Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 17:52:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/10_2023/8kd3_37123_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 100 5.16 5 C 16471 2.51 5 N 4897 2.21 5 O 5779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "U GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 27576 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2620 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 3 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1647 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 2 Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1043 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 848 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.40, per 1000 atoms: 0.52 Number of scatterers: 27576 At special positions: 0 Unit cell: (137.03, 161.17, 188.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 100 16.00 P 328 15.00 O 5779 8.00 N 4897 7.00 C 16471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 263 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 306 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.83 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 5 sheets defined 49.4% alpha, 2.3% beta 139 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 12.11 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.610A pdb=" N MET A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 removed outlier: 3.517A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.011A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.564A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 5.070A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 676 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.550A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 760 through 763 No H-bonds generated for 'chain 'B' and resid 760 through 763' Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 840 removed outlier: 3.667A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.963A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 3.996A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.035A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.808A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 996 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 3.632A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 3.867A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1222 through 1229 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 removed outlier: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 275 through 292 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 369 removed outlier: 3.503A pdb=" N HIS D 369 " --> pdb=" O TRP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.712A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.118A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 558 Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 230 through 240 removed outlier: 4.074A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 240 " --> pdb=" O TRP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 removed outlier: 3.847A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 291 removed outlier: 4.318A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 329 through 342 removed outlier: 4.278A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 349 through 367 Processing helix chain 'G' and resid 304 through 311 Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 326 through 328 No H-bonds generated for 'chain 'G' and resid 326 through 328' Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.999A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 569 Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.680A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.798A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 3.945A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 3.977A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.346A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 Processing helix chain 'R' and resid 53 through 80 Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 78 removed outlier: 3.763A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.812A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 91 Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 35 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.179A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.528A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1136 through 1140 removed outlier: 3.766A pdb=" N ALA B1140 " --> pdb=" O PHE B1301 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B1301 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= D, first strand: chain 'E' and resid 272 through 274 Processing sheet with id= E, first strand: chain 'E' and resid 437 through 439 845 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 16.23 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7213 1.34 - 1.46: 7823 1.46 - 1.58: 12964 1.58 - 1.70: 656 1.70 - 1.82: 153 Bond restraints: 28809 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+01 bond pdb=" N ASP E 288 " pdb=" CA ASP E 288 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" N ILE E 395 " pdb=" CA ILE E 395 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.38e+00 bond pdb=" N ILE E 291 " pdb=" CA ILE E 291 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.93e+00 bond pdb=" N THR E 396 " pdb=" CA THR E 396 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.99e+00 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.27: 1377 104.27 - 111.81: 14056 111.81 - 119.35: 10300 119.35 - 126.89: 13488 126.89 - 134.43: 1064 Bond angle restraints: 40285 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 97.32 14.68 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO B 853 " pdb=" N PRO B 853 " pdb=" CD PRO B 853 " ideal model delta sigma weight residual 112.00 102.60 9.40 1.40e+00 5.10e-01 4.51e+01 angle pdb=" CB MET D 107 " pdb=" CG MET D 107 " pdb=" SD MET D 107 " ideal model delta sigma weight residual 112.70 130.10 -17.40 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 128.61 -15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 40280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14152 35.15 - 70.29: 2004 70.29 - 105.44: 60 105.44 - 140.59: 2 140.59 - 175.74: 1 Dihedral angle restraints: 16219 sinusoidal: 8693 harmonic: 7526 Sorted by residual: dihedral pdb=" CB CYS G 263 " pdb=" SG CYS G 263 " pdb=" SG CYS G 266 " pdb=" CB CYS G 266 " ideal model delta sinusoidal sigma weight residual 93.00 46.45 46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C MET D 107 " pdb=" N MET D 107 " pdb=" CA MET D 107 " pdb=" CB MET D 107 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4154 0.081 - 0.161: 267 0.161 - 0.242: 17 0.242 - 0.323: 3 0.323 - 0.403: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CA ILE E 395 " pdb=" N ILE E 395 " pdb=" C ILE E 395 " pdb=" CB ILE E 395 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA MET D 107 " pdb=" N MET D 107 " pdb=" C MET D 107 " pdb=" CB MET D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4439 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 852 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 853 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.073 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 319 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 88 " -0.023 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" CG TYR P 88 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR P 88 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR P 88 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR P 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR P 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR P 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 5 2.01 - 2.73: 1580 2.73 - 3.45: 38416 3.45 - 4.18: 73271 4.18 - 4.90: 117444 Nonbonded interactions: 230716 Sorted by model distance: nonbonded pdb=" OE2 GLU B 885 " pdb=" CD2 HIS B 886 " model vdw 1.281 3.260 nonbonded pdb=" NE2 HIS O 113 " pdb=" OD1 ASP S 123 " model vdw 1.391 2.520 nonbonded pdb=" OD1 ASP B 872 " pdb=" O ILE E 54 " model vdw 1.709 3.040 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 1.813 3.880 nonbonded pdb=" OE2 GLU B 816 " pdb=" OD1 ASP E 47 " model vdw 1.850 3.040 ... (remaining 230711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 11 through 24 or resid 80 through 113 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 36 through 133) selection = (chain 'S' and resid 36 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.310 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: 0.040 Extract box with map and model: 33.830 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 87.880 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 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 : 0.004 0.185 28809 Z= 0.236 Angle : 0.772 17.397 40285 Z= 0.425 Chirality : 0.043 0.403 4442 Planarity : 0.006 0.137 3978 Dihedral : 24.382 175.735 11344 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.13 % Allowed : 30.60 % Favored : 69.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2507 helix: -0.20 (0.13), residues: 1350 sheet: 0.83 (0.61), residues: 93 loop : -1.83 (0.17), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 326 average time/residue: 1.2071 time to fit residues: 469.4318 Evaluate side-chains 280 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 220 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 690 ASN B 886 HIS ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN O 39 HIS S 55 GLN S 85 GLN S 93 GLN T 25 ASN V 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 28809 Z= 0.250 Angle : 0.593 11.439 40285 Z= 0.321 Chirality : 0.038 0.223 4442 Planarity : 0.004 0.067 3978 Dihedral : 26.514 175.210 6107 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.49 % Allowed : 25.68 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2507 helix: 0.44 (0.14), residues: 1373 sheet: 0.51 (0.59), residues: 98 loop : -1.58 (0.18), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 334 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 38 residues processed: 412 average time/residue: 1.3893 time to fit residues: 674.0248 Evaluate side-chains 338 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 300 time to evaluate : 3.249 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 23 residues processed: 17 average time/residue: 0.8468 time to fit residues: 23.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 chunk 205 optimal weight: 2.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 330 HIS D 393 GLN G 302 HIS O 39 HIS P 25 ASN Q 73 ASN T 25 ASN U 104 GLN V 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28809 Z= 0.203 Angle : 0.540 11.138 40285 Z= 0.295 Chirality : 0.036 0.167 4442 Planarity : 0.004 0.056 3978 Dihedral : 26.652 173.393 6107 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.35 % Allowed : 27.17 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2507 helix: 0.70 (0.14), residues: 1377 sheet: 0.51 (0.59), residues: 96 loop : -1.46 (0.18), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 327 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 32 residues processed: 387 average time/residue: 1.3783 time to fit residues: 625.6522 Evaluate side-chains 336 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 304 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 21 residues processed: 11 average time/residue: 0.4714 time to fit residues: 11.5255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 171 optimal weight: 0.0050 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 330 HIS D 393 GLN F 317 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 60 ASN V 64 ASN V 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28809 Z= 0.285 Angle : 0.587 10.214 40285 Z= 0.319 Chirality : 0.038 0.213 4442 Planarity : 0.004 0.055 3978 Dihedral : 26.795 175.176 6107 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.57 % Allowed : 26.08 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2507 helix: 0.55 (0.14), residues: 1385 sheet: 0.12 (0.56), residues: 94 loop : -1.37 (0.18), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 342 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 45 residues processed: 413 average time/residue: 1.4197 time to fit residues: 682.7491 Evaluate side-chains 354 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 309 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 13 average time/residue: 0.5045 time to fit residues: 12.8992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 0.6980 chunk 154 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN V 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28809 Z= 0.264 Angle : 0.575 8.923 40285 Z= 0.314 Chirality : 0.037 0.199 4442 Planarity : 0.004 0.055 3978 Dihedral : 26.843 174.041 6107 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.65 % Allowed : 26.08 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2507 helix: 0.63 (0.14), residues: 1381 sheet: -0.30 (0.54), residues: 93 loop : -1.32 (0.18), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 310 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 46 residues processed: 389 average time/residue: 1.4301 time to fit residues: 649.1153 Evaluate side-chains 337 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 11 average time/residue: 0.6464 time to fit residues: 12.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN V 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 28809 Z= 0.367 Angle : 0.647 12.827 40285 Z= 0.348 Chirality : 0.041 0.267 4442 Planarity : 0.004 0.055 3978 Dihedral : 27.030 176.053 6107 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 4.08 % Allowed : 26.56 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2507 helix: 0.47 (0.14), residues: 1387 sheet: -0.90 (0.52), residues: 91 loop : -1.38 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 308 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 50 residues processed: 372 average time/residue: 1.4879 time to fit residues: 644.5092 Evaluate side-chains 345 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 295 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 38 residues processed: 14 average time/residue: 0.8942 time to fit residues: 19.5035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 154 optimal weight: 20.0000 chunk 198 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28809 Z= 0.372 Angle : 0.641 15.075 40285 Z= 0.345 Chirality : 0.041 0.262 4442 Planarity : 0.004 0.053 3978 Dihedral : 27.184 175.010 6107 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 3.86 % Allowed : 26.69 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2507 helix: 0.45 (0.14), residues: 1387 sheet: -1.02 (0.52), residues: 91 loop : -1.35 (0.19), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 309 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 48 residues processed: 370 average time/residue: 1.4870 time to fit residues: 638.7397 Evaluate side-chains 343 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 295 time to evaluate : 3.093 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 39 residues processed: 11 average time/residue: 0.7714 time to fit residues: 14.7045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 133 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 HIS ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28809 Z= 0.207 Angle : 0.586 14.158 40285 Z= 0.316 Chirality : 0.037 0.173 4442 Planarity : 0.004 0.053 3978 Dihedral : 27.061 174.471 6107 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 3.16 % Allowed : 27.44 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2507 helix: 0.64 (0.14), residues: 1390 sheet: -0.55 (0.60), residues: 73 loop : -1.33 (0.19), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 303 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 44 residues processed: 360 average time/residue: 1.4314 time to fit residues: 603.4428 Evaluate side-chains 328 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 42 residues processed: 3 average time/residue: 0.8820 time to fit residues: 6.8556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 77 optimal weight: 0.0470 chunk 228 optimal weight: 0.6980 chunk 238 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN V 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28809 Z= 0.193 Angle : 0.572 12.871 40285 Z= 0.310 Chirality : 0.036 0.227 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.949 175.373 6107 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 2.37 % Allowed : 28.27 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2507 helix: 0.78 (0.14), residues: 1382 sheet: -0.69 (0.57), residues: 83 loop : -1.35 (0.19), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 291 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 40 residues processed: 336 average time/residue: 1.4491 time to fit residues: 569.6252 Evaluate side-chains 318 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 278 time to evaluate : 2.854 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 3 average time/residue: 0.8985 time to fit residues: 7.2093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN T 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28809 Z= 0.316 Angle : 0.631 12.965 40285 Z= 0.336 Chirality : 0.039 0.193 4442 Planarity : 0.004 0.055 3978 Dihedral : 27.050 175.201 6107 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 28.67 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2507 helix: 0.63 (0.14), residues: 1389 sheet: -0.99 (0.56), residues: 81 loop : -1.28 (0.19), residues: 1037 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 44 residues processed: 345 average time/residue: 1.4864 time to fit residues: 598.6735 Evaluate side-chains 328 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.686 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 42 residues processed: 3 average time/residue: 0.3315 time to fit residues: 5.2683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN Q 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.126607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093817 restraints weight = 55101.894| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.86 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28809 Z= 0.225 Angle : 0.600 12.476 40285 Z= 0.321 Chirality : 0.038 0.259 4442 Planarity : 0.004 0.054 3978 Dihedral : 27.025 174.197 6107 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.50 % Allowed : 28.36 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2507 helix: 0.69 (0.14), residues: 1388 sheet: -0.62 (0.60), residues: 73 loop : -1.27 (0.19), residues: 1046 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10910.54 seconds wall clock time: 195 minutes 5.27 seconds (11705.27 seconds total)