Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 03:57:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/04_2023/7zc6_14622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/04_2023/7zc6_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_14622/04_2023/7zc6_14622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/04_2023/7zc6_14622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/04_2023/7zc6_14622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc6_14622/04_2023/7zc6_14622_updated.pdb" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 6.61, per 1000 atoms: 0.58 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: 5.02 Conformation dependent library (CDL) restraints added in 1.9 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: 0.95 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: 2.90 Time building geometry restraints manager: 5.38 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: 6577 34.69 - 69.37: 316 69.37 - 104.06: 16 104.06 - 138.74: 1 138.74 - 173.42: 3 Dihedral angle restraints: 6913 sinusoidal: 2637 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 6910 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: 0.920 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: 4.060 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.010 Find NCS groups from input model: 0.390 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- 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 : 19.197 173.425 4183 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 % 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 *********************** 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 : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 46 residues processed: 374 average time/residue: 0.2269 time to fit residues: 120.5377 Evaluate side-chains 230 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1228 time to fit residues: 11.5956 ------------------------------------------------------------------------------- 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: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.274 11653 Z= 1.279 Angle : 3.902 51.065 15862 Z= 2.580 Chirality : 0.763 6.472 1920 Planarity : 0.006 0.070 1946 Dihedral : 11.412 170.651 1600 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.25 % 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: -1.37 (0.20), residues: 1499 helix: -1.43 (0.18), residues: 619 sheet: -2.13 (0.52), residues: 82 loop : -0.15 (0.22), residues: 798 *********************** 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 240 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 240 average time/residue: 0.2087 time to fit residues: 74.5894 Evaluate side-chains 173 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1122 time to fit residues: 2.2881 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.253 11653 Z= 1.275 Angle : 3.912 50.868 15862 Z= 2.585 Chirality : 0.760 6.373 1920 Planarity : 0.005 0.064 1946 Dihedral : 10.791 173.261 1600 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.08 % 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: -0.84 (0.19), residues: 625 sheet: -1.85 (0.56), residues: 79 loop : -0.44 (0.22), residues: 795 *********************** 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 226 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.253 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.2120 time to fit residues: 70.7287 Evaluate side-chains 167 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7747 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 91 optimal weight: 0.0070 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 overall best weight: 1.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN ** C 125 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.245 11653 Z= 1.278 Angle : 3.887 50.610 15862 Z= 2.572 Chirality : 0.760 6.359 1920 Planarity : 0.005 0.084 1946 Dihedral : 10.437 171.107 1600 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.08 % 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: -1.02 (0.21), residues: 1499 helix: -0.61 (0.20), residues: 630 sheet: -1.80 (0.58), residues: 78 loop : -0.47 (0.22), residues: 791 *********************** 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 232 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2080 time to fit residues: 71.9032 Evaluate side-chains 177 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1090 time to fit residues: 2.1202 ------------------------------------------------------------------------------- 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: 0.9980 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7482 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.244 11653 Z= 1.277 Angle : 3.882 50.824 15862 Z= 2.571 Chirality : 0.760 6.389 1920 Planarity : 0.004 0.052 1946 Dihedral : 10.243 174.608 1600 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.00 % 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: -0.95 (0.21), residues: 1499 helix: -0.41 (0.20), residues: 636 sheet: -1.60 (0.58), residues: 72 loop : -0.60 (0.22), residues: 791 *********************** 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 215 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2095 time to fit residues: 66.9812 Evaluate side-chains 167 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8622 ------------------------------------------------------------------------------- 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: 0.9980 chunk 129 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 121 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4308 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 : 3.881 50.668 15862 Z= 2.570 Chirality : 0.760 6.394 1920 Planarity : 0.004 0.048 1946 Dihedral : 10.070 175.029 1600 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.08 % 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: -0.86 (0.21), residues: 1499 helix: -0.33 (0.21), residues: 644 sheet: -1.20 (0.60), residues: 72 loop : -0.60 (0.22), residues: 783 *********************** 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 218 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.2034 time to fit residues: 66.9821 Evaluate side-chains 164 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1063 time to fit residues: 2.0757 ------------------------------------------------------------------------------- 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: 30.0000 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4481 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= 1.284 Angle : 3.877 50.739 15862 Z= 2.568 Chirality : 0.759 6.316 1920 Planarity : 0.004 0.046 1946 Dihedral : 9.900 175.877 1600 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.00 % 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: -0.77 (0.21), residues: 1499 helix: -0.25 (0.21), residues: 652 sheet: -1.16 (0.61), residues: 72 loop : -0.56 (0.22), residues: 775 *********************** 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 213 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2098 time to fit residues: 66.3172 Evaluate side-chains 161 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7802 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 0.0270 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4579 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= 1.272 Angle : 3.887 50.671 15862 Z= 2.573 Chirality : 0.760 6.333 1920 Planarity : 0.004 0.047 1946 Dihedral : 9.942 177.500 1600 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.08 % 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: -0.83 (0.22), residues: 1499 helix: -0.27 (0.21), residues: 642 sheet: -0.93 (0.61), residues: 72 loop : -0.65 (0.22), residues: 785 *********************** 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 202 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.2117 time to fit residues: 64.1594 Evaluate side-chains 159 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1093 time to fit residues: 1.9996 ------------------------------------------------------------------------------- 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: 0.9990 chunk 137 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 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: 0.7489 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.244 11653 Z= 1.275 Angle : 3.881 50.611 15862 Z= 2.570 Chirality : 0.760 6.332 1920 Planarity : 0.004 0.046 1946 Dihedral : 9.885 177.882 1600 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.08 % 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: -0.79 (0.21), residues: 1499 helix: -0.18 (0.21), residues: 637 sheet: -0.82 (0.62), residues: 72 loop : -0.70 (0.22), residues: 790 *********************** 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 205 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2150 time to fit residues: 66.7038 Evaluate side-chains 151 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7823 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 118 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7468 moved from start: 0.4837 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= 1.280 Angle : 3.880 50.614 15862 Z= 2.569 Chirality : 0.760 6.332 1920 Planarity : 0.004 0.046 1946 Dihedral : 9.813 178.589 1600 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.00 % 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: -0.82 (0.21), residues: 1499 helix: -0.12 (0.21), residues: 641 sheet: -0.79 (0.61), residues: 72 loop : -0.81 (0.22), residues: 786 ********************** 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 205 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2086 time to fit residues: 64.1749 Evaluate side-chains 157 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8507 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103869 restraints weight = 18463.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103888 restraints weight = 15946.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104036 restraints weight = 13707.829| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 0.245 11653 Z= 1.275 Angle : 3.888 50.649 15862 Z= 2.573 Chirality : 0.760 6.317 1920 Planarity : 0.004 0.046 1946 Dihedral : 9.880 179.629 1600 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.00 % 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: -0.82 (0.22), residues: 1499 helix: -0.11 (0.21), residues: 639 sheet: -0.75 (0.60), residues: 78 loop : -0.82 (0.22), residues: 782 =============================================================================== Job complete usr+sys time: 2253.76 seconds wall clock time: 41 minutes 38.88 seconds (2498.88 seconds total)