Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 01:09:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_13254_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_13254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_13254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_13254_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8n_13254/04_2023/7p8n_13254_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 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 Residue "a GLU 132": "OE1" <-> "OE2" Residue "a GLU 532": "OE1" <-> "OE2" Residue "b GLU 7": "OE1" <-> "OE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: 14.98, per 1000 atoms: 0.70 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 - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.87 Conformation dependent library (CDL) restraints added in 4.5 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... running ksdssp... Secondary structure from input PDB file: 131 helices and 23 sheets defined 42.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 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 234 No H-bonds generated for 'chain 'a' and resid 232 through 234' Processing helix chain 'a' and resid 244 through 254 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: 4.464A 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 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: 3.564A pdb=" N SER a 382 " --> pdb=" O LEU a 378 " (cutoff:3.500A) 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: 3.761A pdb=" N PHE a 408 " --> pdb=" O ALA a 404 " (cutoff:3.500A) removed outlier: 5.060A 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: 3.719A 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 581 No H-bonds generated for 'chain 'a' and resid 578 through 581' Processing helix chain 'a' and resid 585 through 598 Processing helix chain 'a' and resid 634 through 641 removed outlier: 3.686A pdb=" N GLU a 640 " --> pdb=" O LYS a 636 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 24 Processing helix chain 'b' and resid 41 through 54 Processing helix chain 'b' and resid 105 through 111 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 136 through 138 No H-bonds generated for 'chain 'b' and resid 136 through 138' 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 256 Processing helix chain 'b' and resid 271 through 286 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 368 through 371 No H-bonds generated for 'chain 'b' and resid 368 through 371' Processing helix chain 'b' and resid 404 through 409 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: 3.708A 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 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 556 Processing helix chain 'c' and resid 7 through 15 Processing helix chain 'c' and resid 19 through 33 removed outlier: 4.981A 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: 4.005A 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 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 244 through 254 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: 4.861A pdb=" N ALA A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 5.044A 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 removed outlier: 3.586A pdb=" N SER A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) 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: 3.830A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.188A 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: 3.726A 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 36 through 39 No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 102 through 111 Proline residue: B 106 - end of helix removed outlier: 3.628A 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 191 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 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 445 through 451 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) removed outlier: 3.881A pdb=" N ALA B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) No H-bonds generated for '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: 3.984A 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: 7.097A 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 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: 4.881A 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 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 156 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: 6.630A pdb=" N ILE a 368 " --> pdb=" O SER a 346 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N MET a 348 " --> pdb=" O ILE a 368 " (cutoff:3.500A) removed outlier: 5.942A 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: 3.738A 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 removed outlier: 6.017A pdb=" N GLY a 609 " --> pdb=" O GLU a 560 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU a 560 " --> pdb=" O GLY a 609 " (cutoff:3.500A) 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 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= J, first strand: chain 'b' and resid 347 through 352 removed outlier: 4.089A pdb=" N LYS b 261 " --> pdb=" O LYS b 219 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP b 302 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA b 264 " --> pdb=" O ASP b 302 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU b 304 " --> pdb=" O ALA b 264 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE b 266 " --> pdb=" O GLU b 304 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS b 306 " --> pdb=" O ILE b 266 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'b' and resid 394 through 399 removed outlier: 3.669A pdb=" N VAL b 462 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'c' and resid 112 through 117 removed outlier: 6.591A pdb=" N TYR c 73 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP c 115 " --> pdb=" O TYR c 73 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE c 75 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL c 117 " --> pdb=" O ILE c 75 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL c 77 " --> pdb=" O VAL c 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= N, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= O, first strand: chain 'A' and resid 136 through 138 Processing sheet with id= P, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= Q, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.599A pdb=" N LYS A 259 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 368 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N MET A 348 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU A 370 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 476 through 480 removed outlier: 3.831A pdb=" N LYS A 430 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id= S, 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= T, 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= U, first strand: chain 'B' and resid 348 through 352 removed outlier: 6.742A pdb=" N PHE B 220 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASN B 351 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 222 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 261 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 263 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 302 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA B 264 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 304 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 266 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS B 306 " --> pdb=" O ILE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= W, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.983A pdb=" N TYR C 73 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASP C 115 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 75 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 117 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 77 " --> pdb=" O VAL C 117 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2106 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: 7.08 Time building geometry restraints manager: 9.55 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=" N MET b 1 " pdb=" CA MET b 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N MET a 1 " pdb=" CA MET a 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" CB LYS B 570 " pdb=" CG LYS B 570 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.97e-01 ... (remaining 21485 not shown) Histogram of bond angle deviations from ideal: 73.51 - 85.61: 158 85.61 - 97.70: 0 97.70 - 109.80: 2427 109.80 - 121.90: 22225 121.90 - 134.00: 4242 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 109.81 115.24 -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=" 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 angle pdb=" C TYR c 33 " pdb=" N ARG c 34 " pdb=" CA ARG c 34 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.14e+00 angle pdb=" CB MET b 564 " pdb=" CG MET b 564 " pdb=" SD MET b 564 " ideal model delta sigma weight residual 112.70 106.22 6.48 3.00e+00 1.11e-01 4.67e+00 ... (remaining 29047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 12817 35.79 - 71.58: 213 71.58 - 107.37: 17 107.37 - 143.16: 0 143.16 - 178.95: 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 78.64 178.95 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 97.52 160.07 1 2.00e+01 2.50e-03 4.66e+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 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 13046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2124 0.031 - 0.062: 736 0.062 - 0.094: 226 0.094 - 0.125: 160 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: 3693 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 3690 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 169 2.53 - 3.12: 16824 3.12 - 3.71: 34796 3.71 - 4.31: 51541 4.31 - 4.90: 82775 Nonbonded interactions: 186105 Sorted by model distance: nonbonded pdb=" OG SER c 45 " pdb=" O ILE c 50 " model vdw 1.936 2.440 nonbonded pdb=" O HOH a 883 " pdb=" O HOH a 919 " model vdw 1.975 2.440 nonbonded pdb=" O HOH B 812 " pdb=" O HOH B 820 " model vdw 2.017 2.440 nonbonded pdb=" O HOH b 827 " pdb=" O HOH b 833 " model vdw 2.024 2.440 nonbonded pdb=" O HOH a 852 " pdb=" O HOH a 915 " model vdw 2.063 2.440 ... (remaining 186100 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 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: 2.580 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: 8.950 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 66.710 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.330 ------------------------------------------------------------------------------- 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 : 0.003 0.035 21490 Z= 0.167 Angle : 0.511 6.483 29052 Z= 0.269 Chirality : 0.041 0.156 3268 Planarity : 0.004 0.074 3693 Dihedral : 14.490 178.950 8149 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.14 % Rotamer Outliers : 0.00 % 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: 0.45 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.812 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 402 average time/residue: 1.6158 time to fit residues: 725.1601 Evaluate side-chains 308 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2605 time to fit residues: 4.0328 ------------------------------------------------------------------------------- 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: 0.3980 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 0.0670 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 241 optimal weight: 4.9990 overall best weight: 1.6522 ------------------------------------------------------------------------------- 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 A 538 HIS B 500 ASN C 42 ASN C 132 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 21490 Z= 0.263 Angle : 0.584 9.952 29052 Z= 0.302 Chirality : 0.045 0.243 3268 Planarity : 0.005 0.076 3693 Dihedral : 6.332 174.841 2954 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % 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: 0.32 (0.16), residues: 2669 helix: 1.21 (0.15), residues: 1154 sheet: -0.22 (0.30), residues: 294 loop : -0.60 (0.18), residues: 1221 *********************** 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 362 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 315 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 25 residues processed: 338 average time/residue: 1.5041 time to fit residues: 573.1468 Evaluate side-chains 317 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 14 residues processed: 12 average time/residue: 0.6224 time to fit residues: 12.9933 ------------------------------------------------------------------------------- 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: 7.9990 chunk 201 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 241 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 42 ASN A 403 GLN A 483 ASN C 42 ASN C 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21490 Z= 0.221 Angle : 0.551 9.256 29052 Z= 0.283 Chirality : 0.044 0.187 3268 Planarity : 0.005 0.062 3693 Dihedral : 6.371 174.921 2954 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer Outliers : 2.24 % 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 (0.16), residues: 2669 helix: 1.13 (0.15), residues: 1157 sheet: -0.17 (0.31), residues: 288 loop : -0.53 (0.18), residues: 1224 *********************** 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 361 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 310 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 23 residues processed: 337 average time/residue: 1.5534 time to fit residues: 591.6847 Evaluate side-chains 313 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 290 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 9 average time/residue: 0.8185 time to fit residues: 12.5645 ------------------------------------------------------------------------------- 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: 6.9990 chunk 181 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 257 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 42 ASN A 403 GLN C 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 21490 Z= 0.277 Angle : 0.589 9.044 29052 Z= 0.303 Chirality : 0.045 0.179 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.511 175.229 2954 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.10 % Rotamer Outliers : 2.46 % 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: 0.95 (0.15), residues: 1154 sheet: -0.21 (0.30), residues: 287 loop : -0.59 (0.18), residues: 1228 *********************** 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 362 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 306 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 335 average time/residue: 1.5155 time to fit residues: 572.8209 Evaluate side-chains 323 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 2.564 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 17 residues processed: 12 average time/residue: 0.5088 time to fit residues: 11.9204 ------------------------------------------------------------------------------- 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: 0.6980 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 C 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21490 Z= 0.203 Angle : 0.535 8.839 29052 Z= 0.275 Chirality : 0.043 0.155 3268 Planarity : 0.005 0.066 3693 Dihedral : 6.411 175.353 2954 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer Outliers : 2.20 % 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: 0.25 (0.16), residues: 2669 helix: 1.07 (0.15), residues: 1155 sheet: -0.24 (0.30), residues: 287 loop : -0.53 (0.18), residues: 1227 *********************** 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 354 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 304 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 338 average time/residue: 1.4585 time to fit residues: 559.5161 Evaluate side-chains 320 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 2.490 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 8 average time/residue: 0.9005 time to fit residues: 12.2288 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 257 optimal weight: 0.0670 chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1407 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= 0.236 Angle : 0.556 8.860 29052 Z= 0.286 Chirality : 0.044 0.155 3268 Planarity : 0.005 0.067 3693 Dihedral : 6.472 176.240 2954 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % 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: 0.19 (0.16), residues: 2669 helix: 0.99 (0.15), residues: 1158 sheet: -0.23 (0.30), residues: 285 loop : -0.55 (0.18), residues: 1226 *********************** 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 360 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 307 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 35 residues processed: 341 average time/residue: 1.4933 time to fit residues: 577.0620 Evaluate side-chains 332 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 2.530 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 13 average time/residue: 0.6915 time to fit residues: 14.8912 ------------------------------------------------------------------------------- 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: 0.3980 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN a 73 ASN A 403 GLN C 42 ASN C 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 21490 Z= 0.196 Angle : 0.532 8.917 29052 Z= 0.272 Chirality : 0.043 0.153 3268 Planarity : 0.005 0.066 3693 Dihedral : 6.425 176.486 2954 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % 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: 0.26 (0.16), residues: 2669 helix: 1.07 (0.15), residues: 1156 sheet: -0.25 (0.30), residues: 287 loop : -0.53 (0.18), residues: 1226 *********************** 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 351 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 305 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 336 average time/residue: 1.4982 time to fit residues: 571.0102 Evaluate side-chains 327 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 297 time to evaluate : 2.492 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 24 residues processed: 8 average time/residue: 0.6960 time to fit residues: 10.4951 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 201 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 21490 Z= 0.192 Angle : 0.530 8.938 29052 Z= 0.271 Chirality : 0.043 0.154 3268 Planarity : 0.004 0.066 3693 Dihedral : 6.393 176.176 2954 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.44 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.16), residues: 2669 helix: 1.11 (0.15), residues: 1156 sheet: -0.25 (0.30), residues: 287 loop : -0.52 (0.18), residues: 1226 *********************** 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 346 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 338 average time/residue: 1.4788 time to fit residues: 566.9822 Evaluate side-chains 329 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 303 time to evaluate : 2.614 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 23 residues processed: 5 average time/residue: 0.7874 time to fit residues: 8.5287 ------------------------------------------------------------------------------- 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: 2.9990 chunk 245 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 215 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21490 Z= 0.174 Angle : 0.516 9.005 29052 Z= 0.263 Chirality : 0.042 0.152 3268 Planarity : 0.004 0.068 3693 Dihedral : 6.358 177.817 2954 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % 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: 0.34 (0.16), residues: 2669 helix: 1.17 (0.15), residues: 1156 sheet: -0.25 (0.30), residues: 287 loop : -0.50 (0.18), residues: 1226 *********************** 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 341 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 333 average time/residue: 1.4895 time to fit residues: 563.0635 Evaluate side-chains 322 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 2.408 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 23 residues processed: 4 average time/residue: 0.5204 time to fit residues: 6.3493 ------------------------------------------------------------------------------- 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: 0.8980 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21490 Z= 0.207 Angle : 0.545 8.875 29052 Z= 0.277 Chirality : 0.043 0.153 3268 Planarity : 0.005 0.066 3693 Dihedral : 6.414 177.931 2954 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer Outliers : 1.54 % 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: 0.29 (0.16), residues: 2669 helix: 1.12 (0.15), residues: 1154 sheet: -0.25 (0.30), residues: 285 loop : -0.52 (0.18), residues: 1230 ********************** 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 335 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 300 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 329 average time/residue: 1.5006 time to fit residues: 559.2031 Evaluate side-chains 325 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 297 time to evaluate : 2.600 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 5 average time/residue: 0.4576 time to fit residues: 6.8621 ------------------------------------------------------------------------------- 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: 0.0980 chunk 64 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.152955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122838 restraints weight = 24089.570| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.99 r_work: 0.2925 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 21490 Z= 0.286 Angle : 0.602 8.878 29052 Z= 0.307 Chirality : 0.046 0.160 3268 Planarity : 0.005 0.068 3693 Dihedral : 6.580 177.537 2954 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.15), residues: 1156 sheet: -0.30 (0.30), residues: 285 loop : -0.59 (0.18), residues: 1228 =============================================================================== Job complete usr+sys time: 8651.20 seconds wall clock time: 153 minutes 59.34 seconds (9239.34 seconds total)