Starting phenix.real_space_refine (version: dev) on Sun May 15 14:30:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/05_2022/6zoj_11320.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.138 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 75783 Number of models: 1 Model: "" Number of chains: 45 Chain: "2" Number of atoms: 36367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1704, 36367 Classifications: {'RNA': 1704} Modifications used: {'rna3p_pyr': 695, 'rna2p_pur': 141, 'rna3p_pur': 756, 'rna2p_pyr': 112} Link IDs: {'rna3p': 1450, 'rna2p': 253} Chain breaks: 4 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1501 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 183} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "R" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 95, 'PCIS': 1} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125, 'PCIS': 2} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 135, 'PCIS': 1} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "a" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 441 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "j" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "h" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "2" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Unusual residues: {' MG': 159} Classifications: {'undetermined': 159} Link IDs: {None: 158} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69429 SG CYS a 23 142.745 94.130 130.998 1.00 27.04 S ATOM 69450 SG CYS a 26 139.629 92.849 129.410 1.00 27.87 S ATOM 69833 SG CYS a 74 139.559 96.115 131.314 1.00 26.36 S ATOM 69852 SG CYS a 77 139.804 92.894 133.117 1.00 28.15 S ATOM 71350 SG CYS d 21 84.252 86.263 183.231 1.00 22.30 S ATOM 71374 SG CYS d 24 83.378 87.258 179.731 1.00 22.45 S ATOM 71495 SG CYS d 39 86.765 85.975 180.433 1.00 19.70 S ATOM 71521 SG CYS d 42 86.005 89.297 181.538 1.00 18.45 S ATOM 72456 SG CYS f 121 37.828 67.973 193.036 1.00 74.06 S ATOM 72492 SG CYS f 126 39.563 71.463 193.264 1.00 77.37 S ATOM 72610 SG CYS f 141 38.445 69.934 189.859 1.00 66.42 S ATOM 72629 SG CYS f 144 41.325 68.517 191.701 1.00 69.35 S Time building chain proxies: 32.51, per 1000 atoms: 0.43 Number of scatterers: 75783 At special positions: 0 Unit cell: (206.28, 231.12, 248.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 183 16.00 P 1704 15.00 Mg 166 11.99 O 18777 8.00 N 13924 7.00 C 41026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 59 " 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=0, symmetry=0 Time building additional restraints: 27.43 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " Number of angles added : 18 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9106 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 58 sheets defined 38.2% alpha, 19.7% beta 466 base pairs and 870 stacking pairs defined. Time for finding SS restraints: 22.89 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.685A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.821A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.618A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.668A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 85 removed outlier: 4.037A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.613A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.515A pdb=" N LEU C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.763A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'D' and resid 6 through 30 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.645A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.722A pdb=" N LEU D 96 " --> pdb=" O THR D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.521A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 4.213A pdb=" N TYR D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.015A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.583A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 261 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 33 through 38 removed outlier: 4.246A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 76 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.597A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.507A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 163 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.629A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.085A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.887A pdb=" N LYS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 36 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 87 removed outlier: 3.614A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.781A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.741A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 94 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 153 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 61 removed outlier: 4.178A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.600A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.717A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.784A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.547A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.650A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.592A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.546A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'M' and resid 17 through 28 removed outlier: 4.143A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 58 through 72 Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 117 through 132 removed outlier: 3.562A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.052A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.239A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA N 148 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 69 removed outlier: 4.333A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 66 through 69' Processing helix chain 'O' and resid 70 through 89 removed outlier: 3.506A pdb=" N LEU O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.602A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.814A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.576A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.633A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.643A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.666A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.899A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.708A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.532A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'R' and resid 71 through 83 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.551A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.517A pdb=" N LEU S 59 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.760A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.520A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.801A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.853A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.637A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 145 Processing helix chain 'U' and resid 28 through 46 removed outlier: 3.641A pdb=" N LEU U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 105 removed outlier: 3.623A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.734A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.771A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.739A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.472A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 94 removed outlier: 3.610A pdb=" N ASN X 92 " --> pdb=" O GLY X 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE X 94 " --> pdb=" O LEU X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 removed outlier: 3.551A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 114 Processing helix chain 'Y' and resid 119 through 125 Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.598A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.502A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.480A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'f' and resid 102 through 104 No H-bonds generated for 'chain 'f' and resid 102 through 104' Processing helix chain 'g' and resid 276 through 280 removed outlier: 3.853A pdb=" N LYS g 280 " --> pdb=" O THR g 277 " (cutoff:3.500A) Processing helix chain 'j' and resid 152 through 161 Processing helix chain 'j' and resid 165 through 179 removed outlier: 3.563A pdb=" N ARG j 175 " --> pdb=" O ARG j 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY j 179 " --> pdb=" O ARG j 175 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.995A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.792A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.328A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 128 removed outlier: 3.715A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL B 140 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 213 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N PHE B 142 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N PHE B 211 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 115 removed outlier: 6.601A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 41 removed outlier: 6.633A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 85 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.741A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.519A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 223 through 226 removed outlier: 6.435A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.533A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.730A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.917A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL E 227 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 123 through 129 removed outlier: 25.467A pdb=" N ILE c 43 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 17.997A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 13.439A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS c 27 " --> pdb=" O GLY c 19 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY c 19 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.401A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC2, first strand: chain 'H' and resid 47 through 53 removed outlier: 6.857A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.368A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.274A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.249A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.063A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP I 105 " --> pdb=" O ARG I 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AC9, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.852A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.842A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.709A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 92 through 93 removed outlier: 3.507A pdb=" N LYS M 93 " --> pdb=" O LYS M 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS M 102 " --> pdb=" O LYS M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.860A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AD5, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'Q' and resid 9 through 15 removed outlier: 6.839A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD8, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AD9, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.998A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'U' and resid 50 through 55 removed outlier: 5.792A pdb=" N LEU U 88 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG U 55 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS U 86 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 59 through 66 removed outlier: 8.958A pdb=" N ARG U 79 " --> pdb=" O LEU d 55 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU d 55 " --> pdb=" O ARG U 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 32 through 39 removed outlier: 4.997A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE6, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.568A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.562A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.293A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.882A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF2, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AF3, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AF4, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.709A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AF6, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AF7, first strand: chain 'f' and resid 133 through 135 removed outlier: 3.515A pdb=" N ARG f 138 " --> pdb=" O HIS f 135 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 3 through 11 removed outlier: 5.441A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 18 through 22 removed outlier: 3.555A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.554A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.502A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.181A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.761A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE g 265 " --> pdb=" O ASP g 260 " (cutoff:3.500A) 1626 hydrogen bonds defined for protein. 4563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1178 hydrogen bonds 1904 hydrogen bond angles 0 basepair planarities 466 basepair parallelities 870 stacking parallelities Total time for adding SS restraints: 67.83 Time building geometry restraints manager: 29.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15530 1.33 - 1.46: 27678 1.46 - 1.58: 33690 1.58 - 1.70: 3403 1.70 - 1.82: 279 Bond restraints: 80580 Sorted by residual: bond pdb=" N ALA F 131 " pdb=" CA ALA F 131 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.12e+00 bond pdb=" N LYS Q 17 " pdb=" CA LYS Q 17 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.58e+00 bond pdb=" N ALA S 100 " pdb=" CA ALA S 100 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.58e+00 bond pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.43e+00 ... (remaining 80575 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.53: 10789 106.53 - 113.42: 46557 113.42 - 120.32: 29946 120.32 - 127.21: 25755 127.21 - 134.10: 3878 Bond angle restraints: 116925 Sorted by residual: angle pdb=" N SER U 93 " pdb=" CA SER U 93 " pdb=" C SER U 93 " ideal model delta sigma weight residual 108.22 111.83 -3.61 9.00e-01 1.23e+00 1.61e+01 angle pdb=" N GLU X 53 " pdb=" CA GLU X 53 " pdb=" C GLU X 53 " ideal model delta sigma weight residual 107.88 113.35 -5.47 1.41e+00 5.03e-01 1.51e+01 angle pdb=" N VAL F 41 " pdb=" CA VAL F 41 " pdb=" C VAL F 41 " ideal model delta sigma weight residual 113.20 109.57 3.63 9.60e-01 1.09e+00 1.43e+01 angle pdb=" N SER O 139 " pdb=" CA SER O 139 " pdb=" C SER O 139 " ideal model delta sigma weight residual 108.34 113.00 -4.66 1.31e+00 5.83e-01 1.26e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 ... (remaining 116920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 43756 35.85 - 71.71: 1279 71.71 - 107.56: 111 107.56 - 143.41: 9 143.41 - 179.27: 20 Dihedral angle restraints: 45175 sinusoidal: 31056 harmonic: 14119 Sorted by residual: dihedral pdb=" O4' U 21551 " pdb=" C1' U 21551 " pdb=" N1 U 21551 " pdb=" C2 U 21551 " ideal model delta sinusoidal sigma weight residual -160.00 18.03 -178.03 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual -160.00 13.20 -173.20 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 26.99 173.01 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 45172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 12596 0.048 - 0.096: 1423 0.096 - 0.145: 398 0.145 - 0.193: 19 0.193 - 0.241: 6 Chirality restraints: 14442 Sorted by residual: chirality pdb=" C1' U 2 918 " pdb=" O4' U 2 918 " pdb=" C2' U 2 918 " pdb=" N1 U 2 918 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1' G 2 470 " pdb=" O4' G 2 470 " pdb=" C2' G 2 470 " pdb=" N9 G 2 470 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' U 21445 " pdb=" O4' U 21445 " pdb=" C2' U 21445 " pdb=" N1 U 21445 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 14439 not shown) Planarity restraints: 8511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 21240 " -0.037 2.00e-02 2.50e+03 1.66e-02 7.56e+00 pdb=" N9 A 21240 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A 21240 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 21240 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 21240 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 21240 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 21240 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A 21240 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 21240 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 21240 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 21240 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21311 " -0.032 2.00e-02 2.50e+03 1.68e-02 6.35e+00 pdb=" N1 C 21311 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C 21311 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C 21311 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C 21311 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 21311 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C 21311 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C 21311 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C 21311 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21606 " -0.032 2.00e-02 2.50e+03 1.36e-02 5.59e+00 pdb=" N9 G 21606 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 21606 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 21606 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 21606 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 21606 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G 21606 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G 21606 " 0.005 2.00e-02 2.50e+03 ... (remaining 8508 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 129 2.34 - 2.98: 33868 2.98 - 3.62: 113909 3.62 - 4.26: 208130 4.26 - 4.90: 297892 Nonbonded interactions: 653928 Sorted by model distance: nonbonded pdb="MG MG 22012 " pdb="MG MG 22043 " model vdw 1.694 1.300 nonbonded pdb=" OP1 G 21837 " pdb="MG MG 22090 " model vdw 1.976 2.170 nonbonded pdb=" OP2 A 2 46 " pdb="MG MG 22148 " model vdw 2.007 2.170 nonbonded pdb=" OP2 G 21603 " pdb="MG MG 22031 " model vdw 2.013 2.170 nonbonded pdb=" O6 G 21517 " pdb="MG MG 22001 " model vdw 2.025 2.170 ... (remaining 653923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1704 5.49 5 Mg 166 5.21 5 S 183 5.16 5 C 41026 2.51 5 N 13924 2.21 5 O 18777 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 40.950 Check model and map are aligned: 0.870 Convert atoms to be neutral: 0.540 Process input model: 222.610 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.002 0.037 80580 Z= 0.143 Angle : 0.511 8.114 116925 Z= 0.287 Chirality : 0.034 0.241 14442 Planarity : 0.003 0.046 8511 Dihedral : 14.311 179.267 36066 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4844 helix: 1.63 (0.13), residues: 1614 sheet: 0.46 (0.17), residues: 935 loop : -0.22 (0.12), residues: 2295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 849 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 890 average time/residue: 1.5973 time to fit residues: 1864.1593 Evaluate side-chains 609 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 588 time to evaluate : 4.658 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 3 average time/residue: 1.0050 time to fit residues: 10.0302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 548 optimal weight: 5.9990 chunk 491 optimal weight: 0.8980 chunk 272 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 508 optimal weight: 6.9990 chunk 196 optimal weight: 0.2980 chunk 309 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 589 optimal weight: 9.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 141 ASN B 177 GLN C 178 HIS D 145 GLN E 161 GLN F 36 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 99 ASN I 111 GLN I 168 GLN J 27 GLN O 103 ASN P 24 GLN P 46 ASN P 103 ASN Q 114 GLN R 62 GLN T 137 GLN U 81 GLN V 21 ASN Z 89 GLN a 43 ASN ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS g 296 GLN j 160 ASN j 165 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 80580 Z= 0.268 Angle : 0.583 18.088 116925 Z= 0.300 Chirality : 0.039 0.249 14442 Planarity : 0.005 0.061 8511 Dihedral : 14.828 179.908 25893 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.66 (0.12), residues: 4844 helix: 1.58 (0.13), residues: 1649 sheet: 0.42 (0.17), residues: 935 loop : -0.36 (0.12), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 608 time to evaluate : 4.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 69 residues processed: 686 average time/residue: 1.5859 time to fit residues: 1436.1292 Evaluate side-chains 630 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 561 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 42 residues processed: 27 average time/residue: 0.8157 time to fit residues: 40.9755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 490 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 590 optimal weight: 7.9990 chunk 637 optimal weight: 2.9990 chunk 525 optimal weight: 6.9990 chunk 585 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 473 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS C 113 GLN E 209 HIS ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 165 GLN J 27 GLN K 39 ASN O 103 ASN P 24 GLN P 46 ASN P 103 ASN Q 114 GLN R 62 GLN T 137 GLN T 142 ASN V 47 ASN W 91 ASN Z 89 GLN a 43 ASN j 158 GLN j 160 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 80580 Z= 0.222 Angle : 0.544 9.865 116925 Z= 0.283 Chirality : 0.037 0.251 14442 Planarity : 0.004 0.057 8511 Dihedral : 14.847 179.984 25893 Min Nonbonded Distance : 1.300 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.73 (0.12), residues: 4844 helix: 1.73 (0.13), residues: 1637 sheet: 0.38 (0.16), residues: 940 loop : -0.34 (0.12), residues: 2267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 594 time to evaluate : 4.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 86 residues processed: 687 average time/residue: 1.5870 time to fit residues: 1442.2364 Evaluate side-chains 648 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 562 time to evaluate : 4.686 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 56 residues processed: 30 average time/residue: 0.8041 time to fit residues: 44.3921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 583 optimal weight: 2.9990 chunk 443 optimal weight: 0.0020 chunk 306 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 396 optimal weight: 0.4980 chunk 592 optimal weight: 5.9990 chunk 627 optimal weight: 9.9990 chunk 309 optimal weight: 0.8980 chunk 561 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN E 214 ASN F 203 ASN H 68 GLN H 186 ASN J 27 GLN K 77 GLN O 103 ASN P 46 ASN Q 114 GLN R 62 GLN T 142 ASN U 81 GLN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN j 158 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.094 80580 Z= 0.144 Angle : 0.509 10.143 116925 Z= 0.264 Chirality : 0.035 0.246 14442 Planarity : 0.004 0.065 8511 Dihedral : 14.809 179.826 25893 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.89 (0.12), residues: 4844 helix: 1.88 (0.13), residues: 1638 sheet: 0.44 (0.17), residues: 937 loop : -0.25 (0.12), residues: 2269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 599 time to evaluate : 4.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 83 residues processed: 693 average time/residue: 1.6069 time to fit residues: 1479.8281 Evaluate side-chains 646 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 563 time to evaluate : 4.719 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 61 residues processed: 22 average time/residue: 0.9276 time to fit residues: 36.8942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 522 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 467 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 535 optimal weight: 0.3980 chunk 433 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 chunk 563 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS C 113 GLN D 179 GLN F 36 GLN H 186 ASN I 7 ASN J 27 GLN K 77 GLN P 46 ASN Q 97 GLN Q 114 GLN R 62 GLN T 142 ASN U 81 GLN V 47 ASN W 91 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 160 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 80580 Z= 0.191 Angle : 0.524 10.406 116925 Z= 0.271 Chirality : 0.036 0.246 14442 Planarity : 0.004 0.120 8511 Dihedral : 14.760 179.762 25893 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 4844 helix: 1.92 (0.13), residues: 1633 sheet: 0.42 (0.17), residues: 942 loop : -0.26 (0.12), residues: 2269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 576 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 95 residues processed: 668 average time/residue: 1.5799 time to fit residues: 1404.4680 Evaluate side-chains 658 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 563 time to evaluate : 4.784 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 67 residues processed: 28 average time/residue: 0.7820 time to fit residues: 41.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 211 optimal weight: 30.0000 chunk 564 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 368 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 627 optimal weight: 0.0370 chunk 521 optimal weight: 6.9990 chunk 290 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN F 36 GLN G 197 GLN H 186 ASN J 27 GLN K 77 GLN L 112 HIS O 103 ASN P 46 ASN Q 114 GLN R 62 GLN T 85 ASN T 142 ASN U 81 GLN V 47 ASN W 15 ASN W 91 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN e 39 ASN j 158 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 80580 Z= 0.351 Angle : 0.632 12.016 116925 Z= 0.324 Chirality : 0.042 0.267 14442 Planarity : 0.006 0.122 8511 Dihedral : 14.965 179.167 25893 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.60 (0.12), residues: 4844 helix: 1.63 (0.13), residues: 1633 sheet: 0.29 (0.17), residues: 942 loop : -0.41 (0.12), residues: 2269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 573 time to evaluate : 4.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 106 residues processed: 680 average time/residue: 1.5710 time to fit residues: 1416.8099 Evaluate side-chains 659 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 553 time to evaluate : 7.208 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 78 residues processed: 28 average time/residue: 0.7833 time to fit residues: 42.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 605 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 458 optimal weight: 0.1980 chunk 355 optimal weight: 5.9990 chunk 528 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 625 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 381 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN G 105 ASN H 186 ASN J 27 GLN K 77 GLN N 69 ASN O 103 ASN P 104 GLN Q 114 GLN R 62 GLN T 142 ASN U 81 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN W 91 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 158 GLN j 160 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 80580 Z= 0.228 Angle : 0.558 11.648 116925 Z= 0.289 Chirality : 0.038 0.256 14442 Planarity : 0.005 0.123 8511 Dihedral : 14.909 179.842 25893 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.67 (0.12), residues: 4844 helix: 1.72 (0.13), residues: 1635 sheet: 0.27 (0.17), residues: 940 loop : -0.39 (0.12), residues: 2269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 572 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 104 residues processed: 671 average time/residue: 1.5568 time to fit residues: 1388.5772 Evaluate side-chains 656 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 552 time to evaluate : 4.685 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 80 residues processed: 24 average time/residue: 0.8087 time to fit residues: 37.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 386 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 397 optimal weight: 0.0270 chunk 426 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 491 optimal weight: 0.7980 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN H 186 ASN J 27 GLN K 77 GLN N 69 ASN O 103 ASN P 104 GLN Q 114 GLN R 62 GLN T 142 ASN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 80580 Z= 0.189 Angle : 0.540 11.316 116925 Z= 0.279 Chirality : 0.036 0.251 14442 Planarity : 0.004 0.128 8511 Dihedral : 14.843 179.900 25893 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.75 (0.12), residues: 4844 helix: 1.80 (0.13), residues: 1639 sheet: 0.27 (0.17), residues: 939 loop : -0.32 (0.12), residues: 2266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 567 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 95 residues processed: 658 average time/residue: 1.5488 time to fit residues: 1359.8018 Evaluate side-chains 646 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 551 time to evaluate : 4.759 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 79 residues processed: 17 average time/residue: 0.9298 time to fit residues: 29.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 569 optimal weight: 3.9990 chunk 599 optimal weight: 0.9990 chunk 546 optimal weight: 3.9990 chunk 582 optimal weight: 0.9980 chunk 350 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 457 optimal weight: 0.5980 chunk 178 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 551 optimal weight: 1.9990 chunk 580 optimal weight: 0.0170 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 226 GLN H 186 ASN K 77 GLN N 69 ASN O 103 ASN P 46 ASN P 104 GLN Q 114 GLN R 62 GLN T 142 ASN U 81 GLN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.107 80580 Z= 0.145 Angle : 0.525 11.051 116925 Z= 0.271 Chirality : 0.035 0.246 14442 Planarity : 0.004 0.133 8511 Dihedral : 14.816 179.687 25893 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.82 (0.12), residues: 4844 helix: 1.88 (0.13), residues: 1638 sheet: 0.28 (0.17), residues: 940 loop : -0.28 (0.12), residues: 2266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 559 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 86 residues processed: 647 average time/residue: 1.6320 time to fit residues: 1411.5074 Evaluate side-chains 633 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 547 time to evaluate : 4.780 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 78 residues processed: 8 average time/residue: 0.7455 time to fit residues: 15.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 382 optimal weight: 4.9990 chunk 616 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 292 optimal weight: 0.5980 chunk 428 optimal weight: 0.0980 chunk 646 optimal weight: 0.8980 chunk 595 optimal weight: 8.9990 chunk 514 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 397 optimal weight: 3.9990 chunk 315 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN H 186 ASN K 77 GLN N 69 ASN O 103 ASN P 24 GLN R 62 GLN T 142 ASN U 81 GLN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 158 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.481 80580 Z= 0.220 Angle : 0.542 28.134 116925 Z= 0.280 Chirality : 0.035 0.242 14442 Planarity : 0.004 0.121 8511 Dihedral : 14.749 179.368 25893 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.84 (0.12), residues: 4844 helix: 1.89 (0.13), residues: 1645 sheet: 0.31 (0.17), residues: 937 loop : -0.28 (0.13), residues: 2262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 554 time to evaluate : 4.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 80 residues processed: 634 average time/residue: 1.6026 time to fit residues: 1353.5278 Evaluate side-chains 624 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 544 time to evaluate : 4.691 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 73 residues processed: 7 average time/residue: 0.6053 time to fit residues: 13.3791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 408 optimal weight: 1.9990 chunk 548 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 474 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 515 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 529 optimal weight: 0.0050 chunk 65 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN H 186 ASN K 77 GLN M 19 GLN N 69 ASN O 103 ASN P 104 GLN Q 114 GLN R 62 GLN T 10 ASN T 142 ASN U 81 GLN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073525 restraints weight = 152376.271| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.37 r_work: 0.3038 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.3009 rms_B_bonded: 1.42 restraints_weight: 0.1250 r_work: 0.2993 rms_B_bonded: 1.60 restraints_weight: 0.0625 r_work: 0.2976 rms_B_bonded: 1.83 restraints_weight: 0.0312 r_work: 0.2957 rms_B_bonded: 2.13 restraints_weight: 0.0156 r_work: 0.2935 rms_B_bonded: 2.49 restraints_weight: 0.0078 r_work: 0.2910 rms_B_bonded: 2.94 restraints_weight: 0.0039 r_work: 0.2881 rms_B_bonded: 3.48 restraints_weight: 0.0020 r_work: 0.2847 rms_B_bonded: 4.16 restraints_weight: 0.0010 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.289 80580 Z= 0.424 Angle : 0.675 20.817 116925 Z= 0.345 Chirality : 0.044 0.270 14442 Planarity : 0.006 0.116 8511 Dihedral : 14.989 179.433 25893 Min Nonbonded Distance : 1.068 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.48 (0.12), residues: 4844 helix: 1.57 (0.13), residues: 1634 sheet: 0.17 (0.17), residues: 928 loop : -0.49 (0.12), residues: 2282 =============================================================================== Job complete usr+sys time: 20235.05 seconds wall clock time: 354 minutes 29.91 seconds (21269.91 seconds total)