Starting phenix.real_space_refine on Fri Mar 15 10:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/03_2024/7zc6_14622_updated.pdb" } resolution = 4.27 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= 0.003 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 Fe 29 7.16 5 P 3 5.49 5 S 110 5.16 5 C 7337 2.51 5 N 1857 2.21 5 O 2092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 130": "OD1" <-> "OD2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11428 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1446 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1451 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3291 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 409} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2282 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 16, 'TRANS': 287} Chain: "E" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1435 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1348 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'SF4': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 197 SG CYS A 25 74.119 89.930 41.647 1.00 68.15 S ATOM 870 SG CYS A 113 77.837 89.536 39.704 1.00 86.99 S ATOM 8659 SG CYS E 26 76.801 92.203 41.640 1.00 72.84 S ATOM 9273 SG CYS E 109 74.286 91.482 38.436 1.00 74.88 S ATOM 2249 SG CYS B 177 37.926 72.883 46.538 1.00 70.07 S ATOM 2234 SG CYS B 174 41.882 77.587 44.472 1.00 80.54 S ATOM 2217 SG CYS B 171 36.501 78.904 48.010 1.00101.07 S ATOM 2078 SG CYS B 152 42.351 76.972 49.759 1.00 73.24 S ATOM 2276 SG CYS B 181 37.213 64.066 48.403 1.00 60.39 S ATOM 1899 SG CYS B 124 41.917 63.120 49.815 1.00 57.96 S ATOM 2049 SG CYS B 148 40.617 68.951 51.573 1.00 65.89 S ATOM 2013 SG CYS B 142 37.484 63.946 54.134 1.00 52.52 S ATOM 1988 SG CYS B 138 28.277 57.461 53.661 1.00 65.39 S ATOM 1749 SG CYS B 105 31.277 63.446 55.599 1.00 77.65 S ATOM 2414 SG CYS B 199 24.881 62.694 54.758 1.00 83.08 S ATOM 2511 SG CYS B 212 27.646 57.971 57.780 1.00 82.33 S ATOM 2572 SG CYS B 222 13.707 65.162 50.259 1.00110.31 S ATOM 2554 SG CYS B 219 12.993 61.363 54.806 1.00111.20 S ATOM 2534 SG CYS B 216 18.643 61.459 52.209 1.00 97.19 S ATOM 2815 SG CYS B 255 16.109 66.501 55.513 1.00105.47 S ATOM 2604 SG CYS B 226 11.002 73.165 47.062 1.00119.53 S ATOM 2750 SG CYS B 245 15.934 76.629 47.837 1.00121.69 S ATOM 2772 SG CYS B 248 10.150 77.089 51.366 1.00134.21 S ATOM 2789 SG CYS B 251 14.475 73.473 52.896 1.00115.99 S ATOM 5985 SG CYS C 410 58.404 48.702 46.374 1.00 57.86 S ATOM 5729 SG CYS C 375 61.955 46.682 41.136 1.00 60.27 S ATOM 5969 SG CYS C 407 58.117 43.438 43.701 1.00 64.51 S ATOM 5946 SG CYS C 404 55.779 47.850 40.801 1.00 56.81 S ATOM 5681 SG CYS C 368 67.660 51.898 51.719 1.00 62.42 S ATOM 6015 SG CYS C 414 62.114 52.268 53.715 1.00 61.08 S ATOM 5659 SG CYS C 365 64.667 57.398 51.524 1.00 60.44 S ATOM 5700 SG CYS C 371 64.674 52.081 47.522 1.00 54.07 S Time building chain proxies: 6.71, per 1000 atoms: 0.59 Number of scatterers: 11428 At special positions: 0 Unit cell: (136.431, 128.898, 89.559, 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) Fe 29 26.01 S 110 16.00 P 3 15.00 O 2092 8.00 N 1857 7.00 C 7337 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 300 " pdb="FE1 SF4 B 300 " - pdb=" SG CYS B 177 " pdb="FE2 SF4 B 300 " - pdb=" SG CYS B 174 " pdb="FE3 SF4 B 300 " - pdb=" SG CYS B 171 " pdb="FE4 SF4 B 300 " - pdb=" SG CYS B 152 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 142 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 181 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 148 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 124 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 212 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 105 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 138 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 199 " pdb=" SF4 B 303 " pdb="FE4 SF4 B 303 " - pdb=" SG CYS B 255 " pdb="FE3 SF4 B 303 " - pdb=" SG CYS B 216 " pdb="FE1 SF4 B 303 " - pdb=" SG CYS B 222 " pdb="FE2 SF4 B 303 " - pdb=" SG CYS B 219 " pdb=" SF4 B 304 " pdb="FE2 SF4 B 304 " - pdb=" SG CYS B 245 " pdb="FE3 SF4 B 304 " - pdb=" SG CYS B 248 " pdb="FE1 SF4 B 304 " - pdb=" SG CYS B 226 " pdb="FE4 SF4 B 304 " - pdb=" SG CYS B 251 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 410 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 404 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 407 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 375 " pdb=" SF4 C 502 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 368 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 414 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 365 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 371 " Number of angles added : 84 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 43.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.840A pdb=" N ILE A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 34 through 60 removed outlier: 4.897A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 58 " --> pdb=" O MET A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.057A pdb=" N THR A 73 " --> pdb=" O TYR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.803A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.755A pdb=" N GLY A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 157 removed outlier: 3.815A pdb=" N LYS A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.536A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 removed outlier: 4.108A pdb=" N VAL B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 20 No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'B' and resid 23 through 26 No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 176 through 179 No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 170 through 177 removed outlier: 4.231A pdb=" N MET C 174 " --> pdb=" O CYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 204 through 213 removed outlier: 5.494A pdb=" N ASN C 208 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 210 " --> pdb=" O MET C 207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 211 " --> pdb=" O ASN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 removed outlier: 4.060A pdb=" N ASN C 219 " --> pdb=" O ALA C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 237 through 244 removed outlier: 3.814A pdb=" N ILE C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 275 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 354 through 357 No H-bonds generated for 'chain 'C' and resid 354 through 357' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.912A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 409 through 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' Processing helix chain 'C' and resid 421 through 433 removed outlier: 3.653A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 31 removed outlier: 4.077A pdb=" N ASP D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 48 through 66 removed outlier: 3.607A pdb=" N TRP D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.557A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 154 through 159 removed outlier: 4.109A pdb=" N LYS D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 4.318A pdb=" N PHE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.783A pdb=" N TYR D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 removed outlier: 4.381A pdb=" N SER D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.656A pdb=" N PHE D 234 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 256 through 274 removed outlier: 4.043A pdb=" N ILE D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.957A pdb=" N TRP D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 13 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 58 removed outlier: 3.867A pdb=" N ASN E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 70 through 87 Processing helix chain 'E' and resid 102 through 105 removed outlier: 3.859A pdb=" N ILE E 105 " --> pdb=" O ILE E 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 125 through 151 removed outlier: 4.047A pdb=" N PHE E 129 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP E 130 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.829A pdb=" N THR E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 50 removed outlier: 3.722A pdb=" N ALA G 32 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 130 through 136 removed outlier: 4.481A pdb=" N GLN G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR G 136 " --> pdb=" O PHE G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 184 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 103 Processing sheet with id= B, first strand: chain 'B' and resid 157 through 160 Processing sheet with id= C, first strand: chain 'B' and resid 195 through 197 Processing sheet with id= D, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.378A pdb=" N ASN C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU C 100 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 80 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 156 through 158 removed outlier: 6.170A pdb=" N THR C 197 " --> pdb=" O ILE C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.606A pdb=" N ARG C 284 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 323 through 326 removed outlier: 4.273A pdb=" N LYS C 323 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 352 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.624A pdb=" N SER G 77 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU G 81 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY G 111 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER G 104 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 109 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 145 through 147 367 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 4359 1.40 - 1.62: 7084 1.62 - 1.84: 122 1.84 - 2.06: 4 2.06 - 2.28: 84 Bond restraints: 11653 Sorted by residual: bond pdb=" N PRO C 194 " pdb=" CA PRO C 194 " ideal model delta sigma weight residual 1.469 1.707 -0.238 1.28e-02 6.10e+03 3.46e+02 bond pdb=" C4 FMN G 300 " pdb=" O4 FMN G 300 " ideal model delta sigma weight residual 1.230 1.402 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C2 FMN D 400 " pdb=" O2 FMN D 400 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C2 FMN G 300 " pdb=" O2 FMN G 300 " ideal model delta sigma weight residual 1.230 1.394 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" C2 FMN C 503 " pdb=" O2 FMN C 503 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.58e+01 ... (remaining 11648 not shown) Histogram of bond angle deviations from ideal: 73.69 - 86.59: 84 86.59 - 99.48: 23 99.48 - 112.38: 5281 112.38 - 125.28: 10226 125.28 - 138.18: 248 Bond angle restraints: 15862 Sorted by residual: angle pdb=" C PHE C 193 " pdb=" N PRO C 194 " pdb=" CA PRO C 194 " ideal model delta sigma weight residual 119.84 138.18 -18.34 1.25e+00 6.40e-01 2.15e+02 angle pdb=" CA PRO C 194 " pdb=" N PRO C 194 " pdb=" CD PRO C 194 " ideal model delta sigma weight residual 112.00 100.66 11.34 1.40e+00 5.10e-01 6.56e+01 angle pdb=" N LEU A 170 " pdb=" CA LEU A 170 " pdb=" C LEU A 170 " ideal model delta sigma weight residual 112.75 122.10 -9.35 1.36e+00 5.41e-01 4.73e+01 angle pdb=" CA THR A 176 " pdb=" CB THR A 176 " pdb=" OG1 THR A 176 " ideal model delta sigma weight residual 109.60 99.51 10.09 1.50e+00 4.44e-01 4.52e+01 angle pdb=" CA PRO D 295 " pdb=" N PRO D 295 " pdb=" CD PRO D 295 " ideal model delta sigma weight residual 112.00 102.74 9.26 1.40e+00 5.10e-01 4.37e+01 ... (remaining 15857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 6586 34.69 - 69.37: 322 69.37 - 104.06: 16 104.06 - 138.74: 1 138.74 - 173.42: 3 Dihedral angle restraints: 6928 sinusoidal: 2652 harmonic: 4276 Sorted by residual: dihedral pdb=" C10 FMN D 400 " pdb=" C1' FMN D 400 " pdb=" N10 FMN D 400 " pdb=" C2' FMN D 400 " ideal model delta sinusoidal sigma weight residual -102.41 71.02 -173.42 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN G 300 " pdb=" C1' FMN G 300 " pdb=" N10 FMN G 300 " pdb=" C2' FMN G 300 " ideal model delta sinusoidal sigma weight residual 257.59 93.16 164.43 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C10 FMN C 503 " pdb=" C1' FMN C 503 " pdb=" N10 FMN C 503 " pdb=" C2' FMN C 503 " ideal model delta sinusoidal sigma weight residual 257.59 102.47 155.12 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.261: 1892 4.261 - 8.523: 0 8.523 - 12.784: 0 12.784 - 17.045: 0 17.045 - 21.307: 28 Chirality restraints: 1920 Sorted by residual: chirality pdb="FE2 SF4 B 300 " pdb=" S1 SF4 B 300 " pdb=" S3 SF4 B 300 " pdb=" S4 SF4 B 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.31 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 B 303 " pdb=" S1 SF4 B 303 " pdb=" S3 SF4 B 303 " pdb=" S4 SF4 B 303 " both_signs ideal model delta sigma weight residual False 10.55 -10.71 21.27 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 B 304 " pdb=" S2 SF4 B 304 " pdb=" S3 SF4 B 304 " pdb=" S4 SF4 B 304 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 ... (remaining 1917 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 7 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ARG E 7 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG E 7 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU E 8 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 146 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C VAL G 146 " -0.091 2.00e-02 2.50e+03 pdb=" O VAL G 146 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL G 147 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 248 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" CG ASP D 248 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASP D 248 " -0.028 2.00e-02 2.50e+03 pdb=" OD2 ASP D 248 " -0.028 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 245 2.66 - 3.22: 10223 3.22 - 3.78: 17655 3.78 - 4.34: 22775 4.34 - 4.90: 35668 Nonbonded interactions: 86566 Sorted by model distance: nonbonded pdb=" CG2 VAL B 234 " pdb=" OD1 ASN B 235 " model vdw 2.098 3.460 nonbonded pdb=" O2' FMN G 300 " pdb=" O4' FMN G 300 " model vdw 2.161 2.440 nonbonded pdb=" SG CYS A 25 " pdb="FE FE A 200 " model vdw 2.301 2.620 nonbonded pdb=" NZ LYS G 139 " pdb=" O GLY G 153 " model vdw 2.308 2.520 nonbonded pdb=" SG CYS E 26 " pdb="FE FE A 200 " model vdw 2.312 2.620 ... (remaining 86561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.620 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.880 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.014 0.238 11653 Z= 0.935 Angle : 1.947 18.337 15862 Z= 1.172 Chirality : 2.554 21.307 1920 Planarity : 0.014 0.127 1946 Dihedral : 19.296 173.425 4198 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.14 % Favored : 93.06 % Rotamer: Outliers : 10.79 % Allowed : 9.16 % Favored : 80.05 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 1.45 % 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: -1.59 (0.22), residues: 1499 helix: -2.83 (0.16), residues: 610 sheet: -2.47 (0.48), residues: 96 loop : 0.94 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP D 65 HIS 0.009 0.003 HIS C 419 PHE 0.041 0.005 PHE B 18 TYR 0.037 0.005 TYR C 167 ARG 0.010 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 279 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6867 (t80) cc_final: 0.5942 (t80) REVERT: A 125 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 168 LYS cc_start: 0.8524 (mttt) cc_final: 0.8119 (mmtt) REVERT: B 119 TYR cc_start: 0.8830 (t80) cc_final: 0.8567 (t80) REVERT: B 122 MET cc_start: 0.8303 (mtm) cc_final: 0.8065 (mmt) REVERT: B 158 HIS cc_start: 0.7723 (m-70) cc_final: 0.7248 (m90) REVERT: B 160 GLU cc_start: 0.8276 (pm20) cc_final: 0.8029 (pm20) REVERT: B 231 ILE cc_start: 0.8635 (tp) cc_final: 0.8263 (mp) REVERT: B 238 PRO cc_start: 0.9337 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: B 241 ASP cc_start: 0.8278 (t0) cc_final: 0.7849 (t70) REVERT: C 230 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7969 (t) REVERT: C 323 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8022 (ttmt) REVERT: D 249 TYR cc_start: 0.6844 (m-10) cc_final: 0.6629 (m-10) REVERT: E 57 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8427 (t) REVERT: E 122 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7575 (m110) REVERT: E 167 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5435 (t80) REVERT: E 174 ILE cc_start: 0.7525 (mm) cc_final: 0.7215 (mm) outliers start: 132 outliers final: 46 residues processed: 374 average time/residue: 0.2284 time to fit residues: 121.1068 Evaluate side-chains 240 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 73 HIS ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 ASN ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 121 ASN D 161 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.264 11653 Z= 1.286 Angle : 3.906 50.907 15862 Z= 2.582 Chirality : 0.761 6.410 1920 Planarity : 0.006 0.059 1946 Dihedral : 12.022 170.603 1615 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.25 % Allowed : 6.21 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.42 (0.20), residues: 1499 helix: -1.42 (0.18), residues: 617 sheet: -2.12 (0.52), residues: 82 loop : -0.22 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 65 HIS 0.005 0.001 HIS C 172 PHE 0.021 0.002 PHE B 18 TYR 0.023 0.002 TYR C 167 ARG 0.006 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7588 (mmm) cc_final: 0.7016 (mmp) REVERT: A 168 LYS cc_start: 0.8656 (mttt) cc_final: 0.8429 (mmtt) REVERT: B 122 MET cc_start: 0.8447 (mtt) cc_final: 0.8153 (mmt) REVERT: B 158 HIS cc_start: 0.7498 (m-70) cc_final: 0.7079 (m90) REVERT: B 160 GLU cc_start: 0.8185 (pm20) cc_final: 0.7880 (pm20) REVERT: B 241 ASP cc_start: 0.8561 (t0) cc_final: 0.8097 (t70) REVERT: C 125 ASN cc_start: 0.8070 (m-40) cc_final: 0.7854 (m110) REVERT: C 165 GLU cc_start: 0.8378 (tt0) cc_final: 0.7946 (tt0) REVERT: C 202 ILE cc_start: 0.8737 (mp) cc_final: 0.8288 (mm) REVERT: C 239 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8524 (mm-40) REVERT: C 429 LYS cc_start: 0.7937 (mttt) cc_final: 0.7489 (mptt) REVERT: D 133 LEU cc_start: 0.8298 (tp) cc_final: 0.8057 (tp) REVERT: D 249 TYR cc_start: 0.7441 (m-10) cc_final: 0.6999 (m-80) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.2245 time to fit residues: 80.2327 Evaluate side-chains 178 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN C 143 HIS ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.249 11653 Z= 1.276 Angle : 3.916 51.191 15862 Z= 2.588 Chirality : 0.757 6.337 1920 Planarity : 0.005 0.062 1946 Dihedral : 11.520 176.606 1615 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.22 (0.21), residues: 1499 helix: -0.90 (0.19), residues: 628 sheet: -1.86 (0.56), residues: 79 loop : -0.47 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 65 HIS 0.008 0.002 HIS C 143 PHE 0.023 0.002 PHE D 234 TYR 0.028 0.002 TYR C 199 ARG 0.008 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 230 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7101 (t80) cc_final: 0.6420 (t80) REVERT: A 168 LYS cc_start: 0.8629 (mttt) cc_final: 0.8417 (mmtt) REVERT: B 122 MET cc_start: 0.8457 (mtt) cc_final: 0.8239 (mmt) REVERT: B 158 HIS cc_start: 0.7697 (m-70) cc_final: 0.7437 (m90) REVERT: B 160 GLU cc_start: 0.8221 (pm20) cc_final: 0.8010 (pm20) REVERT: B 241 ASP cc_start: 0.8665 (t0) cc_final: 0.8289 (t70) REVERT: C 125 ASN cc_start: 0.8352 (m-40) cc_final: 0.8043 (m110) REVERT: C 165 GLU cc_start: 0.8645 (tt0) cc_final: 0.7997 (tt0) REVERT: C 239 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8736 (mm-40) REVERT: C 335 MET cc_start: 0.8066 (mmm) cc_final: 0.7461 (mmt) REVERT: C 429 LYS cc_start: 0.8224 (mttt) cc_final: 0.7717 (mptt) REVERT: E 14 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7294 (tppt) REVERT: E 121 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7156 (mtmm) REVERT: E 187 MET cc_start: 0.8538 (ttp) cc_final: 0.8159 (ttp) outliers start: 3 outliers final: 1 residues processed: 232 average time/residue: 0.2010 time to fit residues: 69.1223 Evaluate side-chains 175 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 chunk 91 optimal weight: 0.2980 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.242 11653 Z= 1.274 Angle : 3.893 50.771 15862 Z= 2.576 Chirality : 0.759 6.327 1920 Planarity : 0.005 0.067 1946 Dihedral : 11.271 176.335 1615 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.22 (0.21), residues: 1499 helix: -0.80 (0.20), residues: 647 sheet: -1.75 (0.57), residues: 78 loop : -0.57 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 65 HIS 0.002 0.001 HIS C 143 PHE 0.016 0.002 PHE D 234 TYR 0.021 0.002 TYR D 7 ARG 0.018 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6833 (t80) cc_final: 0.6393 (t80) REVERT: A 168 LYS cc_start: 0.8541 (mttt) cc_final: 0.8333 (mmtt) REVERT: A 180 MET cc_start: 0.8613 (mmm) cc_final: 0.8230 (mmm) REVERT: B 158 HIS cc_start: 0.7771 (m-70) cc_final: 0.7243 (m90) REVERT: B 160 GLU cc_start: 0.8266 (pm20) cc_final: 0.7652 (pm20) REVERT: B 241 ASP cc_start: 0.8623 (t0) cc_final: 0.8252 (t70) REVERT: C 125 ASN cc_start: 0.8420 (m-40) cc_final: 0.8096 (m110) REVERT: C 165 GLU cc_start: 0.8666 (tt0) cc_final: 0.8014 (tt0) REVERT: C 202 ILE cc_start: 0.8589 (mp) cc_final: 0.7976 (mm) REVERT: C 239 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8771 (mm-40) REVERT: C 335 MET cc_start: 0.8089 (mmm) cc_final: 0.7405 (mmt) REVERT: C 429 LYS cc_start: 0.8146 (mttt) cc_final: 0.7735 (mptt) REVERT: E 21 GLN cc_start: 0.7630 (mp10) cc_final: 0.7177 (mp10) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1963 time to fit residues: 69.3236 Evaluate side-chains 181 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.240 11653 Z= 1.271 Angle : 3.897 50.942 15862 Z= 2.578 Chirality : 0.760 6.364 1920 Planarity : 0.005 0.058 1946 Dihedral : 11.185 177.943 1615 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.14 (0.21), residues: 1499 helix: -0.60 (0.20), residues: 630 sheet: -1.53 (0.59), residues: 72 loop : -0.71 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 65 HIS 0.002 0.001 HIS C 73 PHE 0.023 0.002 PHE D 89 TYR 0.021 0.002 TYR D 7 ARG 0.015 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7538 (t80) cc_final: 0.6390 (t80) REVERT: A 168 LYS cc_start: 0.8527 (mttt) cc_final: 0.8309 (mmtt) REVERT: B 158 HIS cc_start: 0.7923 (m-70) cc_final: 0.7535 (m90) REVERT: B 160 GLU cc_start: 0.8397 (pm20) cc_final: 0.7751 (pm20) REVERT: B 241 ASP cc_start: 0.8607 (t0) cc_final: 0.8313 (t70) REVERT: C 125 ASN cc_start: 0.8456 (m-40) cc_final: 0.8123 (m-40) REVERT: C 135 MET cc_start: 0.7972 (mtp) cc_final: 0.7390 (mtp) REVERT: C 165 GLU cc_start: 0.8626 (tt0) cc_final: 0.8033 (tt0) REVERT: C 168 LEU cc_start: 0.8935 (mm) cc_final: 0.8729 (mt) REVERT: C 175 MET cc_start: 0.8903 (tpp) cc_final: 0.8366 (mmm) REVERT: C 335 MET cc_start: 0.8139 (mmm) cc_final: 0.7405 (mmt) REVERT: C 429 LYS cc_start: 0.8288 (mttt) cc_final: 0.7820 (mptt) REVERT: E 14 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7330 (tppt) REVERT: E 21 GLN cc_start: 0.7597 (mp10) cc_final: 0.7378 (mp10) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.2038 time to fit residues: 66.4205 Evaluate side-chains 175 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.241 11653 Z= 1.276 Angle : 3.917 51.203 15862 Z= 2.587 Chirality : 0.760 6.380 1920 Planarity : 0.005 0.058 1946 Dihedral : 11.205 179.744 1615 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.47 (0.21), residues: 1499 helix: -0.79 (0.20), residues: 634 sheet: -1.22 (0.58), residues: 78 loop : -1.03 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 65 HIS 0.004 0.001 HIS C 419 PHE 0.023 0.003 PHE D 89 TYR 0.029 0.003 TYR C 199 ARG 0.010 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7318 (t80) cc_final: 0.6734 (t80) REVERT: B 122 MET cc_start: 0.8530 (mmt) cc_final: 0.8061 (mmt) REVERT: B 241 ASP cc_start: 0.8622 (t0) cc_final: 0.8111 (t70) REVERT: C 125 ASN cc_start: 0.8414 (m-40) cc_final: 0.8084 (m110) REVERT: C 135 MET cc_start: 0.7948 (mtp) cc_final: 0.7557 (mtp) REVERT: C 262 VAL cc_start: 0.8771 (m) cc_final: 0.8480 (p) REVERT: C 287 THR cc_start: 0.9326 (m) cc_final: 0.9023 (p) REVERT: C 335 MET cc_start: 0.8310 (mmm) cc_final: 0.7393 (mmt) REVERT: C 429 LYS cc_start: 0.8377 (mttt) cc_final: 0.7889 (mptt) REVERT: E 121 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7066 (mtmm) REVERT: E 187 MET cc_start: 0.8659 (ttp) cc_final: 0.8280 (ttp) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.2025 time to fit residues: 67.4996 Evaluate side-chains 168 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.247 11653 Z= 1.282 Angle : 3.877 50.526 15862 Z= 2.567 Chirality : 0.763 6.510 1920 Planarity : 0.004 0.052 1946 Dihedral : 10.676 179.406 1615 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.08 % Allowed : 1.55 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.16 (0.21), residues: 1499 helix: -0.47 (0.20), residues: 643 sheet: -1.23 (0.59), residues: 72 loop : -0.90 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 300 HIS 0.002 0.001 HIS D 202 PHE 0.026 0.001 PHE B 18 TYR 0.023 0.002 TYR D 7 ARG 0.008 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7727 (t80) cc_final: 0.6645 (t80) REVERT: B 122 MET cc_start: 0.8430 (mmt) cc_final: 0.7948 (mmt) REVERT: B 158 HIS cc_start: 0.7902 (m90) cc_final: 0.7652 (m90) REVERT: B 241 ASP cc_start: 0.8543 (t0) cc_final: 0.8219 (t70) REVERT: C 125 ASN cc_start: 0.8480 (m-40) cc_final: 0.8157 (m110) REVERT: C 135 MET cc_start: 0.7860 (mtp) cc_final: 0.7613 (mtp) REVERT: C 165 GLU cc_start: 0.8674 (tt0) cc_final: 0.8095 (tt0) REVERT: C 168 LEU cc_start: 0.8911 (mm) cc_final: 0.8661 (mt) REVERT: C 239 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8745 (mm-40) REVERT: C 262 VAL cc_start: 0.8645 (m) cc_final: 0.8373 (p) REVERT: C 331 MET cc_start: 0.8236 (ttm) cc_final: 0.7951 (ttt) REVERT: C 429 LYS cc_start: 0.8050 (mttt) cc_final: 0.7691 (mptt) REVERT: D 41 TYR cc_start: 0.7050 (p90) cc_final: 0.5256 (t80) REVERT: E 14 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7238 (tppt) REVERT: E 121 LYS cc_start: 0.7434 (mtmm) cc_final: 0.6858 (mtmm) REVERT: E 187 MET cc_start: 0.8437 (ttp) cc_final: 0.7965 (ttp) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.2016 time to fit residues: 64.9763 Evaluate side-chains 166 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.239 11653 Z= 1.272 Angle : 3.899 50.807 15862 Z= 2.578 Chirality : 0.760 6.349 1920 Planarity : 0.004 0.052 1946 Dihedral : 10.770 179.792 1615 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.08 % Allowed : 1.39 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.24 (0.21), residues: 1499 helix: -0.49 (0.20), residues: 631 sheet: -1.23 (0.57), residues: 78 loop : -0.99 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 98 HIS 0.003 0.001 HIS C 419 PHE 0.019 0.002 PHE D 217 TYR 0.022 0.002 TYR C 269 ARG 0.008 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7772 (t80) cc_final: 0.6562 (t80) REVERT: B 122 MET cc_start: 0.8470 (mmt) cc_final: 0.8047 (mmt) REVERT: B 158 HIS cc_start: 0.8023 (m90) cc_final: 0.7674 (m90) REVERT: B 241 ASP cc_start: 0.8610 (t0) cc_final: 0.8153 (t70) REVERT: C 125 ASN cc_start: 0.8457 (m-40) cc_final: 0.8129 (m110) REVERT: C 135 MET cc_start: 0.7971 (mtp) cc_final: 0.7644 (mtp) REVERT: C 165 GLU cc_start: 0.8806 (tt0) cc_final: 0.8297 (tt0) REVERT: C 239 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8759 (mm-40) REVERT: C 262 VAL cc_start: 0.8781 (m) cc_final: 0.8547 (p) REVERT: C 330 MET cc_start: 0.8272 (mtm) cc_final: 0.8060 (mtm) REVERT: C 331 MET cc_start: 0.8304 (ttm) cc_final: 0.8083 (ttm) REVERT: C 429 LYS cc_start: 0.8214 (mttt) cc_final: 0.7840 (mptt) REVERT: D 41 TYR cc_start: 0.7271 (p90) cc_final: 0.5438 (t80) REVERT: E 121 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7016 (mtmm) REVERT: E 187 MET cc_start: 0.8575 (ttp) cc_final: 0.8112 (ttp) outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.2039 time to fit residues: 65.4126 Evaluate side-chains 169 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.246 11653 Z= 1.279 Angle : 3.881 50.580 15862 Z= 2.569 Chirality : 0.760 6.321 1920 Planarity : 0.004 0.049 1946 Dihedral : 10.432 179.389 1615 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.17 (0.21), residues: 1499 helix: -0.43 (0.20), residues: 649 sheet: -1.24 (0.56), residues: 78 loop : -0.96 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 98 HIS 0.009 0.001 HIS C 172 PHE 0.025 0.001 PHE B 18 TYR 0.019 0.001 TYR C 269 ARG 0.008 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7228 (t80) cc_final: 0.6918 (t80) REVERT: B 122 MET cc_start: 0.8419 (mmt) cc_final: 0.7973 (mmt) REVERT: B 158 HIS cc_start: 0.7917 (m90) cc_final: 0.7620 (m90) REVERT: B 241 ASP cc_start: 0.8554 (t0) cc_final: 0.8150 (t70) REVERT: C 125 ASN cc_start: 0.8446 (m-40) cc_final: 0.8139 (m110) REVERT: C 165 GLU cc_start: 0.8779 (tt0) cc_final: 0.8195 (tt0) REVERT: C 175 MET cc_start: 0.8741 (tpp) cc_final: 0.8477 (mmm) REVERT: C 202 ILE cc_start: 0.8387 (mp) cc_final: 0.7884 (mm) REVERT: C 213 MET cc_start: 0.8086 (tpp) cc_final: 0.7850 (mmm) REVERT: C 239 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8742 (mm-40) REVERT: C 262 VAL cc_start: 0.8690 (m) cc_final: 0.8382 (p) REVERT: C 263 GLN cc_start: 0.8558 (mm110) cc_final: 0.8147 (mp10) REVERT: C 411 SER cc_start: 0.9429 (p) cc_final: 0.9118 (t) REVERT: C 429 LYS cc_start: 0.7999 (mttt) cc_final: 0.7666 (mptt) REVERT: D 41 TYR cc_start: 0.7139 (p90) cc_final: 0.5266 (t80) REVERT: D 213 ILE cc_start: 0.8210 (mm) cc_final: 0.7945 (mm) REVERT: E 21 GLN cc_start: 0.7442 (mp10) cc_final: 0.7216 (mp10) REVERT: E 121 LYS cc_start: 0.7441 (mtmm) cc_final: 0.6899 (mtmm) REVERT: E 187 MET cc_start: 0.8454 (ttp) cc_final: 0.8015 (ttp) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.2039 time to fit residues: 66.8987 Evaluate side-chains 169 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 67 optimal weight: 0.0270 chunk 98 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 118 optimal weight: 0.0770 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 HIS C 364 ASN D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.249 11653 Z= 1.290 Angle : 3.877 50.550 15862 Z= 2.567 Chirality : 0.760 6.310 1920 Planarity : 0.004 0.048 1946 Dihedral : 10.194 178.791 1615 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.08 (0.21), residues: 1499 helix: -0.32 (0.21), residues: 645 sheet: -1.03 (0.61), residues: 72 loop : -0.96 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 98 HIS 0.003 0.001 HIS C 172 PHE 0.016 0.001 PHE D 217 TYR 0.019 0.001 TYR C 272 ARG 0.012 0.001 ARG C 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.8365 (mmt) cc_final: 0.7882 (mmt) REVERT: B 158 HIS cc_start: 0.7885 (m90) cc_final: 0.7647 (m90) REVERT: B 241 ASP cc_start: 0.8565 (t0) cc_final: 0.8172 (t70) REVERT: C 125 ASN cc_start: 0.8460 (m-40) cc_final: 0.8134 (m110) REVERT: C 165 GLU cc_start: 0.8706 (tt0) cc_final: 0.8188 (tt0) REVERT: C 175 MET cc_start: 0.8712 (tpp) cc_final: 0.8504 (mmm) REVERT: C 202 ILE cc_start: 0.8397 (mp) cc_final: 0.7903 (mm) REVERT: C 263 GLN cc_start: 0.8514 (mm110) cc_final: 0.8203 (mp10) REVERT: C 411 SER cc_start: 0.9355 (p) cc_final: 0.9128 (t) REVERT: C 429 LYS cc_start: 0.8021 (mttt) cc_final: 0.7713 (mptt) REVERT: D 41 TYR cc_start: 0.6965 (p90) cc_final: 0.5128 (t80) REVERT: D 290 MET cc_start: 0.7828 (tpt) cc_final: 0.7602 (mmt) REVERT: E 121 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6813 (mtmm) REVERT: E 187 MET cc_start: 0.8457 (ttp) cc_final: 0.8045 (ttp) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.1927 time to fit residues: 63.9619 Evaluate side-chains 168 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104630 restraints weight = 18418.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104501 restraints weight = 15507.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104463 restraints weight = 13846.391| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.242 11653 Z= 1.273 Angle : 3.892 50.734 15862 Z= 2.574 Chirality : 0.760 6.334 1920 Planarity : 0.004 0.053 1946 Dihedral : 10.278 178.273 1615 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -1.15 (0.21), residues: 1499 helix: -0.39 (0.21), residues: 643 sheet: -1.01 (0.59), residues: 78 loop : -0.98 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 98 HIS 0.006 0.001 HIS C 172 PHE 0.021 0.002 PHE B 18 TYR 0.032 0.002 TYR B 118 ARG 0.011 0.001 ARG C 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.47 seconds wall clock time: 43 minutes 23.97 seconds (2603.97 seconds total)