Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:48:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdj_14651/02_2023/7zdj_14651_updated.pdb" } resolution = 3.25 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= 0.008 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "4 GLU 172": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "X GLU 9": "OE1" <-> "OE2" Residue "Z GLU 171": "OE1" <-> "OE2" Residue "k GLU 178": "OE1" <-> "OE2" Residue "k GLU 216": "OE1" <-> "OE2" Residue "k PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 41": "OE1" <-> "OE2" Residue "n GLU 24": "OE1" <-> "OE2" Residue "p GLU 34": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "u GLU 8": "OE1" <-> "OE2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "v GLU 18": "OE1" <-> "OE2" Residue "v GLU 57": "OE1" <-> "OE2" Residue "w GLU 39": "OE1" <-> "OE2" Residue "x GLU 6": "OE1" <-> "OE2" Residue "y GLU 47": "OE1" <-> "OE2" Residue "1 GLU 248": "OE1" <-> "OE2" Residue "1 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 18": "OE1" <-> "OE2" Residue "3 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 58": "OE1" <-> "OE2" Residue "6 GLU 109": "OE1" <-> "OE2" Residue "9 GLU 9": "OE1" <-> "OE2" Residue "9 GLU 133": "OE1" <-> "OE2" Residue "9 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 27": "OE1" <-> "OE2" Residue "e GLU 37": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "i TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 13": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65812 Number of models: 1 Model: "" Number of chains: 55 Chain: "4" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1294 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43918 SG CYS 1 365 105.528 54.711 242.157 1.00 52.10 S ATOM 44242 SG CYS 1 405 109.004 49.289 241.170 1.00 42.94 S ATOM 43898 SG CYS 1 362 108.437 54.630 237.161 1.00 43.44 S ATOM 43879 SG CYS 1 359 112.330 54.577 242.528 1.00 47.82 S ATOM 45319 SG CYS 2 103 103.381 49.186 261.464 1.00127.58 S ATOM 45353 SG CYS 2 108 101.502 46.849 263.319 1.00 71.07 S ATOM 45633 SG CYS 2 144 105.112 45.542 257.765 1.00 80.93 S ATOM 45656 SG CYS 2 148 103.413 42.896 259.119 1.00 71.93 S ATOM 46996 SG CYS 3 114 107.926 73.408 227.819 1.00 40.01 S ATOM 46935 SG CYS 3 105 102.862 76.972 230.037 1.00 35.63 S ATOM 46956 SG CYS 3 108 109.042 78.610 231.378 1.00 36.35 S ATOM 47328 SG CYS 3 156 115.659 65.698 232.346 1.00 47.09 S ATOM 47305 SG CYS 3 153 113.385 68.653 237.705 1.00 35.44 S ATOM 47352 SG CYS 3 159 119.697 69.537 235.930 1.00 65.33 S ATOM 47682 SG CYS 3 203 115.248 72.085 232.376 1.00 61.22 S ATOM 46441 SG CYS 3 41 114.042 59.359 230.051 1.00 63.12 S ATOM 46527 SG CYS 3 52 110.471 60.139 229.149 1.00 53.10 S ATOM 46552 SG CYS 3 55 111.155 55.380 225.711 1.00 40.79 S ATOM 46653 SG CYS 3 69 114.589 55.411 227.132 1.00 40.72 S ATOM 53924 SG CYS 6 119 92.222 100.527 205.251 1.00 57.04 S ATOM 54154 SG CYS 6 149 89.419 98.179 210.368 1.00 70.43 S ATOM 53426 SG CYS 6 55 86.819 103.601 207.575 1.00 39.86 S ATOM 53420 SG CYS 6 54 85.891 98.002 204.956 1.00 54.21 S ATOM 55372 SG CYS 9 119 92.025 91.895 216.202 1.00 36.23 S ATOM 55346 SG CYS 9 116 93.751 98.289 216.972 1.00 34.77 S ATOM 55393 SG CYS 9 122 94.419 93.940 221.759 1.00 47.87 S ATOM 55120 SG CYS 9 87 98.228 93.709 216.372 1.00 47.86 S ATOM 55422 SG CYS 9 126 96.642 90.337 229.158 1.00 52.84 S ATOM 55093 SG CYS 9 83 100.264 92.098 223.957 1.00 50.95 S ATOM 55051 SG CYS 9 77 102.464 93.240 229.892 1.00 42.07 S ATOM 55070 SG CYS 9 80 101.726 86.960 227.533 1.00 48.56 S ATOM 56669 SG CYS b 59 98.534 85.479 244.543 1.00 52.43 S ATOM 56847 SG CYS b 84 101.538 85.551 242.253 1.00 46.04 S ATOM 56869 SG CYS b 87 99.992 88.336 243.242 1.00 45.92 S Time building chain proxies: 27.71, per 1000 atoms: 0.42 Number of scatterers: 65812 At special positions: 0 Unit cell: (179.34, 204.96, 294.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 466 16.00 P 9 15.00 O 11796 8.00 N 11125 7.00 C 42386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.08 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 300 " pdb="FE2 SF4 6 300 " - pdb=" SG CYS 6 149 " pdb="FE1 SF4 6 300 " - pdb=" SG CYS 6 119 " pdb="FE4 SF4 6 300 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 300 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 202 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 80 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 29 sheets defined 51.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain '4' and resid 8 through 13 Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.182A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 104 removed outlier: 3.945A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 100 through 104' Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.939A pdb=" N HIS 4 157 " --> pdb=" O ALA 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 184 removed outlier: 3.650A pdb=" N TRP 4 169 " --> pdb=" O THR 4 165 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE 4 180 " --> pdb=" O LYS 4 176 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.874A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 removed outlier: 3.537A pdb=" N LEU 4 251 " --> pdb=" O ALA 4 247 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN 4 252 " --> pdb=" O GLU 4 248 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 247 through 252' Processing helix chain '4' and resid 258 through 263 removed outlier: 3.766A pdb=" N SER 4 263 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 removed outlier: 3.506A pdb=" N ASN 4 316 " --> pdb=" O SER 4 312 " (cutoff:3.500A) Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 351 Processing helix chain '4' and resid 394 through 405 removed outlier: 3.586A pdb=" N ALA 4 400 " --> pdb=" O PHE 4 396 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY 4 401 " --> pdb=" O ALA 4 397 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 4 402 " --> pdb=" O HIS 4 398 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.150A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.827A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.572A pdb=" N GLN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 removed outlier: 3.502A pdb=" N ILE H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 3.868A pdb=" N MET H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.480A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 removed outlier: 3.531A pdb=" N PHE J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 Processing helix chain 'J' and resid 50 through 59 Processing helix chain 'J' and resid 64 through 74 removed outlier: 3.759A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.797A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.351A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 27 through 50 Processing helix chain 'K' and resid 55 through 84 Proline residue: K 60 - end of helix removed outlier: 4.656A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 23 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 56 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 235 Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.438A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.321A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.750A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP L 393 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 Processing helix chain 'L' and resid 448 through 471 removed outlier: 5.890A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 508 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 5.401A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 5.032A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.268A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 41 removed outlier: 4.194A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 Proline residue: M 74 - end of helix removed outlier: 3.972A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.594A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.668A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 150 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.421A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.628A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.648A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.397A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 266 removed outlier: 3.835A pdb=" N MET M 263 " --> pdb=" O TYR M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 278 removed outlier: 3.709A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 391 through 415 removed outlier: 4.686A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 447 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 4.302A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 5.424A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 169 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.636A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 269 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 4.349A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 79 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.236A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 19 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 56 through 76 removed outlier: 4.139A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 114 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 4.145A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 44 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 141 removed outlier: 3.825A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 159 Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 189 through 193 removed outlier: 3.970A pdb=" N MET k 192 " --> pdb=" O PRO k 189 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS k 193 " --> pdb=" O HIS k 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 189 through 193' Processing helix chain 'k' and resid 196 through 209 removed outlier: 3.591A pdb=" N THR k 209 " --> pdb=" O VAL k 205 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 238 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 15 through 17 No H-bonds generated for 'chain 'l' and resid 15 through 17' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 48 through 54 Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 31 Processing helix chain 'm' and resid 38 through 46 Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 37 Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 removed outlier: 3.634A pdb=" N GLU n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 Processing helix chain 'p' and resid 19 through 21 No H-bonds generated for 'chain 'p' and resid 19 through 21' Processing helix chain 'p' and resid 26 through 50 Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 137 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 68 through 72 removed outlier: 4.073A pdb=" N THR r 72 " --> pdb=" O PHE r 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 9 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 5.065A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 70 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 5.882A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 33 removed outlier: 4.893A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.316A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.651A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 3.928A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain 'z' and resid 66 through 68 No H-bonds generated for 'chain 'z' and resid 66 through 68' Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.617A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 62 Processing helix chain '1' and resid 75 through 80 Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 311 through 314 removed outlier: 3.793A pdb=" N THR 1 314 " --> pdb=" O VAL 1 311 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 311 through 314' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.467A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 4.059A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 4.254A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 197 through 202 Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 271 through 274 No H-bonds generated for 'chain '3' and resid 271 through 274' Processing helix chain '3' and resid 296 through 308 Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 427 through 434 Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 463 through 479 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 650 Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 4.706A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix Processing helix chain '5' and resid 126 through 138 removed outlier: 5.303A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 118 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 175 removed outlier: 5.729A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.393A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 Processing helix chain 'b' and resid 40 through 45 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.159A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.558A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 30 through 41 removed outlier: 3.616A pdb=" N ARG d 40 " --> pdb=" O ASN d 36 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 4.735A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 310 through 321 removed outlier: 4.636A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 36 removed outlier: 4.718A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 44 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.295A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.983A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.136A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 83 Processing sheet with id= A, first strand: chain '4' and resid 47 through 51 removed outlier: 3.554A pdb=" N ARG 4 63 " --> pdb=" O HIS 4 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '4' and resid 361 through 368 Processing sheet with id= C, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= E, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.594A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.591A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 219 through 224 removed outlier: 6.140A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 266 through 271 Processing sheet with id= I, first strand: chain '2' and resid 137 through 142 removed outlier: 6.612A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 9 through 13 Processing sheet with id= K, first strand: chain '3' and resid 146 through 148 Processing sheet with id= L, first strand: chain '3' and resid 173 through 175 Processing sheet with id= M, first strand: chain '3' and resid 223 through 228 Processing sheet with id= N, first strand: chain '3' and resid 283 through 285 Processing sheet with id= O, first strand: chain '3' and resid 343 through 345 removed outlier: 8.526A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 490 through 493 removed outlier: 8.222A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '3' and resid 572 through 574 Processing sheet with id= R, first strand: chain '5' and resid 74 through 82 removed outlier: 6.753A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '5' and resid 172 through 177 Processing sheet with id= T, first strand: chain '6' and resid 47 through 51 removed outlier: 6.651A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '9' and resid 65 through 67 Processing sheet with id= V, first strand: chain '9' and resid 92 through 98 removed outlier: 5.751A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= X, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Y, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.617A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.971A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.336A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 2846 hydrogen bonds defined for protein. 7884 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: 19.12 Time building geometry restraints manager: 23.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 28520 1.43 - 1.65: 38127 1.65 - 1.87: 759 1.87 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 67486 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+01 bond pdb=" C13 ZMP j 101 " pdb=" N1 ZMP j 101 " ideal model delta sigma weight residual 1.451 1.337 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C ILE H 87 " pdb=" N PRO H 88 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.22e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.339 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.339 0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 67481 not shown) Histogram of bond angle deviations from ideal: 69.99 - 83.13: 78 83.13 - 96.27: 3 96.27 - 109.40: 6419 109.40 - 122.54: 77783 122.54 - 135.68: 7248 Bond angle restraints: 91531 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 73.65 46.95 3.00e+00 1.11e-01 2.45e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.95 38.35 3.00e+00 1.11e-01 1.63e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.75 -24.01 1.95e+00 2.62e-01 1.51e+02 angle pdb=" C5B NDP d 401 " pdb=" O5B NDP d 401 " pdb=" PA NDP d 401 " ideal model delta sigma weight residual 103.84 119.60 -15.76 1.91e+00 2.73e-01 6.77e+01 angle pdb=" C5D NDP d 401 " pdb=" O5D NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 104.93 124.62 -19.69 2.66e+00 1.41e-01 5.48e+01 ... (remaining 91526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 39036 33.99 - 67.99: 1380 67.99 - 101.98: 88 101.98 - 135.98: 1 135.98 - 169.97: 1 Dihedral angle restraints: 40506 sinusoidal: 16736 harmonic: 23770 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -136.41 -43.59 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -145.09 -34.91 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" C10 FMN 1 502 " pdb=" C1' FMN 1 502 " pdb=" N10 FMN 1 502 " pdb=" C2' FMN 1 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.62 169.97 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 40503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.250: 10048 4.250 - 8.499: 0 8.499 - 12.749: 0 12.749 - 16.999: 0 16.999 - 21.249: 24 Chirality restraints: 10072 Sorted by residual: chirality pdb="FE3 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S4 SF4 6 300 " both_signs ideal model delta sigma weight residual False -10.55 10.69 -21.25 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 6 300 " pdb=" S1 SF4 6 300 " pdb=" S2 SF4 6 300 " pdb=" S3 SF4 6 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.60 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10069 not shown) Planarity restraints: 11566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Z 12 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO Z 13 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO Z 13 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO Z 13 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 37 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO 4 38 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO 4 38 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO 4 38 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL 3 338 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C VAL 3 338 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL 3 338 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP 3 339 " -0.017 2.00e-02 2.50e+03 ... (remaining 11563 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 15014 2.78 - 3.37: 69712 3.37 - 3.96: 128233 3.96 - 4.55: 182008 4.55 - 5.14: 269001 Nonbonded interactions: 663968 Sorted by model distance: nonbonded pdb=" O MET M 243 " pdb=" OG1 THR M 247 " model vdw 2.195 2.440 nonbonded pdb=" O LEU N 337 " pdb=" OG1 THR N 340 " model vdw 2.220 2.440 nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.223 2.440 nonbonded pdb=" O PHE H 293 " pdb=" OG1 THR H 297 " model vdw 2.238 2.440 nonbonded pdb=" OE2 GLU 4 143 " pdb=" OH TYR 4 278 " model vdw 2.240 2.440 ... (remaining 663963 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 'X' and (resid 5 through 86 or resid 101)) selection = (chain 'j' and (resid 5 through 86 or (resid 101 and (name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 o \ r name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or n \ ame O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or name \ S1 )))) } 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 9 5.49 5 S 466 5.16 5 C 42386 2.51 5 N 11125 2.21 5 O 11796 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=1.00 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: 0.220 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: 0.040 Extract box with map and model: 6.410 Check model and map are aligned: 0.720 Process input model: 150.410 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.490 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 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 : 0.005 0.221 67486 Z= 0.295 Angle : 0.766 46.954 91531 Z= 0.383 Chirality : 1.032 21.249 10072 Planarity : 0.006 0.109 11566 Dihedral : 16.214 169.974 25155 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.84 % Favored : 97.15 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.38 (0.09), residues: 8039 helix: 0.18 (0.07), residues: 4275 sheet: 0.08 (0.26), residues: 413 loop : -0.74 (0.10), residues: 3351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 987 time to evaluate : 6.502 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 1000 average time/residue: 0.6852 time to fit residues: 1152.8236 Evaluate side-chains 965 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 958 time to evaluate : 6.217 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5125 time to fit residues: 15.0486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 0.9980 chunk 602 optimal weight: 5.9990 chunk 334 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 623 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 721 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 320 ASN L 447 ASN M 103 GLN M 188 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN N 235 ASN Z 114 GLN Z 120 HIS k 141 GLN n 20 GLN o 12 GLN p 78 ASN ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 65 HIS b 51 GLN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 GLN e 61 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 112 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.257 67486 Z= 0.561 Angle : 1.557 50.658 91531 Z= 1.013 Chirality : 0.315 6.488 10072 Planarity : 0.004 0.071 11566 Dihedral : 5.650 170.755 9022 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.65 % Favored : 97.34 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.39 (0.09), residues: 8039 helix: 0.99 (0.08), residues: 4270 sheet: 0.00 (0.26), residues: 421 loop : -0.59 (0.10), residues: 3348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 983 time to evaluate : 6.366 Fit side-chains outliers start: 141 outliers final: 74 residues processed: 1066 average time/residue: 0.6531 time to fit residues: 1176.4822 Evaluate side-chains 1024 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 950 time to evaluate : 6.207 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.4969 time to fit residues: 77.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 600 optimal weight: 20.0000 chunk 491 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 723 optimal weight: 10.0000 chunk 781 optimal weight: 3.9990 chunk 644 optimal weight: 0.0370 chunk 717 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 580 optimal weight: 8.9990 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN n 20 GLN ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 ASN e 61 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.251 67486 Z= 0.547 Angle : 1.551 50.589 91531 Z= 1.012 Chirality : 0.310 6.383 10072 Planarity : 0.004 0.057 11566 Dihedral : 5.301 170.572 9022 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.31 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.74 (0.09), residues: 8039 helix: 1.30 (0.08), residues: 4275 sheet: 0.02 (0.26), residues: 423 loop : -0.45 (0.11), residues: 3341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 992 time to evaluate : 6.901 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 40 residues processed: 1062 average time/residue: 0.6919 time to fit residues: 1251.3452 Evaluate side-chains 1001 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 961 time to evaluate : 6.225 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5233 time to fit residues: 47.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 7.9990 chunk 543 optimal weight: 0.0970 chunk 375 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 485 optimal weight: 7.9990 chunk 725 optimal weight: 10.0000 chunk 768 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 687 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN L 514 ASN M 169 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 HIS ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 ASN 6 106 GLN b 51 GLN c 46 GLN d 119 GLN e 61 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.251 67486 Z= 0.593 Angle : 1.569 50.988 91531 Z= 1.019 Chirality : 0.311 6.498 10072 Planarity : 0.004 0.050 11566 Dihedral : 5.276 170.534 9022 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.99 % Favored : 97.00 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.81 (0.09), residues: 8039 helix: 1.39 (0.08), residues: 4262 sheet: -0.01 (0.26), residues: 419 loop : -0.43 (0.11), residues: 3358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 966 time to evaluate : 6.284 Fit side-chains revert: symmetry clash outliers start: 130 outliers final: 64 residues processed: 1058 average time/residue: 0.6885 time to fit residues: 1234.7154 Evaluate side-chains 1004 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 940 time to evaluate : 6.228 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5112 time to fit residues: 70.0288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 3.9990 chunk 436 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 572 optimal weight: 0.0170 chunk 317 optimal weight: 6.9990 chunk 655 optimal weight: 6.9990 chunk 531 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 689 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN K 7 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN M 169 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 155 HIS 6 106 GLN c 46 GLN d 119 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 67486 Z= 0.562 Angle : 1.559 50.873 91531 Z= 1.015 Chirality : 0.310 6.388 10072 Planarity : 0.004 0.047 11566 Dihedral : 5.174 170.370 9022 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.72 % Favored : 97.26 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.94 (0.10), residues: 8039 helix: 1.50 (0.08), residues: 4258 sheet: -0.01 (0.25), residues: 421 loop : -0.36 (0.11), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 982 time to evaluate : 6.399 Fit side-chains outliers start: 88 outliers final: 37 residues processed: 1036 average time/residue: 0.6765 time to fit residues: 1184.7762 Evaluate side-chains 985 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 948 time to evaluate : 6.239 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.5565 time to fit residues: 45.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 20.0000 chunk 692 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 451 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 769 optimal weight: 9.9990 chunk 638 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 31 ASN L 320 ASN M 169 ASN M 188 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 ASN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 459 GLN 6 106 GLN e 61 GLN ** f 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.248 67486 Z= 0.588 Angle : 1.569 51.109 91531 Z= 1.019 Chirality : 0.311 6.508 10072 Planarity : 0.004 0.046 11566 Dihedral : 5.208 170.384 9022 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.18 % Favored : 96.80 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.92 (0.10), residues: 8039 helix: 1.46 (0.08), residues: 4267 sheet: -0.03 (0.25), residues: 419 loop : -0.36 (0.11), residues: 3353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 952 time to evaluate : 6.451 Fit side-chains outliers start: 99 outliers final: 54 residues processed: 1021 average time/residue: 0.6793 time to fit residues: 1177.8921 Evaluate side-chains 982 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 928 time to evaluate : 6.274 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5531 time to fit residues: 63.5117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 5.9990 chunk 86 optimal weight: 0.0770 chunk 438 optimal weight: 8.9990 chunk 561 optimal weight: 7.9990 chunk 435 optimal weight: 10.0000 chunk 647 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 766 optimal weight: 4.9990 chunk 479 optimal weight: 5.9990 chunk 467 optimal weight: 0.8980 chunk 353 optimal weight: 10.0000 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 86 ASN K 7 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 ASN N 235 ASN V 18 HIS n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 GLN e 61 GLN ** f 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 67486 Z= 0.557 Angle : 1.560 50.787 91531 Z= 1.015 Chirality : 0.310 6.415 10072 Planarity : 0.004 0.045 11566 Dihedral : 5.134 170.252 9022 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.77 % Favored : 97.21 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.03 (0.10), residues: 8039 helix: 1.55 (0.08), residues: 4262 sheet: -0.02 (0.25), residues: 422 loop : -0.30 (0.11), residues: 3355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 963 time to evaluate : 6.299 Fit side-chains outliers start: 44 outliers final: 21 residues processed: 995 average time/residue: 0.6729 time to fit residues: 1130.2890 Evaluate side-chains 969 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 948 time to evaluate : 6.342 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5321 time to fit residues: 29.0466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 457 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 487 optimal weight: 10.0000 chunk 522 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 602 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 GLN e 61 GLN ** f 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.253 67486 Z= 0.561 Angle : 1.560 51.004 91531 Z= 1.016 Chirality : 0.310 6.519 10072 Planarity : 0.004 0.045 11566 Dihedral : 5.104 170.130 9022 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.08 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.05 (0.10), residues: 8039 helix: 1.57 (0.08), residues: 4264 sheet: -0.03 (0.25), residues: 423 loop : -0.28 (0.11), residues: 3352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 966 time to evaluate : 7.590 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 987 average time/residue: 0.6831 time to fit residues: 1141.5906 Evaluate side-chains 954 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 936 time to evaluate : 6.335 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5437 time to fit residues: 26.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.5980 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 5.9990 chunk 714 optimal weight: 10.0000 chunk 733 optimal weight: 7.9990 chunk 429 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 645 optimal weight: 4.9990 chunk 675 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 25 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 GLN e 61 GLN ** f 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.250 67486 Z= 0.559 Angle : 1.560 50.820 91531 Z= 1.016 Chirality : 0.310 6.450 10072 Planarity : 0.004 0.047 11566 Dihedral : 5.081 170.027 9022 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.84 % Favored : 97.15 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.07 (0.10), residues: 8039 helix: 1.60 (0.08), residues: 4253 sheet: 0.00 (0.25), residues: 423 loop : -0.28 (0.11), residues: 3363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 941 time to evaluate : 6.380 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 958 average time/residue: 0.6871 time to fit residues: 1114.6933 Evaluate side-chains 953 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 934 time to evaluate : 6.563 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5464 time to fit residues: 27.6659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 9.9990 chunk 468 optimal weight: 10.0000 chunk 755 optimal weight: 0.9990 chunk 460 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 524 optimal weight: 5.9990 chunk 792 optimal weight: 20.0000 chunk 728 optimal weight: 9.9990 chunk 630 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 487 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN n 20 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 ASN 6 106 GLN b 51 GLN e 61 GLN f 49 GLN ** f 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.250 67486 Z= 0.552 Angle : 1.559 50.770 91531 Z= 1.015 Chirality : 0.310 6.433 10072 Planarity : 0.004 0.051 11566 Dihedral : 5.025 169.862 9022 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.87 % Favored : 97.11 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.13 (0.10), residues: 8039 helix: 1.63 (0.08), residues: 4259 sheet: 0.02 (0.25), residues: 422 loop : -0.24 (0.11), residues: 3358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16078 Ramachandran restraints generated. 8039 Oldfield, 0 Emsley, 8039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 967 time to evaluate : 6.446 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 974 average time/residue: 0.7146 time to fit residues: 1178.7698 Evaluate side-chains 949 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 946 time to evaluate : 6.341 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6893 time to fit residues: 11.9281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 30.0000 chunk 500 optimal weight: 6.9990 chunk 671 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 581 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 631 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 648 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN L 320 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN n 20 GLN p 47 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 ASN 6 106 GLN b 51 GLN e 61 GLN ** g 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 5 GLN i 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061543 restraints weight = 136354.415| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.72 r_work: 0.2755 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.251 67486 Z= 0.546 Angle : 1.555 50.747 91531 Z= 1.014 Chirality : 0.310 6.426 10072 Planarity : 0.004 0.051 11566 Dihedral : 4.956 169.645 9022 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.74 % Favored : 97.25 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.19 (0.10), residues: 8039 helix: 1.68 (0.08), residues: 4259 sheet: 0.07 (0.25), residues: 423 loop : -0.22 (0.11), residues: 3357 =============================================================================== Job complete usr+sys time: 17802.78 seconds wall clock time: 312 minutes 17.06 seconds (18737.06 seconds total)