.2639 (ttp) REVERT: a 615 ASN cc_start: 0.7157 (t0) cc_final: 0.6408 (t0) REVERT: b 150 MET cc_start: 0.7450 (mtm) cc_final: 0.6709 (mtp) REVERT: b 226 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.5957 (m-30) REVERT: b 250 MET cc_start: 0.7999 (mtp) cc_final: 0.7655 (mtp) REVERT: b 285 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7250 (mtt180) REVERT: b 404 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6756 (mt) REVERT: b 471 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7544 (tp30) REVERT: b 513 GLU cc_start: 0.7090 (pt0) cc_final: 0.6497 (mp0) REVERT: c 72 LYS cc_start: 0.7896 (tttp) cc_final: 0.6915 (tmtm) REVERT: c 136 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: A 1 MET cc_start: 0.6603 (tpp) cc_final: 0.6273 (ttt) REVERT: A 14 ASP cc_start: 0.6782 (m-30) cc_final: 0.6567 (m-30) REVERT: A 55 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7343 (mm110) REVERT: A 163 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: A 429 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: A 498 SER cc_start: 0.7939 (p) cc_final: 0.7636 (m) REVERT: B 55 ARG cc_start: 0.5818 (mmp80) cc_final: 0.4867 (mmm-85) REVERT: B 157 GLU cc_start: 0.5982 (tp30) cc_final: 0.5513 (mm-30) REVERT: B 369 ASN cc_start: 0.6600 (t0) cc_final: 0.6235 (t0) REVERT: B 377 ASN cc_start: 0.6516 (m-40) cc_final: 0.5756 (p0) REVERT: B 493 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8098 (mp0) REVERT: C 136 TYR cc_start: 0.7881 (m-80) cc_final: 0.7377 (m-80) outliers start: 43 outliers final: 31 residues processed: 322 average time/residue: 0.7163 time to fit residues: 259.5136 Evaluate side-chains 330 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 337 VAL Chi-restraints excluded: chain a residue 400 VAL Chi-restraints excluded: chain a residue 483 ASN Chi-restraints excluded: chain a residue 517 LEU Chi-restraints excluded: chain a residue 547 THR Chi-restraints excluded: chain a residue 585 SER Chi-restraints excluded: chain a residue 601 MET Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain b residue 234 MET Chi-restraints excluded: chain b residue 327 LYS Chi-restraints excluded: chain b residue 351 ASN Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain c residue 32 ILE Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 136 TYR Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 117 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 173 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 403 GLN A 403 GLN C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.125471 restraints weight = 32179.046| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.96 r_work: 0.2898 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21575 Z= 0.110 Angle : 0.781 33.340 29238 Z= 0.271 Chirality : 0.042 0.148 3268 Planarity : 0.004 0.064 3695 Dihedral : 4.082 25.823 2958 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.72 % Allowed : 16.36 % Favored : 81.93 % 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: 0.59 (0.17), residues: 2669 helix: 1.50 (0.15), residues: 1171 sheet: -0.43 (0.30), residues: 297 loop : -0.44 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 130 TYR 0.014 0.001 TYR c 136 PHE 0.025 0.001 PHE b 421 TRP 0.006 0.001 TRP b 344 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00255 (21490) covalent geometry : angle 0.52175 (29052) hydrogen bonds : bond 0.03589 ( 949) hydrogen bonds : angle 4.62326 ( 2644) metal coordination : bond 0.00795 ( 84) metal coordination : angle 7.30362 ( 186) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7681.18 seconds wall clock time: 131 minutes 47.63 seconds (7907.63 seconds total)