Starting phenix.real_space_refine on Fri Aug 9 22:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb6_39110/08_2024/8yb6_39110.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 115 5.16 5 C 17387 2.51 5 N 4884 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 318": "OE1" <-> "OE2" Residue "H GLU 207": "OE1" <-> "OE2" Residue "I GLU 224": "OE1" <-> "OE2" Residue "J GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27758 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2768 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2166 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 20, 'TRANS': 246} Chain: "C" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1303 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna2p': 25, 'rna3p': 35} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2897 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain: "E" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2882 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain: "F" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2911 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "H" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "I" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2072 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 2 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 28, 'TRANS': 414} Chain: "K" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1356 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} 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: "J" 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 2101 SG CYS A 298 41.464 47.449 71.635 1.00 53.53 S ATOM 2122 SG CYS A 301 40.017 49.331 68.641 1.00 54.72 S ATOM 2338 SG CYS A 329 43.654 49.799 69.543 1.00 62.09 S ATOM 2363 SG CYS A 332 40.965 51.236 71.750 1.00 63.65 S ATOM 23999 SG CYS J 215 61.978 39.812 166.800 1.00 87.93 S ATOM 24019 SG CYS J 218 62.860 42.864 164.829 1.00 84.22 S ATOM 24738 SG CYS J 311 59.725 40.770 163.884 1.00 91.10 S ATOM 24756 SG CYS J 314 62.965 39.363 163.113 1.00 94.58 S Time building chain proxies: 14.94, per 1000 atoms: 0.54 Number of scatterers: 27758 At special positions: 0 Unit cell: (113.9, 139.4, 196.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 115 16.00 P 60 15.00 O 5310 8.00 N 4884 7.00 C 17387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.54 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 329 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 332 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 298 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 311 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 215 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 314 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 218 " Number of angles added : 12 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6268 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 31 sheets defined 38.1% alpha, 16.7% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 8.97 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.512A pdb=" N GLY A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.089A pdb=" N LYS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.610A pdb=" N ALA A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.613A pdb=" N ALA A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.836A pdb=" N ARG A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.681A pdb=" N GLU B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.628A pdb=" N CYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.961A pdb=" N LYS B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.881A pdb=" N LYS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.635A pdb=" N ARG D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 4.218A pdb=" N ALA D 54 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.525A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.792A pdb=" N TRP D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS D 80 " --> pdb=" O CYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 removed outlier: 4.115A pdb=" N LYS D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.716A pdb=" N LEU D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.547A pdb=" N VAL D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.717A pdb=" N ALA D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 192 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.583A pdb=" N LYS D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.776A pdb=" N VAL D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 349 through 362 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.290A pdb=" N ALA E 54 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.577A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 88 removed outlier: 5.860A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 removed outlier: 4.025A pdb=" N ASP E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 279 through 286 removed outlier: 4.409A pdb=" N ASN E 282 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 285 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 74 through 89 removed outlier: 4.306A pdb=" N TRP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.811A pdb=" N LYS F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.508A pdb=" N HIS F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.583A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 315 removed outlier: 3.514A pdb=" N GLN F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 removed outlier: 3.658A pdb=" N GLN F 370 " --> pdb=" O TRP F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 49 through 56 removed outlier: 5.248A pdb=" N ALA G 54 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 56 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 76 through 89 removed outlier: 3.936A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.547A pdb=" N ASP G 95 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 122 through 135 removed outlier: 3.510A pdb=" N GLN G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.528A pdb=" N LYS G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.616A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 314 removed outlier: 3.528A pdb=" N GLN G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 Processing helix chain 'G' and resid 349 through 363 Processing helix chain 'G' and resid 368 through 372 removed outlier: 3.782A pdb=" N LYS G 371 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.534A pdb=" N LEU H 56 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.665A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 250 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.652A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 363 Processing helix chain 'H' and resid 365 through 370 removed outlier: 3.643A pdb=" N GLN H 370 " --> pdb=" O TRP H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 47 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 223 through 231 Processing helix chain 'I' and resid 233 through 248 Processing helix chain 'I' and resid 281 through 286 removed outlier: 3.622A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 315 Processing helix chain 'I' and resid 328 through 332 Processing helix chain 'I' and resid 339 through 343 Processing helix chain 'I' and resid 349 through 362 removed outlier: 3.603A pdb=" N GLY I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 110 Processing helix chain 'J' and resid 120 through 143 removed outlier: 3.541A pdb=" N ARG J 124 " --> pdb=" O ASN J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 163 removed outlier: 3.636A pdb=" N ASN J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 167 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 217 through 225 Processing helix chain 'J' and resid 255 through 263 removed outlier: 3.606A pdb=" N ALA J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN J 262 " --> pdb=" O GLY J 258 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 418 through 426 Processing helix chain 'J' and resid 427 through 438 removed outlier: 3.777A pdb=" N LYS J 438 " --> pdb=" O ALA J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 465 removed outlier: 3.809A pdb=" N ALA J 454 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE J 456 " --> pdb=" O GLN J 452 " (cutoff:3.500A) Proline residue: J 458 - end of helix removed outlier: 3.502A pdb=" N ASN J 462 " --> pdb=" O PRO J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 474 removed outlier: 3.933A pdb=" N GLU J 473 " --> pdb=" O GLY J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 483 Processing helix chain 'J' and resid 486 through 498 removed outlier: 3.669A pdb=" N THR J 491 " --> pdb=" O GLY J 487 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER J 496 " --> pdb=" O LYS J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 514 removed outlier: 3.819A pdb=" N ARG J 506 " --> pdb=" O THR J 502 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER J 514 " --> pdb=" O GLY J 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 Processing helix chain 'K' and resid 16 through 25 Processing helix chain 'K' and resid 34 through 52 Proline residue: K 47 - end of helix Processing helix chain 'K' and resid 57 through 71 Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'K' and resid 96 through 107 removed outlier: 3.544A pdb=" N ARG K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'K' and resid 116 through 130 removed outlier: 3.549A pdb=" N LEU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 149 through 165 removed outlier: 4.057A pdb=" N LYS K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR A 124 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 85 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 126 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS A 83 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 128 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 81 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 130 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 79 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU A 132 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 77 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 134 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 68 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG A 74 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N ILE A 207 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ARG A 241 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 243 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 74 removed outlier: 4.039A pdb=" N TYR B 3 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B 8 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 186 through 207 removed outlier: 6.650A pdb=" N VAL B 235 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS B 189 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 233 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 191 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 231 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN B 193 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 229 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 195 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 227 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 197 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 225 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 199 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 223 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS B 201 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 221 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU B 203 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B 219 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS B 205 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP B 217 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 268 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.706A pdb=" N VAL D 101 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 327 removed outlier: 6.297A pdb=" N TRP D 326 " --> pdb=" O ILE D 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY E 268 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL E 271 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE E 323 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY E 324 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE E 347 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP E 326 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLY F 324 " --> pdb=" O ARG F 345 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 347 " --> pdb=" O GLY F 324 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 323 " --> pdb=" O PHE G 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 29 removed outlier: 3.647A pdb=" N CYS H 27 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY H 324 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE H 347 " --> pdb=" O GLY H 324 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 326 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 61 removed outlier: 3.529A pdb=" N THR H 61 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL H 101 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.815A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AC9, first strand: chain 'J' and resid 99 through 102 Processing sheet with id=AD1, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AD2, first strand: chain 'J' and resid 248 through 252 removed outlier: 4.477A pdb=" N LYS J 389 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP J 398 " --> pdb=" O SER J 402 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER J 402 " --> pdb=" O ASP J 398 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 305 through 306 Processing sheet with id=AD4, first strand: chain 'K' and resid 74 through 75 removed outlier: 5.622A pdb=" N GLU K 74 " --> pdb=" O LEU K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 1030 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 8.62 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8258 1.34 - 1.46: 4996 1.46 - 1.57: 14958 1.57 - 1.69: 120 1.69 - 1.81: 171 Bond restraints: 28503 Sorted by residual: bond pdb=" N PRO J 331 " pdb=" CD PRO J 331 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.62e+00 bond pdb=" C SER E 12 " pdb=" N PRO E 13 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.28e+00 bond pdb=" C SER F 12 " pdb=" N PRO F 13 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" O5' U C 20 " pdb=" C5' U C 20 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.67e+00 bond pdb=" O5' U C 32 " pdb=" C5' U C 32 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 ... (remaining 28498 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.62: 833 105.62 - 112.76: 15082 112.76 - 119.89: 9549 119.89 - 127.02: 12892 127.02 - 134.15: 533 Bond angle restraints: 38889 Sorted by residual: angle pdb=" C THR D 123 " pdb=" N GLU D 124 " pdb=" CA GLU D 124 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C GLN F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta sigma weight residual 122.83 126.47 -3.64 1.08e+00 8.57e-01 1.14e+01 angle pdb=" C THR A 31 " pdb=" N ALA A 32 " pdb=" CA ALA A 32 " ideal model delta sigma weight residual 121.54 115.45 6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C ASP I 317 " pdb=" N GLU I 318 " pdb=" CA GLU I 318 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 113.18 105.67 7.51 2.37e+00 1.78e-01 1.01e+01 ... (remaining 38884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 16131 34.77 - 69.54: 993 69.54 - 104.31: 80 104.31 - 139.08: 1 139.08 - 173.85: 3 Dihedral angle restraints: 17208 sinusoidal: 7483 harmonic: 9725 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual 200.00 34.90 165.10 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U C 32 " pdb=" C1' U C 32 " pdb=" N1 U C 32 " pdb=" C2 U C 32 " ideal model delta sinusoidal sigma weight residual 200.00 47.39 152.61 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U C 2 " pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C2 U C 2 " ideal model delta sinusoidal sigma weight residual -128.00 45.85 -173.85 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3009 0.041 - 0.082: 945 0.082 - 0.123: 281 0.123 - 0.164: 47 0.164 - 0.204: 1 Chirality restraints: 4283 Sorted by residual: chirality pdb=" C1' G C 14 " pdb=" O4' G C 14 " pdb=" C2' G C 14 " pdb=" N9 G C 14 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2' U C 20 " pdb=" C3' U C 20 " pdb=" O2' U C 20 " pdb=" C1' U C 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB VAL H 129 " pdb=" CA VAL H 129 " pdb=" CG1 VAL H 129 " pdb=" CG2 VAL H 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 4280 not shown) Planarity restraints: 4830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO A 145 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 398 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP J 398 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP J 398 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 398 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 361 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE E 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY E 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 4827 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4697 2.77 - 3.30: 24552 3.30 - 3.83: 45788 3.83 - 4.37: 52539 4.37 - 4.90: 92745 Nonbonded interactions: 220321 Sorted by model distance: nonbonded pdb=" ND1 HIS B 135 " pdb=" OP1 U C 55 " model vdw 2.234 3.120 nonbonded pdb=" O ALA H 247 " pdb=" CG2 THR H 251 " model vdw 2.237 3.460 nonbonded pdb=" O LEU D 149 " pdb=" OG1 THR D 165 " model vdw 2.256 3.040 nonbonded pdb=" O LEU J 226 " pdb=" OG1 THR J 230 " model vdw 2.270 3.040 nonbonded pdb=" O CYS J 138 " pdb=" OG1 THR J 142 " model vdw 2.274 3.040 ... (remaining 220316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 1 through 370) selection = chain 'E' selection = (chain 'F' and resid 1 through 370) selection = (chain 'G' and resid 1 through 370) selection = (chain 'H' and resid 1 through 370) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.690 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 81.510 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28503 Z= 0.229 Angle : 0.625 9.981 38889 Z= 0.332 Chirality : 0.044 0.204 4283 Planarity : 0.005 0.060 4830 Dihedral : 20.077 173.850 10940 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.14 % Allowed : 35.80 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3337 helix: -0.49 (0.15), residues: 1165 sheet: 0.19 (0.22), residues: 555 loop : -1.80 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 159 HIS 0.005 0.001 HIS F 6 PHE 0.016 0.001 PHE F 260 TYR 0.020 0.001 TYR E 360 ARG 0.008 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 284 average time/residue: 0.4023 time to fit residues: 180.1850 Evaluate side-chains 279 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain G residue 233 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 306 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 225 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28503 Z= 0.230 Angle : 0.544 8.318 38889 Z= 0.285 Chirality : 0.041 0.196 4283 Planarity : 0.004 0.050 4830 Dihedral : 12.812 177.051 4563 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.65 % Allowed : 32.36 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3337 helix: 0.28 (0.16), residues: 1161 sheet: 0.32 (0.22), residues: 537 loop : -1.61 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 156 HIS 0.004 0.001 HIS F 6 PHE 0.014 0.001 PHE G 219 TYR 0.013 0.001 TYR D 337 ARG 0.007 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 298 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7265 (ttp) cc_final: 0.7053 (ttp) REVERT: G 4 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: G 148 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8267 (tmm) REVERT: G 337 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6722 (m-10) REVERT: G 352 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: H 4 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: H 47 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7965 (ptt-90) REVERT: J 262 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: J 363 ARG cc_start: 0.7732 (ptt-90) cc_final: 0.7507 (ptt-90) REVERT: K 92 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6892 (mt) outliers start: 103 outliers final: 50 residues processed: 378 average time/residue: 0.4246 time to fit residues: 255.7657 Evaluate side-chains 329 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 271 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 246 optimal weight: 0.0000 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 17 ASN E 86 ASN E 225 GLN E 229 ASN F 82 GLN F 135 GLN H 131 ASN I 172 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28503 Z= 0.230 Angle : 0.531 8.174 38889 Z= 0.277 Chirality : 0.041 0.196 4283 Planarity : 0.004 0.058 4830 Dihedral : 12.690 173.633 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.83 % Allowed : 32.58 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3337 helix: 0.52 (0.16), residues: 1165 sheet: 0.32 (0.22), residues: 545 loop : -1.58 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 156 HIS 0.004 0.001 HIS F 6 PHE 0.013 0.001 PHE G 219 TYR 0.012 0.001 TYR F 316 ARG 0.004 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 291 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 165 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8020 (t) REVERT: E 1 MET cc_start: 0.7246 (ttp) cc_final: 0.6999 (ttp) REVERT: E 76 GLU cc_start: 0.4420 (OUTLIER) cc_final: 0.3131 (pm20) REVERT: F 82 GLN cc_start: 0.5360 (OUTLIER) cc_final: 0.4427 (mp-120) REVERT: F 103 MET cc_start: 0.7630 (ppp) cc_final: 0.7307 (ptm) REVERT: G 4 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: G 148 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8286 (tmm) REVERT: G 337 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: G 352 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: H 4 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: H 47 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7940 (ptt-90) REVERT: J 262 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: J 319 GLU cc_start: 0.6245 (tm-30) cc_final: 0.5985 (tm-30) REVERT: J 445 LYS cc_start: 0.7317 (tttt) cc_final: 0.6796 (tttt) REVERT: K 92 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6925 (mt) outliers start: 108 outliers final: 59 residues processed: 377 average time/residue: 0.4025 time to fit residues: 238.8538 Evaluate side-chains 346 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 276 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 28503 Z= 0.302 Angle : 0.559 8.686 38889 Z= 0.292 Chirality : 0.042 0.208 4283 Planarity : 0.004 0.047 4830 Dihedral : 12.649 170.159 4559 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.57 % Allowed : 31.83 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3337 helix: 0.57 (0.16), residues: 1160 sheet: 0.28 (0.22), residues: 545 loop : -1.59 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 156 HIS 0.008 0.001 HIS I 204 PHE 0.016 0.001 PHE G 219 TYR 0.015 0.001 TYR F 316 ARG 0.006 0.000 ARG H 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 291 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 165 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8017 (t) REVERT: E 1 MET cc_start: 0.7225 (ttp) cc_final: 0.7005 (ttp) REVERT: E 76 GLU cc_start: 0.4340 (OUTLIER) cc_final: 0.2926 (pm20) REVERT: F 103 MET cc_start: 0.7624 (ppp) cc_final: 0.7347 (ptm) REVERT: F 367 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 4 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: G 337 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: G 352 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: H 4 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: H 47 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7972 (ptt-90) REVERT: J 262 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: J 445 LYS cc_start: 0.7260 (tttt) cc_final: 0.6570 (tttt) REVERT: K 92 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6966 (mt) outliers start: 129 outliers final: 78 residues processed: 397 average time/residue: 0.4132 time to fit residues: 257.3135 Evaluate side-chains 363 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 276 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 82 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28503 Z= 0.135 Angle : 0.493 8.808 38889 Z= 0.256 Chirality : 0.040 0.172 4283 Planarity : 0.003 0.048 4830 Dihedral : 12.525 169.659 4559 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.19 % Allowed : 33.18 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3337 helix: 0.86 (0.16), residues: 1172 sheet: 0.45 (0.22), residues: 525 loop : -1.54 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 156 HIS 0.005 0.000 HIS I 204 PHE 0.009 0.001 PHE I 244 TYR 0.010 0.001 TYR E 360 ARG 0.006 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 301 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7705 (ttm-80) REVERT: D 165 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7975 (t) REVERT: E 1 MET cc_start: 0.7157 (ttp) cc_final: 0.6914 (ttp) REVERT: F 103 MET cc_start: 0.7508 (ppp) cc_final: 0.7265 (ptm) REVERT: G 4 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: G 76 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5542 (pm20) REVERT: G 337 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: G 352 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: H 47 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7907 (ptt-90) REVERT: J 259 MET cc_start: 0.7092 (tpp) cc_final: 0.6671 (ttp) REVERT: J 262 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: J 298 LYS cc_start: 0.7405 (mptt) cc_final: 0.7069 (mptt) REVERT: J 445 LYS cc_start: 0.7254 (tttt) cc_final: 0.6719 (tttt) REVERT: K 92 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6875 (mt) outliers start: 90 outliers final: 52 residues processed: 376 average time/residue: 0.4115 time to fit residues: 241.5541 Evaluate side-chains 345 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 64 optimal weight: 10.9990 chunk 191 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 327 optimal weight: 0.0970 chunk 271 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28503 Z= 0.163 Angle : 0.495 8.899 38889 Z= 0.257 Chirality : 0.040 0.172 4283 Planarity : 0.003 0.044 4830 Dihedral : 12.453 167.653 4559 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.58 % Allowed : 32.72 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3337 helix: 0.96 (0.16), residues: 1173 sheet: 0.54 (0.22), residues: 533 loop : -1.51 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 156 HIS 0.003 0.001 HIS I 204 PHE 0.013 0.001 PHE D 102 TYR 0.010 0.001 TYR B 29 ARG 0.006 0.000 ARG J 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 292 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7115 (ttp) cc_final: 0.6889 (ttp) REVERT: E 76 GLU cc_start: 0.4288 (OUTLIER) cc_final: 0.2882 (pm20) REVERT: F 82 GLN cc_start: 0.4880 (OUTLIER) cc_final: 0.4089 (mp10) REVERT: F 103 MET cc_start: 0.7528 (ppp) cc_final: 0.7300 (ptm) REVERT: F 367 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7617 (mm-30) REVERT: G 4 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: G 337 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: G 352 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: H 47 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7924 (ptt-90) REVERT: J 259 MET cc_start: 0.7072 (tpp) cc_final: 0.6703 (ttp) REVERT: J 262 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: J 418 ASN cc_start: 0.7443 (p0) cc_final: 0.7205 (p0) REVERT: J 445 LYS cc_start: 0.7278 (tttt) cc_final: 0.6792 (tttt) REVERT: K 92 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6909 (mt) outliers start: 101 outliers final: 67 residues processed: 374 average time/residue: 0.4122 time to fit residues: 239.3186 Evaluate side-chains 358 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 283 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 0.0270 chunk 36 optimal weight: 0.5980 chunk 186 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 150 optimal weight: 0.0970 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 70 GLN G 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28503 Z= 0.131 Angle : 0.483 8.511 38889 Z= 0.249 Chirality : 0.039 0.165 4283 Planarity : 0.003 0.043 4830 Dihedral : 12.401 166.732 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.37 % Allowed : 33.11 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3337 helix: 1.11 (0.16), residues: 1168 sheet: 0.58 (0.22), residues: 525 loop : -1.47 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 159 HIS 0.003 0.000 HIS I 204 PHE 0.012 0.001 PHE D 102 TYR 0.013 0.001 TYR E 316 ARG 0.006 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 296 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.8312 (tp) cc_final: 0.7207 (mm) REVERT: D 103 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6818 (tpt) REVERT: E 1 MET cc_start: 0.7180 (ttp) cc_final: 0.6962 (ttp) REVERT: E 319 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7208 (tm-30) REVERT: F 82 GLN cc_start: 0.4850 (OUTLIER) cc_final: 0.4039 (mp10) REVERT: F 103 MET cc_start: 0.7468 (ppp) cc_final: 0.7240 (ptm) REVERT: F 367 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7661 (mm-30) REVERT: G 4 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: G 337 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: G 352 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: H 47 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: J 259 MET cc_start: 0.6997 (tpp) cc_final: 0.6549 (ttp) REVERT: J 262 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: J 418 ASN cc_start: 0.7379 (p0) cc_final: 0.7161 (p0) REVERT: J 445 LYS cc_start: 0.7339 (tttt) cc_final: 0.6900 (tttt) REVERT: K 92 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6858 (mt) REVERT: K 124 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7412 (mtt) outliers start: 95 outliers final: 67 residues processed: 374 average time/residue: 0.4246 time to fit residues: 249.2656 Evaluate side-chains 358 residues out of total 2822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 282 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4801 > 50: distance: 83 - 235: 32.432 distance: 142 - 166: 6.220 distance: 150 - 177: 27.504 distance: 162 - 166: 3.208 distance: 166 - 167: 12.165 distance: 167 - 168: 9.780 distance: 167 - 170: 36.241 distance: 168 - 169: 15.434 distance: 168 - 177: 16.135 distance: 170 - 171: 8.008 distance: 171 - 172: 5.519 distance: 173 - 175: 3.369 distance: 174 - 176: 7.786 distance: 175 - 176: 10.179 distance: 177 - 178: 32.188 distance: 178 - 179: 6.975 distance: 178 - 181: 20.646 distance: 179 - 180: 12.624 distance: 179 - 182: 5.047 distance: 182 - 183: 46.160 distance: 183 - 184: 17.002 distance: 183 - 186: 17.016 distance: 184 - 185: 31.152 distance: 184 - 187: 23.525 distance: 187 - 188: 15.263 distance: 188 - 189: 5.755 distance: 188 - 191: 6.687 distance: 189 - 190: 14.855 distance: 189 - 197: 13.289 distance: 191 - 192: 31.437 distance: 192 - 193: 18.760 distance: 192 - 194: 18.631 distance: 193 - 195: 15.873 distance: 194 - 196: 7.659 distance: 195 - 196: 9.193 distance: 197 - 198: 28.538 distance: 198 - 199: 16.679 distance: 198 - 201: 20.534 distance: 199 - 200: 5.061 distance: 199 - 205: 52.317 distance: 201 - 202: 39.756 distance: 202 - 204: 29.565 distance: 205 - 206: 6.918 distance: 206 - 207: 20.920 distance: 206 - 209: 25.226 distance: 207 - 208: 8.364 distance: 207 - 217: 36.607 distance: 209 - 210: 6.239 distance: 210 - 211: 17.488 distance: 210 - 212: 5.474 distance: 211 - 213: 11.215 distance: 212 - 214: 3.642 distance: 213 - 215: 20.347 distance: 214 - 215: 5.500 distance: 215 - 216: 5.438 distance: 217 - 218: 23.854 distance: 217 - 223: 25.835 distance: 218 - 219: 5.177 distance: 218 - 221: 39.249 distance: 219 - 220: 10.668 distance: 219 - 224: 16.327 distance: 221 - 222: 7.184 distance: 222 - 223: 19.757 distance: 225 - 226: 12.984 distance: 225 - 228: 6.355 distance: 226 - 227: 27.368 distance: 226 - 232: 6.472 distance: 228 - 229: 6.738 distance: 229 - 230: 10.470 distance: 229 - 231: 28.577 distance: 232 - 233: 31.945 distance: 233 - 234: 3.985 distance: 234 - 235: 23.709 distance: 234 - 236: 37.744 distance: 236 - 237: 25.031 distance: 236 - 273: 37.005 distance: 237 - 238: 14.978 distance: 237 - 240: 28.401 distance: 238 - 239: 22.639 distance: 238 - 244: 24.649 distance: 239 - 270: 21.602 distance: 240 - 241: 21.431 distance: 240 - 242: 29.887 distance: 241 - 243: 22.426