Starting phenix.real_space_refine (version: dev) on Sat Feb 25 16:55:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zd6_14637/02_2023/7zd6_14637_updated.pdb" } resolution = 3.16 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= 0.011 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 9": "OE1" <-> "OE2" Residue "X GLU 28": "OE1" <-> "OE2" Residue "k GLU 178": "OE1" <-> "OE2" Residue "m GLU 15": "OE1" <-> "OE2" Residue "m GLU 78": "OE1" <-> "OE2" Residue "p GLU 21": "OE1" <-> "OE2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "u GLU 8": "OE1" <-> "OE2" Residue "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 6": "OE1" <-> "OE2" Residue "x GLU 37": "OE1" <-> "OE2" Residue "3 GLU 287": "OE1" <-> "OE2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 37": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "g TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 2": "OE1" <-> "OE2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 57": "OE1" <-> "OE2" Residue "j GLU 75": "OE1" <-> "OE2" 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: 66748 Number of models: 1 Model: "" Number of chains: 63 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: "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: "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: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "H" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 179 Unusual residues: {'3PE': 2, 'DCQ': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'3PE': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "V" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 53 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: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'3PE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 40528 SG CYS 1 365 103.033 55.736 244.744 1.00 42.86 S ATOM 40852 SG CYS 1 405 106.292 50.075 243.843 1.00 30.63 S ATOM 40508 SG CYS 1 362 105.659 55.257 239.660 1.00 47.78 S ATOM 40489 SG CYS 1 359 109.808 55.251 244.841 1.00 30.86 S ATOM 41929 SG CYS 2 103 101.324 50.882 264.281 1.00104.54 S ATOM 41963 SG CYS 2 108 99.380 48.677 266.204 1.00 61.94 S ATOM 42243 SG CYS 2 144 102.907 47.094 260.710 1.00 70.59 S ATOM 42266 SG CYS 2 148 101.027 44.518 262.172 1.00 91.19 S ATOM 43606 SG CYS 3 114 105.732 73.898 229.589 1.00 28.50 S ATOM 43545 SG CYS 3 105 100.771 77.597 231.792 1.00 35.91 S ATOM 43566 SG CYS 3 108 107.065 79.110 233.019 1.00 28.32 S ATOM 43938 SG CYS 3 156 113.179 66.075 234.237 1.00 27.52 S ATOM 43915 SG CYS 3 153 111.258 69.320 239.599 1.00 25.65 S ATOM 43962 SG CYS 3 159 117.501 69.810 237.542 1.00 87.22 S ATOM 44292 SG CYS 3 203 113.105 72.421 234.019 1.00 35.83 S ATOM 43051 SG CYS 3 41 111.251 59.787 232.103 1.00 39.55 S ATOM 43137 SG CYS 3 52 107.751 60.579 231.370 1.00 54.11 S ATOM 43162 SG CYS 3 55 108.008 55.671 228.118 1.00 34.34 S ATOM 43263 SG CYS 3 69 111.551 55.581 229.309 1.00 40.83 S ATOM 53924 SG CYS 6 119 90.122 100.491 206.766 1.00 25.26 S ATOM 54154 SG CYS 6 149 87.441 98.576 212.081 1.00 27.01 S ATOM 53426 SG CYS 6 55 84.900 103.843 209.123 1.00 15.46 S ATOM 53420 SG CYS 6 54 83.706 98.226 206.711 1.00 47.28 S ATOM 55372 SG CYS 9 119 89.982 92.430 217.901 1.00 25.14 S ATOM 55346 SG CYS 9 116 91.955 98.765 218.338 1.00 35.35 S ATOM 55393 SG CYS 9 122 92.664 94.536 223.260 1.00 28.80 S ATOM 55120 SG CYS 9 87 96.245 93.996 217.770 1.00 21.44 S ATOM 55422 SG CYS 9 126 94.999 91.108 230.777 1.00 25.71 S ATOM 55093 SG CYS 9 83 98.491 92.666 225.445 1.00 43.22 S ATOM 55051 SG CYS 9 77 100.876 93.998 231.216 1.00 22.13 S ATOM 55070 SG CYS 9 80 99.872 87.585 229.086 1.00 27.07 S ATOM 56669 SG CYS b 59 97.064 86.709 246.253 1.00 52.84 S ATOM 56847 SG CYS b 84 100.101 86.620 243.895 1.00 29.90 S ATOM 56869 SG CYS b 87 98.588 89.566 244.825 1.00 55.57 S Time building chain proxies: 27.52, per 1000 atoms: 0.41 Number of scatterers: 66748 At special positions: 0 Unit cell: (176.9, 198.86, 295.24, 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 30 15.00 O 11967 8.00 N 11149 7.00 C 43106 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=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 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: 22.71 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " 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 6 201 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " 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="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " 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 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " 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: 339 helices and 30 sheets defined 51.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... 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: 5.727A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.495A 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 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 56 Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.551A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 4.061A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.669A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) 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 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 275 removed outlier: 3.636A pdb=" N ALA H 275 " --> pdb=" O LEU H 271 " (cutoff:3.500A) 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 2 through 21 removed outlier: 3.577A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 65 through 73 Processing helix chain 'J' and resid 87 through 110 removed outlier: 3.755A pdb=" N ASP J 110 " --> pdb=" O TYR J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.354A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 4 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 4.083A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.538A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 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 155 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 232 through 238 removed outlier: 4.398A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.233A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.500A 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: 4.332A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.086A 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 388 through 400 removed outlier: 3.502A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 394 " --> pdb=" O SER L 391 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 removed outlier: 6.074A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.502A 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 547 removed outlier: 3.565A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.844A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.548A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 558 through 561 No H-bonds generated for 'chain 'L' and resid 558 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: 4.032A 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 42 removed outlier: 4.269A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.656A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.765A 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 142 through 171 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.648A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.448A 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 237 through 249 removed outlier: 4.907A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.701A pdb=" N PHE M 256 " --> pdb=" O ILE M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.171A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.643A 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 392 through 415 Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.085A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.628A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for '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 113 through 121 removed outlier: 4.697A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 133 Processing helix chain 'N' and resid 135 through 144 removed outlier: 3.733A pdb=" N MET N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) 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 171 removed outlier: 4.421A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) 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 235 removed outlier: 4.208A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 259 through 272 removed outlier: 4.524A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS N 272 " --> pdb=" O GLN N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 4.333A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 315 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 removed outlier: 3.565A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) 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 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.336A 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 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 20 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 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 76 removed outlier: 3.950A 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 removed outlier: 3.553A pdb=" N LYS Z 57 " --> pdb=" O ARG Z 53 " (cutoff:3.500A) 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 115 Processing helix chain 'Z' and resid 117 through 123 removed outlier: 3.576A pdb=" N HIS Z 120 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG Z 121 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN Z 123 " --> pdb=" O HIS Z 120 " (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 9 Processing helix chain 'k' and resid 35 through 43 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 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.338A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.236A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 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 306 through 308 No H-bonds generated for 'chain 'k' and resid 306 through 308' Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'l' and resid 5 through 9 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 43 Processing helix chain 'l' and resid 47 through 51 Processing helix chain 'l' and resid 56 through 66 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 removed outlier: 3.525A pdb=" N LYS m 9 " --> pdb=" O ALA m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 45 Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 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 16 through 20 removed outlier: 3.534A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 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 126 removed outlier: 5.803A pdb=" N LEU q 126 " --> pdb=" O GLU q 122 " (cutoff:3.500A) Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 81 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: 5.025A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.537A 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 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 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.859A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (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 13 No H-bonds generated for 'chain 'y' and resid 11 through 13' Processing helix chain 'y' and resid 15 through 33 Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 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: 3.531A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 50 Processing helix chain '1' and resid 53 through 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.537A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 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 184 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 243 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 301 through 303 No H-bonds generated for 'chain '1' and resid 301 through 303' Processing helix chain '1' and resid 309 through 314 removed outlier: 3.646A pdb=" N GLU 1 313 " --> pdb=" O LYS 1 309 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR 1 314 " --> pdb=" O SER 1 310 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 309 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: 4.486A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 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: 4.492A 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 removed outlier: 3.865A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 97 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 123 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 309 removed outlier: 3.820A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) 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 373 removed outlier: 3.696A pdb=" N GLU 3 372 " --> pdb=" O ALA 3 369 " (cutoff:3.500A) 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 426 through 433 removed outlier: 3.626A pdb=" N ALA 3 433 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 456 through 459 removed outlier: 3.543A pdb=" N GLN 3 459 " --> pdb=" O SER 3 456 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 456 through 459' Processing helix chain '3' and resid 463 through 480 removed outlier: 3.514A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 499 through 505 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 607 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 649 Processing helix chain '3' and resid 669 through 672 No H-bonds generated for 'chain '3' and resid 669 through 672' 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 '4' and resid 8 through 14 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 92 Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 185 removed outlier: 4.264A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.169A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 removed outlier: 3.609A pdb=" N ARG 4 238 " --> pdb=" O ILE 4 234 " (cutoff:3.500A) Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 258 through 263 removed outlier: 4.112A 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 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 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.586A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 17 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.669A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.917A 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 125 through 138 removed outlier: 3.599A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (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 106 Processing helix chain '6' and resid 117 through 121 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 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.785A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.895A 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 60 removed outlier: 4.634A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.662A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 46 removed outlier: 3.845A pdb=" N GLU b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) 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 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.504A 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 118 through 122 Processing helix chain 'd' and resid 30 through 41 removed outlier: 4.070A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 4.712A pdb=" N HIS d 58 " --> pdb=" O TYR d 54 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU d 59 " --> 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 185 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 318 removed outlier: 4.934A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 46 removed outlier: 4.842A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR e 40 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL e 41 " --> pdb=" O LYS e 38 " (cutoff:3.500A) 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: 4.279A 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 105 removed outlier: 4.465A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) 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: 3.856A 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 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.210A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 20 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 82 Processing sheet with id= A, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= B, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.291A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.515A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 219 through 224 removed outlier: 6.478A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 266 through 271 Processing sheet with id= G, first strand: chain '2' and resid 137 through 142 removed outlier: 6.718A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 9 through 13 Processing sheet with id= I, first strand: chain '3' and resid 56 through 58 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 removed outlier: 6.354A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 343 through 345 removed outlier: 8.532A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '3' and resid 490 through 493 removed outlier: 8.264A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '3' and resid 571 through 574 Processing sheet with id= Q, first strand: chain '4' and resid 47 through 51 Processing sheet with id= R, first strand: chain '4' and resid 361 through 369 Processing sheet with id= S, first strand: chain '5' and resid 74 through 82 removed outlier: 6.836A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '5' and resid 172 through 177 Processing sheet with id= U, first strand: chain '6' and resid 47 through 51 removed outlier: 6.572A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '9' and resid 65 through 67 Processing sheet with id= W, first strand: chain '9' and resid 92 through 98 removed outlier: 5.934A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= Y, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Z, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= AA, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AB, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.484A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.867A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.410A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 2889 hydrogen bonds defined for protein. 8214 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: 21.03 Time building geometry restraints manager: 24.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28089 1.42 - 1.64: 39476 1.64 - 1.86: 759 1.86 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 68404 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.606 0.227 3.80e-02 6.93e+02 3.55e+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 3.23e+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 3.21e+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 3.15e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.452 1.345 0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 68399 not shown) Histogram of bond angle deviations from ideal: 69.72 - 83.48: 78 83.48 - 97.24: 5 97.24 - 111.00: 25963 111.00 - 124.77: 65042 124.77 - 138.53: 1498 Bond angle restraints: 92586 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 74.48 46.12 3.00e+00 1.11e-01 2.36e+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 70.69 38.61 3.00e+00 1.11e-01 1.66e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.72 -23.98 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 103.84 118.87 -15.03 1.91e+00 2.73e-01 6.16e+01 angle pdb=" O3 NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 98.63 121.66 -23.03 3.00e+00 1.11e-01 5.89e+01 ... (remaining 92581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 39812 34.19 - 68.38: 1226 68.38 - 102.57: 89 102.57 - 136.76: 1 136.76 - 170.95: 2 Dihedral angle restraints: 41130 sinusoidal: 17360 harmonic: 23770 Sorted by residual: dihedral pdb=" CB CYS l 42 " pdb=" SG CYS l 42 " pdb=" SG CYS l 55 " pdb=" CB CYS l 55 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS s 68 " pdb=" SG CYS s 68 " pdb=" SG CYS s 79 " pdb=" CB CYS s 79 " ideal model delta sinusoidal sigma weight residual -86.00 -163.16 77.16 1 1.00e+01 1.00e-02 7.47e+01 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 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 41127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.241: 10072 4.241 - 8.483: 0 8.483 - 12.724: 0 12.724 - 16.965: 0 16.965 - 21.206: 24 Chirality restraints: 10096 Sorted by residual: chirality pdb="FE3 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S4 SF4 6 201 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 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 10.58 -21.14 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10093 not shown) Planarity restraints: 11608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " -0.039 2.00e-02 2.50e+03 5.00e-02 7.51e+01 pdb=" C1M DCQ H 501 " -0.083 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.002 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.012 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " 0.020 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.115 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " 0.016 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " 0.063 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " -0.042 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Y 36 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" CG ASP Y 36 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP Y 36 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP Y 36 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP w 54 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" CG ASP w 54 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP w 54 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP w 54 " 0.017 2.00e-02 2.50e+03 ... (remaining 11605 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.78: 13952 2.78 - 3.37: 70017 3.37 - 3.96: 130535 3.96 - 4.55: 186121 4.55 - 5.14: 275901 Nonbonded interactions: 676526 Sorted by model distance: nonbonded pdb=" OE1 GLU H 24 " pdb=" OH TYR H 228 " model vdw 2.184 2.440 nonbonded pdb=" OE2 GLU N 34 " pdb=" OG SER N 67 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASP g 116 " pdb=" OG SER g 119 " model vdw 2.232 2.440 nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.243 2.440 ... (remaining 676521 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 30 5.49 5 S 466 5.16 5 C 43106 2.51 5 N 11149 2.21 5 O 11967 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: 0.260 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: 0.050 Extract box with map and model: 6.270 Check model and map are aligned: 0.700 Process input model: 153.030 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.460 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 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 : 0.006 0.227 68404 Z= 0.398 Angle : 0.797 46.115 92586 Z= 0.391 Chirality : 1.030 21.206 10096 Planarity : 0.006 0.068 11608 Dihedral : 15.779 170.954 25779 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -0.24 (0.09), residues: 8039 helix: 0.36 (0.07), residues: 4310 sheet: 0.19 (0.26), residues: 413 loop : -0.78 (0.10), residues: 3316 *********************** 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 720 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 701 time to evaluate : 6.159 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 712 average time/residue: 0.6892 time to fit residues: 832.4403 Evaluate side-chains 690 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 682 time to evaluate : 6.118 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6153 time to fit residues: 17.1365 ------------------------------------------------------------------------------- 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: 20.0000 chunk 602 optimal weight: 1.9990 chunk 334 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 321 optimal weight: 5.9990 chunk 623 optimal weight: 5.9990 chunk 241 optimal weight: 0.0970 chunk 378 optimal weight: 8.9990 chunk 463 optimal weight: 2.9990 chunk 721 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN L 447 ASN M 43 ASN M 399 ASN k 287 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 88 HIS y 30 ASN ** y 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 65 HIS f 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.0492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.256 68404 Z= 0.554 Angle : 1.546 50.728 92586 Z= 1.008 Chirality : 0.310 6.416 10096 Planarity : 0.004 0.057 11608 Dihedral : 7.693 171.260 9646 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 1.42 % 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: 0.52 (0.09), residues: 8039 helix: 1.10 (0.08), residues: 4323 sheet: 0.15 (0.26), residues: 397 loop : -0.57 (0.11), residues: 3319 *********************** 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 790 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 689 time to evaluate : 6.187 Fit side-chains outliers start: 101 outliers final: 46 residues processed: 759 average time/residue: 0.6622 time to fit residues: 854.5744 Evaluate side-chains 719 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 673 time to evaluate : 6.024 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.5053 time to fit residues: 51.9920 ------------------------------------------------------------------------------- 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: 10.0000 chunk 224 optimal weight: 9.9990 chunk 600 optimal weight: 20.0000 chunk 491 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 723 optimal weight: 20.0000 chunk 781 optimal weight: 0.5980 chunk 644 optimal weight: 10.0000 chunk 717 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 580 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS L 31 ASN M 399 ASN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 GLN ** y 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN 2 55 GLN f 70 GLN g 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.252 68404 Z= 0.574 Angle : 1.554 51.098 92586 Z= 1.011 Chirality : 0.309 6.379 10096 Planarity : 0.004 0.056 11608 Dihedral : 7.460 171.425 9646 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.43 % 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: 0.76 (0.09), residues: 8039 helix: 1.32 (0.08), residues: 4329 sheet: 0.15 (0.26), residues: 397 loop : -0.49 (0.11), residues: 3313 *********************** 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 788 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 686 time to evaluate : 6.116 Fit side-chains outliers start: 102 outliers final: 45 residues processed: 766 average time/residue: 0.6765 time to fit residues: 881.7574 Evaluate side-chains 705 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 660 time to evaluate : 6.155 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5422 time to fit residues: 53.7433 ------------------------------------------------------------------------------- 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: 6.9990 chunk 543 optimal weight: 6.9990 chunk 375 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 725 optimal weight: 20.0000 chunk 768 optimal weight: 10.0000 chunk 379 optimal weight: 0.0050 chunk 687 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 overall best weight: 6.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 81 GLN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 621 ASN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 68404 Z= 0.578 Angle : 1.554 50.960 92586 Z= 1.011 Chirality : 0.310 6.429 10096 Planarity : 0.004 0.056 11608 Dihedral : 7.339 171.624 9646 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.49 % 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: 0.87 (0.09), residues: 8039 helix: 1.44 (0.08), residues: 4306 sheet: 0.11 (0.26), residues: 402 loop : -0.44 (0.11), residues: 3331 *********************** 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 796 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 690 time to evaluate : 6.205 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 48 residues processed: 772 average time/residue: 0.6852 time to fit residues: 902.3336 Evaluate side-chains 713 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 665 time to evaluate : 6.094 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5318 time to fit residues: 55.9338 ------------------------------------------------------------------------------- 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: 7.9990 chunk 436 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 572 optimal weight: 30.0000 chunk 317 optimal weight: 20.0000 chunk 655 optimal weight: 7.9990 chunk 531 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 689 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 192 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 121 GLN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 517 ASN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 93 ASN f 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 68404 Z= 0.608 Angle : 1.566 50.735 92586 Z= 1.016 Chirality : 0.310 6.419 10096 Planarity : 0.004 0.056 11608 Dihedral : 7.485 171.866 9646 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.01 % 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: 0.83 (0.09), residues: 8039 helix: 1.40 (0.08), residues: 4318 sheet: 0.08 (0.26), residues: 407 loop : -0.47 (0.11), residues: 3314 *********************** 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 752 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 680 time to evaluate : 6.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 34 residues processed: 735 average time/residue: 0.7006 time to fit residues: 878.4491 Evaluate side-chains 691 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 657 time to evaluate : 6.246 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6174 time to fit residues: 45.8371 ------------------------------------------------------------------------------- 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: 8.9990 chunk 692 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 451 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 769 optimal weight: 9.9990 chunk 638 optimal weight: 7.9990 chunk 356 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 254 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.246 68404 Z= 0.567 Angle : 1.552 50.953 92586 Z= 1.010 Chirality : 0.310 6.429 10096 Planarity : 0.004 0.055 11608 Dihedral : 7.383 171.902 9646 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.83 % 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: 0.96 (0.10), residues: 8039 helix: 1.52 (0.08), residues: 4305 sheet: 0.07 (0.26), residues: 399 loop : -0.40 (0.11), residues: 3335 *********************** 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 743 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 684 time to evaluate : 6.151 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 29 residues processed: 728 average time/residue: 0.6838 time to fit residues: 846.0358 Evaluate side-chains 694 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 665 time to evaluate : 6.261 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5384 time to fit residues: 37.3606 ------------------------------------------------------------------------------- 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: 10.0000 chunk 438 optimal weight: 0.0270 chunk 561 optimal weight: 9.9990 chunk 435 optimal weight: 6.9990 chunk 647 optimal weight: 10.0000 chunk 429 optimal weight: 20.0000 chunk 766 optimal weight: 20.0000 chunk 479 optimal weight: 5.9990 chunk 467 optimal weight: 20.0000 chunk 353 optimal weight: 3.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 68404 Z= 0.560 Angle : 1.551 50.795 92586 Z= 1.010 Chirality : 0.310 6.418 10096 Planarity : 0.004 0.052 11608 Dihedral : 7.325 171.809 9646 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.65 % 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: 1.57 (0.08), residues: 4302 sheet: 0.14 (0.26), residues: 411 loop : -0.36 (0.11), residues: 3326 *********************** 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 723 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 677 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 18 residues processed: 709 average time/residue: 0.6855 time to fit residues: 828.1748 Evaluate side-chains 681 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 663 time to evaluate : 6.114 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5251 time to fit residues: 26.1519 ------------------------------------------------------------------------------- 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: 8.9990 chunk 305 optimal weight: 8.9990 chunk 457 optimal weight: 0.0570 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 487 optimal weight: 7.9990 chunk 522 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 602 optimal weight: 3.9990 overall best weight: 3.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 39 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 68404 Z= 0.551 Angle : 1.547 50.928 92586 Z= 1.008 Chirality : 0.310 6.463 10096 Planarity : 0.004 0.052 11608 Dihedral : 7.220 171.569 9646 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.38 % 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: 1.10 (0.10), residues: 8039 helix: 1.62 (0.08), residues: 4314 sheet: 0.16 (0.26), residues: 411 loop : -0.32 (0.11), residues: 3314 *********************** 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 704 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 677 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 697 average time/residue: 0.7244 time to fit residues: 861.4375 Evaluate side-chains 681 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 671 time to evaluate : 6.324 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5752 time to fit residues: 19.0996 ------------------------------------------------------------------------------- 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: 9.9990 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 5.9990 chunk 714 optimal weight: 3.9990 chunk 733 optimal weight: 6.9990 chunk 429 optimal weight: 20.0000 chunk 311 optimal weight: 0.6980 chunk 560 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 645 optimal weight: 10.0000 chunk 675 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.248 68404 Z= 0.565 Angle : 1.553 50.825 92586 Z= 1.010 Chirality : 0.310 6.447 10096 Planarity : 0.004 0.052 11608 Dihedral : 7.261 171.591 9646 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.25 % 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: 1.09 (0.10), residues: 8039 helix: 1.62 (0.08), residues: 4303 sheet: 0.15 (0.26), residues: 411 loop : -0.33 (0.11), residues: 3325 *********************** 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 690 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 672 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 684 average time/residue: 0.7060 time to fit residues: 818.0279 Evaluate side-chains 674 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 665 time to evaluate : 6.101 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5855 time to fit residues: 17.7206 ------------------------------------------------------------------------------- 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: 20.0000 chunk 468 optimal weight: 20.0000 chunk 755 optimal weight: 6.9990 chunk 460 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 524 optimal weight: 7.9990 chunk 792 optimal weight: 0.0570 chunk 728 optimal weight: 0.4980 chunk 630 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 487 optimal weight: 6.9990 overall best weight: 3.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.250 68404 Z= 0.550 Angle : 1.547 50.794 92586 Z= 1.008 Chirality : 0.310 6.437 10096 Planarity : 0.004 0.052 11608 Dihedral : 7.172 171.502 9646 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.14 % 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: 1.17 (0.10), residues: 8039 helix: 1.68 (0.08), residues: 4297 sheet: 0.17 (0.26), residues: 411 loop : -0.29 (0.11), residues: 3331 ********************** 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 678 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 668 time to evaluate : 6.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 676 average time/residue: 0.7203 time to fit residues: 828.8019 Evaluate side-chains 666 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 663 time to evaluate : 6.169 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5742 time to fit residues: 11.3594 ------------------------------------------------------------------------------- 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: 10.0000 chunk 500 optimal weight: 6.9990 chunk 671 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 581 optimal weight: 0.0010 chunk 93 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 631 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 648 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055090 restraints weight = 148261.774| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.70 r_work: 0.2755 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 68404 Z= 0.554 Angle : 1.549 50.790 92586 Z= 1.009 Chirality : 0.310 6.435 10096 Planarity : 0.004 0.052 11608 Dihedral : 7.164 171.418 9646 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.13 % 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: 1.17 (0.10), residues: 8039 helix: 1.68 (0.08), residues: 4300 sheet: 0.19 (0.26), residues: 409 loop : -0.29 (0.11), residues: 3330 =============================================================================== Job complete usr+sys time: 14396.55 seconds wall clock time: 254 minutes 55.61 seconds (15295.61 seconds total)