Starting phenix.real_space_refine (version: dev) on Fri Feb 24 00:58:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p91_13257/02_2023/7p91_13257_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "a GLU 86": "OE1" <-> "OE2" Residue "a GLU 122": "OE1" <-> "OE2" Residue "b GLU 157": "OE1" <-> "OE2" Residue "b GLU 368": "OE1" <-> "OE2" Residue "b PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 155": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21419 Number of models: 1 Model: "" Number of chains: 18 Chain: "a" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5037 Classifications: {'peptide': 642} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 616} Chain: "b" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4320 Classifications: {'peptide': 560} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 532} Chain breaks: 1 Chain: "c" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "A" Number of atoms: 4376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 4425 Chain: "B" Number of atoms: 4716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 613, 4708 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 31, 'TRANS': 581} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 613, 4708 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 31, 'TRANS': 581} Chain breaks: 1 bond proxies already assigned to first conformer: 4787 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "a" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 40 Unusual residues: {'FES': 2, 'SF4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "b" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "c" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4818 SG CYS a 612 50.942 88.423 34.824 1.00 27.14 S ATOM 4848 SG CYS a 616 48.073 88.389 32.503 1.00 36.72 S ATOM 4528 SG CYS a 575 54.288 87.219 30.790 1.00 29.12 S ATOM 4559 SG CYS a 580 51.868 87.717 28.285 1.00 31.77 S ATOM 2747 SG CYS a 350 75.420 88.863 68.749 1.00 8.79 S ATOM 2305 SG CYS a 295 69.843 91.274 70.272 1.00 16.50 S ATOM 3795 SG CYS a 486 74.226 90.178 74.981 1.00 16.50 S ATOM 3765 SG CYS a 482 71.286 85.277 71.266 1.00 9.41 S ATOM 1464 SG CYS a 186 70.382 84.592 59.972 1.00 16.50 S ATOM 1485 SG CYS a 189 69.287 83.660 66.309 1.00 16.50 S ATOM 1504 SG CYS a 192 71.681 79.105 62.941 1.00 16.50 S ATOM 1211 SG CYS a 153 65.493 80.666 62.024 1.00 16.50 S ATOM 1180 SG CYS a 149 68.952 73.464 61.116 1.00 16.50 S ATOM 1162 SG CYS a 146 70.029 68.006 64.159 1.00 16.50 S ATOM 1534 SG CYS a 196 74.747 72.042 63.219 1.00 16.50 S ATOM 1140 SG CYS a 143 71.815 68.987 57.941 1.00 16.50 S ATOM 782 SG CYS a 99 83.141 69.859 61.975 1.00 16.50 S ATOM 825 SG CYS a 105 80.445 65.144 65.319 1.00 16.50 S ATOM 762 SG CYS a 96 86.033 64.231 61.720 1.00 16.50 S ATOM 377 SG CYS a 48 65.456 54.353 69.520 1.00 9.24 S ATOM 464 SG CYS a 60 62.829 56.855 69.455 1.00 10.72 S ATOM 271 SG CYS a 34 66.504 60.378 66.875 1.00 10.87 S ATOM 352 SG CYS a 45 68.633 57.461 66.614 1.00 16.50 S ATOM 8691 SG CYS b 485 59.829 60.976 55.037 1.00 7.98 S ATOM 8730 SG CYS b 491 62.851 55.464 53.001 1.00 11.24 S ATOM 9049 SG CYS b 531 57.076 55.563 56.017 1.00 9.30 S ATOM 8710 SG CYS b 488 63.447 56.390 58.256 1.00 16.50 S ATOM 5293 SG CYS b 31 35.252 53.197 29.539 1.00 26.40 S ATOM 5321 SG CYS b 36 38.027 52.639 27.207 1.00 24.25 S ATOM 5564 SG CYS b 78 37.721 50.295 33.385 1.00 29.04 S ATOM 5591 SG CYS b 82 40.655 50.157 31.270 1.00 29.41 S ATOM 8547 SG CYS b 468 67.917 41.130 34.548 1.00 23.29 S ATOM 9273 SG CYS b 560 70.423 40.306 31.676 1.00 30.69 S ATOM 9304 SG CYS b 565 70.257 43.844 33.139 1.00 33.07 S ATOM 10272 SG CYS c 119 49.011 53.082 35.116 1.00 15.53 S ATOM 10295 SG CYS c 123 48.779 50.271 33.197 1.00 17.33 S ATOM 9978 SG CYS c 78 53.439 55.211 32.964 1.00 16.71 S ATOM 10008 SG CYS c 83 53.525 52.882 30.377 1.00 15.89 S ATOM 13333 SG CYS A 350 101.102 39.250 69.129 1.00 7.37 S ATOM 12891 SG CYS A 295 106.640 36.774 70.674 1.00 16.50 S ATOM 14381 SG CYS A 486 102.177 37.905 75.350 1.00 16.50 S ATOM 14351 SG CYS A 482 105.158 42.785 71.651 1.00 10.37 S ATOM 12090 SG CYS A 192 104.810 48.977 63.224 1.00 16.50 S ATOM 12050 SG CYS A 186 106.057 43.372 60.288 1.00 16.50 S ATOM 12071 SG CYS A 189 107.120 44.186 66.518 1.00 16.50 S ATOM 11797 SG CYS A 153 110.903 47.333 62.188 1.00 16.50 S ATOM 11766 SG CYS A 149 107.527 54.577 61.263 1.00 16.50 S ATOM 11748 SG CYS A 146 106.477 60.079 64.172 1.00 16.50 S ATOM 12120 SG CYS A 196 101.711 55.990 63.254 1.00 16.50 S ATOM 11726 SG CYS A 143 104.647 59.117 58.041 1.00 16.50 S ATOM 11400 SG CYS A 105 96.077 62.739 65.350 1.00 16.50 S ATOM 11337 SG CYS A 96 90.415 63.703 61.971 1.00 16.50 S ATOM 11357 SG CYS A 99 93.343 58.085 62.205 1.00 16.50 S ATOM 10952 SG CYS A 48 110.963 73.672 69.360 1.00 7.10 S ATOM 11039 SG CYS A 60 113.584 71.282 69.216 1.00 9.93 S ATOM 10846 SG CYS A 34 110.094 67.607 66.718 1.00 9.02 S ATOM 10927 SG CYS A 45 107.842 70.549 66.345 1.00 16.50 S ATOM 19574 SG CYS B 611 95.206 90.539 23.743 1.00 42.65 S ATOM 19592 SG CYS B 614 90.916 86.828 24.887 1.00 46.54 S ATOM 19552 SG CYS B 608 95.862 84.198 21.328 1.00 48.74 S ATOM 19396 SG CYS B 588 90.988 88.629 19.705 1.00 45.94 S ATOM 19331 SG CYS B 578 83.019 80.019 27.690 1.00 43.58 S ATOM 19368 SG CYS B 584 85.964 85.713 25.772 1.00 43.64 S ATOM 19618 SG CYS B 618 86.125 84.529 31.296 1.00 41.14 S ATOM 19350 SG CYS B 581 80.316 85.827 28.903 1.00 38.79 S ATOM 18613 SG CYS B 485 116.527 66.878 54.975 1.00 11.06 S ATOM 18652 SG CYS B 491 113.616 72.543 52.837 1.00 8.58 S ATOM 18971 SG CYS B 531 119.345 72.357 55.809 1.00 16.50 S ATOM 18632 SG CYS B 488 113.018 71.598 58.042 1.00 16.50 S ATOM 15207 SG CYS B 31 140.893 74.109 28.870 1.00 30.10 S ATOM 15235 SG CYS B 36 138.137 75.154 26.670 1.00 27.51 S ATOM 15478 SG CYS B 78 138.765 77.421 32.811 1.00 30.90 S ATOM 15505 SG CYS B 82 135.907 78.002 30.838 1.00 31.26 S ATOM 18469 SG CYS B 468 108.426 86.182 34.641 1.00 22.52 S ATOM 19195 SG CYS B 560 106.557 87.111 31.464 1.00 29.09 S ATOM 19226 SG CYS B 565 106.060 83.657 33.051 1.00 28.48 S ATOM 20582 SG CYS C 119 127.039 74.727 34.959 1.00 20.24 S ATOM 20605 SG CYS C 123 127.180 77.219 32.671 1.00 22.24 S ATOM 20288 SG CYS C 78 122.911 72.216 32.525 1.00 19.40 S ATOM 20318 SG CYS C 83 122.587 74.495 29.869 1.00 18.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 Time building chain proxies: 15.08, per 1000 atoms: 0.70 Number of scatterers: 21419 At special positions: 0 Unit cell: (177.16, 128.544, 104.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 62 26.01 S 219 16.00 P 2 15.00 O 4305 8.00 N 3525 7.00 C 13304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.96 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 705 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 48 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 60 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 45 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 34 " pdb=" FES B 705 " pdb="FE2 FES B 705 " - pdb=" SG CYS B 78 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 36 " pdb="FE2 FES B 705 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 705 " - pdb=" SG CYS B 31 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb=" FES a 701 " pdb="FE2 FES a 701 " - pdb=" SG CYS a 580 " pdb="FE2 FES a 701 " - pdb=" SG CYS a 575 " pdb="FE1 FES a 701 " - pdb=" SG CYS a 616 " pdb="FE1 FES a 701 " - pdb=" SG CYS a 612 " pdb=" FES a 706 " pdb="FE1 FES a 706 " - pdb=" SG CYS a 48 " pdb="FE2 FES a 706 " - pdb=" SG CYS a 45 " pdb="FE1 FES a 706 " - pdb=" SG CYS a 60 " pdb="FE2 FES a 706 " - pdb=" SG CYS a 34 " pdb=" FES b 703 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 82 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 36 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 78 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 31 " pdb=" FES c 201 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 78 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 83 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 119 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 123 " pdb=" SF4 A 701 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 153 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 189 " pdb=" SF4 A 703 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 149 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 143 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 196 " pdb=" SF4 A 704 " pdb="FE4 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 105 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 99 " pdb=" SF4 B 701 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 614 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 588 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 611 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 608 " pdb=" SF4 B 702 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 584 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 581 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 618 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 578 " pdb=" SF4 B 703 " pdb="FE1 SF4 B 703 " - pdb=" SG CYS B 485 " pdb="FE4 SF4 B 703 " - pdb=" SG CYS B 488 " pdb="FE3 SF4 B 703 " - pdb=" SG CYS B 531 " pdb="FE2 SF4 B 703 " - pdb=" SG CYS B 491 " pdb=" SF4 a 702 " pdb="FE1 SF4 a 702 " - pdb=" SG CYS a 350 " pdb="FE4 SF4 a 702 " - pdb=" SG CYS a 482 " pdb="FE2 SF4 a 702 " - pdb=" SG CYS a 295 " pdb="FE3 SF4 a 702 " - pdb=" SG CYS a 486 " pdb=" SF4 a 703 " pdb="FE1 SF4 a 703 " - pdb=" SG CYS a 186 " pdb="FE2 SF4 a 703 " - pdb=" SG CYS a 189 " pdb="FE3 SF4 a 703 " - pdb=" SG CYS a 192 " pdb="FE4 SF4 a 703 " - pdb=" SG CYS a 153 " pdb=" SF4 a 704 " pdb="FE4 SF4 a 704 " - pdb=" SG CYS a 143 " pdb="FE1 SF4 a 704 " - pdb=" SG CYS a 149 " pdb="FE2 SF4 a 704 " - pdb=" SG CYS a 146 " pdb="FE3 SF4 a 704 " - pdb=" SG CYS a 196 " pdb=" SF4 a 705 " pdb="FE2 SF4 a 705 " - pdb=" NE2 HIS a 92 " pdb="FE1 SF4 a 705 " - pdb=" SG CYS a 99 " pdb="FE4 SF4 a 705 " - pdb=" SG CYS a 96 " pdb="FE3 SF4 a 705 " - pdb=" SG CYS a 105 " pdb=" SF4 b 701 " pdb="FE1 SF4 b 701 " - pdb=" SG CYS b 485 " pdb="FE3 SF4 b 701 " - pdb=" SG CYS b 531 " pdb="FE4 SF4 b 701 " - pdb=" SG CYS b 488 " pdb="FE2 SF4 b 701 " - pdb=" SG CYS b 491 " Number of angles added : 180 Zn2+ tetrahedral coordination pdb=" ZN B 706 " pdb="ZN ZN B 706 " - pdb=" NE2 HIS B 555 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 468 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 560 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 565 " pdb=" ZN b 704 " pdb="ZN ZN b 704 " - pdb=" NE2 HIS b 555 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 560 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 565 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 468 " Number of angles added : 6 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 22 sheets defined 43.1% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'a' and resid 19 through 26 Processing helix chain 'a' and resid 59 through 61 No H-bonds generated for 'chain 'a' and resid 59 through 61' Processing helix chain 'a' and resid 75 through 90 Processing helix chain 'a' and resid 106 through 113 Processing helix chain 'a' and resid 140 through 142 No H-bonds generated for 'chain 'a' and resid 140 through 142' Processing helix chain 'a' and resid 148 through 155 Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'a' and resid 181 through 183 No H-bonds generated for 'chain 'a' and resid 181 through 183' Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 207 through 215 Processing helix chain 'a' and resid 232 through 236 removed outlier: 3.549A pdb=" N PHE a 236 " --> pdb=" O GLN a 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 255 Processing helix chain 'a' and resid 263 through 284 Processing helix chain 'a' and resid 296 through 305 Processing helix chain 'a' and resid 307 through 309 No H-bonds generated for 'chain 'a' and resid 307 through 309' Processing helix chain 'a' and resid 319 through 335 removed outlier: 4.547A pdb=" N ALA a 332 " --> pdb=" O LYS a 328 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG a 333 " --> pdb=" O LYS a 329 " (cutoff:3.500A) Processing helix chain 'a' and resid 339 through 341 No H-bonds generated for 'chain 'a' and resid 339 through 341' Processing helix chain 'a' and resid 352 through 358 Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 382 removed outlier: 3.591A pdb=" N SER a 382 " --> pdb=" O LEU a 378 " (cutoff:3.500A) Processing helix chain 'a' and resid 403 through 409 removed outlier: 3.752A pdb=" N PHE a 408 " --> pdb=" O ALA a 404 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLY a 409 " --> pdb=" O GLY a 405 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 425 Processing helix chain 'a' and resid 464 through 470 Processing helix chain 'a' and resid 485 through 488 Processing helix chain 'a' and resid 498 through 514 removed outlier: 3.729A pdb=" N ILE a 514 " --> pdb=" O ASP a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 522 No H-bonds generated for 'chain 'a' and resid 520 through 522' Processing helix chain 'a' and resid 524 through 532 Processing helix chain 'a' and resid 537 through 544 Processing helix chain 'a' and resid 578 through 583 removed outlier: 4.391A pdb=" N LYS a 583 " --> pdb=" O SER a 579 " (cutoff:3.500A) Processing helix chain 'a' and resid 585 through 598 Processing helix chain 'a' and resid 634 through 641 Processing helix chain 'b' and resid 5 through 24 Processing helix chain 'b' and resid 36 through 39 No H-bonds generated for 'chain 'b' and resid 36 through 39' Processing helix chain 'b' and resid 41 through 54 Processing helix chain 'b' and resid 102 through 111 removed outlier: 3.708A pdb=" N VAL b 105 " --> pdb=" O PRO b 102 " (cutoff:3.500A) Proline residue: b 106 - end of helix Processing helix chain 'b' and resid 120 through 122 No H-bonds generated for 'chain 'b' and resid 120 through 122' Processing helix chain 'b' and resid 140 through 144 Processing helix chain 'b' and resid 161 through 166 Processing helix chain 'b' and resid 171 through 178 Processing helix chain 'b' and resid 182 through 192 Processing helix chain 'b' and resid 204 through 213 Processing helix chain 'b' and resid 234 through 241 Processing helix chain 'b' and resid 243 through 257 Processing helix chain 'b' and resid 271 through 287 Processing helix chain 'b' and resid 312 through 315 Processing helix chain 'b' and resid 317 through 324 Processing helix chain 'b' and resid 343 through 345 No H-bonds generated for 'chain 'b' and resid 343 through 345' Processing helix chain 'b' and resid 353 through 364 Proline residue: b 360 - end of helix Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 404 through 408 Processing helix chain 'b' and resid 428 through 430 No H-bonds generated for 'chain 'b' and resid 428 through 430' Processing helix chain 'b' and resid 436 through 438 No H-bonds generated for 'chain 'b' and resid 436 through 438' Processing helix chain 'b' and resid 469 through 483 Processing helix chain 'b' and resid 489 through 506 removed outlier: 4.128A pdb=" N MET b 496 " --> pdb=" O ARG b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 512 through 528 removed outlier: 3.669A pdb=" N LYS b 523 " --> pdb=" O GLU b 519 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR b 524 " --> pdb=" O HIS b 520 " (cutoff:3.500A) Processing helix chain 'b' and resid 532 through 535 No H-bonds generated for 'chain 'b' and resid 532 through 535' Processing helix chain 'b' and resid 537 through 547 Proline residue: b 540 - end of helix Processing helix chain 'b' and resid 549 through 557 Processing helix chain 'c' and resid 7 through 15 Processing helix chain 'c' and resid 19 through 33 removed outlier: 4.968A pdb=" N ILE c 23 " --> pdb=" O GLU c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 48 Processing helix chain 'c' and resid 52 through 59 Processing helix chain 'c' and resid 81 through 86 Processing helix chain 'c' and resid 88 through 99 Processing helix chain 'c' and resid 123 through 125 No H-bonds generated for 'chain 'c' and resid 123 through 125' Processing helix chain 'c' and resid 141 through 157 Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 75 through 91 removed outlier: 4.003A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 232 through 236 removed outlier: 4.039A pdb=" N PHE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 236' Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 263 through 284 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 319 through 334 removed outlier: 4.917A pdb=" N ALA A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.720A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.728A pdb=" N ILE A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 102 through 111 removed outlier: 3.620A pdb=" N VAL B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.685A pdb=" N ARG B 111 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 243 through 256 Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 353 through 364 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 489 through 507 removed outlier: 4.020A pdb=" N MET B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 Processing helix chain 'B' and resid 532 through 535 No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 539 through 556 removed outlier: 7.145A pdb=" N GLU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 605 through 607 No H-bonds generated for 'chain 'B' and resid 605 through 607' Processing helix chain 'B' and resid 613 through 616 No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 19 through 33 removed outlier: 4.860A pdb=" N ILE C 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR C 33 " --> pdb=" O GLN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 52 through 61 Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 141 through 157 Processing sheet with id= A, first strand: chain 'a' and resid 2 through 5 Processing sheet with id= B, first strand: chain 'a' and resid 49 through 52 Processing sheet with id= C, first strand: chain 'a' and resid 136 through 138 Processing sheet with id= D, first strand: chain 'a' and resid 163 through 165 Processing sheet with id= E, first strand: chain 'a' and resid 259 through 262 removed outlier: 3.525A pdb=" N LYS a 259 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE a 368 " --> pdb=" O SER a 346 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N MET a 348 " --> pdb=" O ILE a 368 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU a 370 " --> pdb=" O MET a 348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'a' and resid 476 through 480 removed outlier: 3.712A pdb=" N ILE a 476 " --> pdb=" O LYS a 454 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS a 430 " --> pdb=" O THR a 446 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'a' and resid 572 through 575 Processing sheet with id= H, first strand: chain 'b' and resid 72 through 76 Processing sheet with id= I, first strand: chain 'b' and resid 347 through 352 Processing sheet with id= J, first strand: chain 'b' and resid 394 through 399 removed outlier: 3.709A pdb=" N VAL b 462 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'c' and resid 112 through 117 removed outlier: 6.615A pdb=" N TYR c 73 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP c 115 " --> pdb=" O TYR c 73 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE c 75 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL c 117 " --> pdb=" O ILE c 75 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL c 77 " --> pdb=" O VAL c 117 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= M, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= N, first strand: chain 'A' and resid 136 through 138 Processing sheet with id= O, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= P, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.689A pdb=" N LYS A 259 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 368 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET A 348 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU A 370 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 476 through 480 removed outlier: 3.698A pdb=" N LYS A 430 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.561A pdb=" N VAL B 30 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.929A pdb=" N LEU B 124 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 348 through 352 removed outlier: 6.812A pdb=" N PHE B 220 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN B 351 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 222 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B 261 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR B 263 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 302 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA B 264 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 304 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 266 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS B 306 " --> pdb=" O ILE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= V, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.861A pdb=" N TYR C 73 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP C 115 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 75 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 117 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL C 77 " --> pdb=" O VAL C 117 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 2148 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: 7.52 Time building geometry restraints manager: 9.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 8525 1.42 - 1.63: 12575 1.63 - 1.85: 218 1.85 - 2.07: 0 2.07 - 2.28: 172 Bond restraints: 21490 Sorted by residual: bond pdb=" CA THR C 102 " pdb=" C THR C 102 " ideal model delta sigma weight residual 1.524 1.581 -0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" C THR C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 1.332 1.375 -0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 1.526 1.491 0.035 1.29e-02 6.01e+03 7.28e+00 bond pdb=" C ASN C 138 " pdb=" O ASN C 138 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.30e-02 5.92e+03 5.95e+00 bond pdb=" C LYS A 209 " pdb=" O LYS A 209 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.15e-02 7.56e+03 4.40e+00 ... (remaining 21485 not shown) Histogram of bond angle deviations from ideal: 73.51 - 85.61: 158 85.61 - 97.71: 1 97.71 - 109.81: 2454 109.81 - 121.91: 22264 121.91 - 134.02: 4175 Bond angle restraints: 29052 Sorted by residual: angle pdb=" N MET b 91 " pdb=" CA MET b 91 " pdb=" C MET b 91 " ideal model delta sigma weight residual 109.81 115.65 -5.84 2.21e+00 2.05e-01 6.98e+00 angle pdb=" CB LYS A 506 " pdb=" CG LYS A 506 " pdb=" CD LYS A 506 " ideal model delta sigma weight residual 111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00 angle pdb=" O LEU C 101 " pdb=" C LEU C 101 " pdb=" N THR C 102 " ideal model delta sigma weight residual 123.19 126.38 -3.19 1.30e+00 5.92e-01 6.01e+00 angle pdb=" CA ASN C 138 " pdb=" C ASN C 138 " pdb=" O ASN C 138 " ideal model delta sigma weight residual 121.54 118.76 2.78 1.16e+00 7.43e-01 5.75e+00 angle pdb=" N GLN B 10 " pdb=" CA GLN B 10 " pdb=" CB GLN B 10 " ideal model delta sigma weight residual 110.12 113.55 -3.43 1.47e+00 4.63e-01 5.44e+00 ... (remaining 29047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12795 35.65 - 71.31: 228 71.31 - 106.96: 24 106.96 - 142.62: 0 142.62 - 178.27: 2 Dihedral angle restraints: 13049 sinusoidal: 5372 harmonic: 7677 Sorted by residual: dihedral pdb=" C10 FMN b 702 " pdb=" C1' FMN b 702 " pdb=" N10 FMN b 702 " pdb=" C2' FMN b 702 " ideal model delta sinusoidal sigma weight residual 257.59 79.32 178.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN B 704 " pdb=" C1' FMN B 704 " pdb=" N10 FMN B 704 " pdb=" C2' FMN B 704 " ideal model delta sinusoidal sigma weight residual 257.59 96.05 161.54 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" CA LYS B 334 " pdb=" C LYS B 334 " pdb=" N PRO B 335 " pdb=" CA PRO B 335 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 13046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2645 0.048 - 0.096: 453 0.096 - 0.143: 166 0.143 - 0.191: 3 0.191 - 0.239: 1 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CA ASN C 138 " pdb=" N ASN C 138 " pdb=" C ASN C 138 " pdb=" CB ASN C 138 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA THR C 102 " pdb=" N THR C 102 " pdb=" C THR C 102 " pdb=" CB THR C 102 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU a 526 " pdb=" CB LEU a 526 " pdb=" CD1 LEU a 526 " pdb=" CD2 LEU a 526 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 3265 not shown) Planarity restraints: 3693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 138 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ASN C 138 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN C 138 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 139 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 121 " -0.228 9.50e-02 1.11e+02 1.02e-01 6.98e+00 pdb=" NE ARG b 121 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG b 121 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG b 121 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG b 121 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 101 " 0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 102 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " 0.034 5.00e-02 4.00e+02 ... (remaining 3690 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 341 2.63 - 3.20: 20040 3.20 - 3.76: 34564 3.76 - 4.33: 50808 4.33 - 4.90: 80373 Nonbonded interactions: 186126 Sorted by model distance: nonbonded pdb=" O GLY b 486 " pdb=" O HOH b 801 " model vdw 2.062 2.440 nonbonded pdb=" O PHE A 394 " pdb=" O HOH A 801 " model vdw 2.068 2.440 nonbonded pdb=" O HOH A 825 " pdb=" O HOH A 870 " model vdw 2.077 2.440 nonbonded pdb=" O HOH A 877 " pdb=" O HOH A 890 " model vdw 2.094 2.440 nonbonded pdb=" O CYS a 143 " pdb=" O HOH a 801 " model vdw 2.098 2.440 ... (remaining 186121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 129 or resid 131 through 554 or resid 701 throug \ h 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 571 or resid 701 throug \ h 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 62 7.16 5 Zn 2 6.06 5 P 2 5.49 5 S 219 5.16 5 C 13304 2.51 5 N 3525 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.830 Check model and map are aligned: 0.290 Process input model: 68.060 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 21490 Z= 0.175 Angle : 0.517 7.879 29052 Z= 0.275 Chirality : 0.041 0.239 3268 Planarity : 0.004 0.102 3693 Dihedral : 14.728 178.274 8149 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2669 helix: 1.33 (0.15), residues: 1180 sheet: -0.59 (0.30), residues: 318 loop : -0.68 (0.18), residues: 1171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 393 time to evaluate : 2.563 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 393 average time/residue: 1.5998 time to fit residues: 702.7629 Evaluate side-chains 314 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN b 507 HIS A 53 ASN A 392 GLN A 483 ASN C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 21490 Z= 0.251 Angle : 0.586 11.602 29052 Z= 0.301 Chirality : 0.045 0.164 3268 Planarity : 0.005 0.059 3693 Dihedral : 6.420 178.268 2954 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2669 helix: 1.05 (0.15), residues: 1178 sheet: -0.43 (0.30), residues: 312 loop : -0.67 (0.18), residues: 1179 *********************** 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 379 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 333 time to evaluate : 2.744 Fit side-chains outliers start: 46 outliers final: 18 residues processed: 355 average time/residue: 1.5780 time to fit residues: 628.3323 Evaluate side-chains 326 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 10 average time/residue: 0.5799 time to fit residues: 11.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 201 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 241 optimal weight: 0.5980 chunk 261 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 507 HIS A 392 GLN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 21490 Z= 0.220 Angle : 0.554 12.877 29052 Z= 0.283 Chirality : 0.044 0.173 3268 Planarity : 0.005 0.062 3693 Dihedral : 6.437 179.032 2954 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2669 helix: 1.07 (0.15), residues: 1171 sheet: -0.46 (0.29), residues: 312 loop : -0.67 (0.18), residues: 1186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5338 Ramachandran restraints generated. 2669 Oldfield, 0 Emsley, 2669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 329 time to evaluate : 2.535 Fit side-chains outliers start: 44 outliers final: 22 residues processed: 348 average time/residue: 1.5559 time to fit residues: 612.1817 Evaluate side-chains 333 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 311 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 9 average time/residue: 0.6785 time to fit residues: 11.4657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 162 optimal weight: 8.9990 chunk 242 optimal weight: 0.4980 chunk 257 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 403 GLN b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 507 HIS A 392 GLN A 403 GLN C 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 21490 Z= 0.278 Angle : 0.592 13.146 29052 Z= 0.302 Chirality : 0.045 0.181 3268 Planarity : 0.005 0.066 3693 Dihedral : 6.588 178.649 2954 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2669 helix: 0.90 (0.15), residues: 1170 sheet: -0.49 (0.29), residues: 311 loop : -0.74 (0.18), residues: 1188 *********************** 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 383 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 323 time to evaluate : 2.640 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 355 average time/residue: 1.5406 time to fit residues: 616.2003 Evaluate side-chains 336 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 2.696 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 17 residues processed: 13 average time/residue: 0.4104 time to fit residues: 11.2391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 403 GLN a 483 ASN b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN C 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 21490 Z= 0.356 Angle : 0.650 12.529 29052 Z= 0.333 Chirality : 0.047 0.193 3268 Planarity : 0.006 0.068 3693 Dihedral : 6.781 178.292 2954 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2669 helix: 0.65 (0.15), residues: 1167 sheet: -0.59 (0.29), residues: 312 loop : -0.84 (0.18), residues: 1190 *********************** 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 383 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 316 time to evaluate : 2.691 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 38 residues processed: 350 average time/residue: 1.5220 time to fit residues: 601.2020 Evaluate side-chains 344 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 306 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 19 residues processed: 19 average time/residue: 0.5705 time to fit residues: 18.5769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 507 HIS A 392 GLN B 340 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21490 Z= 0.191 Angle : 0.540 10.726 29052 Z= 0.275 Chirality : 0.043 0.145 3268 Planarity : 0.005 0.066 3693 Dihedral : 6.514 178.938 2954 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2669 helix: 0.94 (0.15), residues: 1169 sheet: -0.47 (0.29), residues: 311 loop : -0.76 (0.18), residues: 1189 *********************** 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 375 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 322 time to evaluate : 2.554 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 25 residues processed: 356 average time/residue: 1.4958 time to fit residues: 602.8574 Evaluate side-chains 329 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.9355 time to fit residues: 9.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 503 HIS C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 21490 Z= 0.266 Angle : 0.591 11.702 29052 Z= 0.300 Chirality : 0.045 0.148 3268 Planarity : 0.005 0.069 3693 Dihedral : 6.606 177.518 2954 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2669 helix: 0.82 (0.15), residues: 1172 sheet: -0.51 (0.29), residues: 312 loop : -0.76 (0.18), residues: 1185 *********************** 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 364 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 302 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 38 residues processed: 345 average time/residue: 1.5265 time to fit residues: 595.5549 Evaluate side-chains 339 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 2.580 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 25 residues processed: 13 average time/residue: 0.5647 time to fit residues: 13.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 23 optimal weight: 0.0670 chunk 201 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 507 HIS A 392 GLN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21490 Z= 0.191 Angle : 0.543 10.576 29052 Z= 0.275 Chirality : 0.043 0.145 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.481 178.330 2954 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2669 helix: 0.98 (0.15), residues: 1169 sheet: -0.41 (0.29), residues: 309 loop : -0.71 (0.18), residues: 1191 *********************** 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 352 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 305 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 338 average time/residue: 1.5051 time to fit residues: 575.6722 Evaluate side-chains 327 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 295 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 7 average time/residue: 0.5587 time to fit residues: 8.8581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 156 optimal weight: 0.0670 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21490 Z= 0.167 Angle : 0.525 10.028 29052 Z= 0.265 Chirality : 0.042 0.146 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.375 177.495 2954 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2669 helix: 1.09 (0.15), residues: 1174 sheet: -0.36 (0.29), residues: 309 loop : -0.64 (0.18), residues: 1186 *********************** 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 345 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 306 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 29 residues processed: 335 average time/residue: 1.4818 time to fit residues: 564.9337 Evaluate side-chains 326 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.5894 time to fit residues: 7.5054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9990 chunk 154 optimal weight: 0.0470 chunk 119 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 0.0370 chunk 129 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21490 Z= 0.211 Angle : 0.554 13.182 29052 Z= 0.280 Chirality : 0.043 0.154 3268 Planarity : 0.005 0.069 3693 Dihedral : 6.448 176.867 2954 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2669 helix: 1.02 (0.15), residues: 1168 sheet: -0.39 (0.29), residues: 311 loop : -0.64 (0.18), residues: 1190 ********************** 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 333 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 301 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 29 residues processed: 328 average time/residue: 1.5350 time to fit residues: 568.4019 Evaluate side-chains 326 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 297 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 1.1963 time to fit residues: 7.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 185 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 ASN ** b 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 13 ASN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121081 restraints weight = 23669.381| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.03 r_work: 0.2936 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 21490 Z= 0.232 Angle : 0.569 12.358 29052 Z= 0.288 Chirality : 0.044 0.151 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.509 176.672 2954 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2669 helix: 0.96 (0.15), residues: 1165 sheet: -0.42 (0.29), residues: 311 loop : -0.65 (0.18), residues: 1193 =============================================================================== Job complete usr+sys time: 8895.22 seconds wall clock time: 158 minutes 0.46 seconds (9480.46 seconds total)