Starting phenix.real_space_refine on Sat Mar 16 02:02:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi0_33845/03_2024/7yi0_33845.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 83 5.16 5 C 8599 2.51 5 N 2248 2.21 5 O 2493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 670": "OE1" <-> "OE2" Residue "A TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "D PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "F PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13430 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4233 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 7, 'TRANS': 495} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2553 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 5 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1259 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9039 SG CYS D 263 41.201 36.453 82.439 1.00 61.30 S ATOM 9056 SG CYS D 266 44.396 38.503 81.827 1.00 45.48 S ATOM 9209 SG CYS D 286 41.321 39.307 79.739 1.00 44.47 S ATOM 9120 SG CYS D 275 32.091 27.627 84.823 1.00 91.60 S ATOM 9141 SG CYS D 278 35.407 25.729 84.699 1.00100.47 S ATOM 9344 SG CYS D 303 34.533 27.734 81.648 1.00 97.48 S ATOM 9367 SG CYS D 306 33.034 24.499 82.584 1.00 96.48 S ATOM 10288 SG CYS D 440 76.941 54.356 80.421 1.00 27.45 S ATOM 10314 SG CYS D 443 80.030 53.856 78.101 1.00 20.60 S ATOM 10503 SG CYS D 466 78.101 57.037 77.898 1.00 27.76 S ATOM 10100 SG CYS D 417 82.257 64.253 84.254 1.00 23.71 S ATOM 10127 SG CYS D 420 84.485 67.113 85.478 1.00 37.16 S ATOM 10383 SG CYS D 451 80.921 67.832 84.252 1.00 46.26 S ATOM 11280 SG CYS F 275 95.951 11.973 36.652 1.00118.29 S ATOM 11301 SG CYS F 278 92.897 13.490 36.787 1.00108.57 S ATOM 11199 SG CYS F 263 96.088 18.843 25.157 1.00 96.00 S ATOM 11216 SG CYS F 266 95.207 20.546 21.917 1.00104.06 S ATOM 11369 SG CYS F 286 98.591 21.687 24.196 1.00106.90 S Time building chain proxies: 6.56, per 1000 atoms: 0.49 Number of scatterers: 13430 At special positions: 0 Unit cell: (129.8, 111.1, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 83 16.00 O 2493 8.00 N 2248 7.00 C 8599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 275 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 278 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 275 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 286 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 263 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 266 " Number of angles added : 15 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3132 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 9 sheets defined 56.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.714A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 714 through 725 removed outlier: 3.571A pdb=" N THR A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.620A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 837 removed outlier: 3.765A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 4.187A pdb=" N LYS A 864 " --> pdb=" O MET A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 891 through 928 removed outlier: 3.841A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 6.095A pdb=" N LYS A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.738A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.593A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1141 through 1163 Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.532A pdb=" N TYR A1240 " --> pdb=" O PHE A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1256 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.719A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.085A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A1287 " --> pdb=" O GLN A1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.751A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.762A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.551A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 105 removed outlier: 4.050A pdb=" N VAL B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.532A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.504A pdb=" N LYS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 263 removed outlier: 3.522A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.021A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.263A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.664A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 removed outlier: 3.520A pdb=" N GLU B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.533A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.876A pdb=" N GLN C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.547A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.756A pdb=" N SER C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 348 through 369 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.732A pdb=" N VAL C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 168 through 175 removed outlier: 4.283A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET D 175 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.816A pdb=" N THR D 405 " --> pdb=" O ASN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.719A pdb=" N SER D 434 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 removed outlier: 3.520A pdb=" N ILE D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 321 through 330 Processing helix chain 'F' and resid 331 through 334 removed outlier: 3.814A pdb=" N LYS F 334 " --> pdb=" O ASN F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 331 through 334' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.676A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 567 removed outlier: 3.953A pdb=" N ASP F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 241 Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.531A pdb=" N SER E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 271 through 297 removed outlier: 3.819A pdb=" N LYS E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 317 removed outlier: 4.397A pdb=" N LEU E 304 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.663A pdb=" N ILE E 325 " --> pdb=" O PRO E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 removed outlier: 3.719A pdb=" N ARG E 333 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 350 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 238 removed outlier: 8.286A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLU D 177 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 63 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER D 179 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 65 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'D' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA8, first strand: chain 'D' and resid 505 through 506 removed outlier: 7.381A pdb=" N TYR D 506 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 273 through 274 635 hydrogen bonds defined for protein. 1812 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: 3.87 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4281 1.34 - 1.46: 3135 1.46 - 1.58: 6182 1.58 - 1.70: 0 1.70 - 1.81: 122 Bond restraints: 13720 Sorted by residual: bond pdb=" C LEU E 248 " pdb=" N PRO E 249 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.42e+00 bond pdb=" CA THR D 439 " pdb=" CB THR D 439 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.37e-02 5.33e+03 1.20e+00 bond pdb=" CB GLU E 340 " pdb=" CG GLU E 340 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" N THR D 439 " pdb=" CA THR D 439 " ideal model delta sigma weight residual 1.462 1.474 -0.013 1.31e-02 5.83e+03 9.20e-01 bond pdb=" CB GLU A1171 " pdb=" CG GLU A1171 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.77e-01 ... (remaining 13715 not shown) Histogram of bond angle deviations from ideal: 97.72 - 104.99: 198 104.99 - 112.27: 6678 112.27 - 119.54: 4736 119.54 - 126.81: 6712 126.81 - 134.09: 170 Bond angle restraints: 18494 Sorted by residual: angle pdb=" N GLN A 937 " pdb=" CA GLN A 937 " pdb=" C GLN A 937 " ideal model delta sigma weight residual 114.62 107.49 7.13 1.14e+00 7.69e-01 3.91e+01 angle pdb=" CA GLN A 937 " pdb=" C GLN A 937 " pdb=" N ALA A 938 " ideal model delta sigma weight residual 119.71 115.10 4.61 1.17e+00 7.31e-01 1.55e+01 angle pdb=" CA LYS A 936 " pdb=" CB LYS A 936 " pdb=" CG LYS A 936 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA GLU A1171 " pdb=" CB GLU A1171 " pdb=" CG GLU A1171 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA THR D 439 " pdb=" CB THR D 439 " pdb=" CG2 THR D 439 " ideal model delta sigma weight residual 110.50 116.19 -5.69 1.70e+00 3.46e-01 1.12e+01 ... (remaining 18489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7316 17.93 - 35.86: 724 35.86 - 53.79: 211 53.79 - 71.72: 30 71.72 - 89.65: 8 Dihedral angle restraints: 8289 sinusoidal: 3454 harmonic: 4835 Sorted by residual: dihedral pdb=" CA LEU E 248 " pdb=" C LEU E 248 " pdb=" N PRO E 249 " pdb=" CA PRO E 249 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LYS A 936 " pdb=" C LYS A 936 " pdb=" N GLN A 937 " pdb=" CA GLN A 937 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1613 0.052 - 0.104: 341 0.104 - 0.156: 40 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CB THR A1000 " pdb=" CA THR A1000 " pdb=" OG1 THR A1000 " pdb=" CG2 THR A1000 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA THR D 439 " pdb=" N THR D 439 " pdb=" C THR D 439 " pdb=" CB THR D 439 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA HIS A 785 " pdb=" N HIS A 785 " pdb=" C HIS A 785 " pdb=" CB HIS A 785 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 1995 not shown) Planarity restraints: 2351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 90 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 91 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 248 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO E 249 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 249 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 249 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 466 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 467 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 467 " -0.024 5.00e-02 4.00e+02 ... (remaining 2348 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 186 2.66 - 3.22: 12477 3.22 - 3.78: 20357 3.78 - 4.34: 28988 4.34 - 4.90: 46732 Nonbonded interactions: 108740 Sorted by model distance: nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.105 2.440 nonbonded pdb=" OG SER B 123 " pdb=" OD2 ASP B 165 " model vdw 2.109 2.440 nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.165 2.230 nonbonded pdb=" O ILE E 342 " pdb=" OG1 THR E 345 " model vdw 2.172 2.440 nonbonded pdb=" N ASP B 140 " pdb=" OD1 ASP B 140 " model vdw 2.187 2.520 ... (remaining 108735 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 4.110 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.610 Find NCS groups from input model: 0.380 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13720 Z= 0.180 Angle : 0.568 11.685 18494 Z= 0.305 Chirality : 0.042 0.260 1998 Planarity : 0.004 0.051 2351 Dihedral : 15.666 89.653 5157 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.93 % Allowed : 15.07 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.27 (0.21), residues: 1604 helix: 1.01 (0.18), residues: 805 sheet: 0.09 (0.55), residues: 91 loop : -1.66 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 428 HIS 0.017 0.001 HIS A 785 PHE 0.017 0.001 PHE A 935 TYR 0.018 0.001 TYR F 556 ARG 0.008 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 365 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1168 VAL cc_start: 0.8215 (t) cc_final: 0.7809 (t) REVERT: B 40 MET cc_start: 0.7028 (tpt) cc_final: 0.6422 (tpp) outliers start: 14 outliers final: 4 residues processed: 376 average time/residue: 0.2854 time to fit residues: 149.3617 Evaluate side-chains 197 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 214 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN A 909 GLN A 913 ASN A 947 GLN A1299 ASN C 393 GLN ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN E 317 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13720 Z= 0.177 Angle : 0.572 11.302 18494 Z= 0.304 Chirality : 0.042 0.201 1998 Planarity : 0.004 0.058 2351 Dihedral : 4.900 51.765 1779 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.19 % Allowed : 16.53 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.05 (0.21), residues: 1604 helix: 1.30 (0.18), residues: 824 sheet: 0.15 (0.53), residues: 90 loop : -1.62 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 782 HIS 0.013 0.001 HIS A 785 PHE 0.027 0.001 PHE E 289 TYR 0.017 0.002 TYR B 347 ARG 0.006 0.001 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.3951 (t80) REVERT: A 952 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.6943 (tp) REVERT: A 1008 GLU cc_start: 0.7735 (mp0) cc_final: 0.7178 (mp0) REVERT: A 1194 MET cc_start: 0.5986 (mtp) cc_final: 0.5544 (mpp) REVERT: B 40 MET cc_start: 0.6995 (tpt) cc_final: 0.6240 (tpp) REVERT: B 73 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5943 (mm-30) REVERT: B 155 SER cc_start: 0.8097 (t) cc_final: 0.7761 (m) REVERT: B 244 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 261 TRP cc_start: 0.6304 (m-10) cc_final: 0.5863 (m-10) REVERT: B 305 MET cc_start: 0.5831 (ptp) cc_final: 0.5398 (ptm) REVERT: D 549 TYR cc_start: 0.5677 (m-80) cc_final: 0.5376 (m-80) REVERT: D 553 ASP cc_start: 0.4850 (OUTLIER) cc_final: 0.4414 (m-30) REVERT: F 316 MET cc_start: 0.2224 (OUTLIER) cc_final: 0.1722 (ppp) REVERT: F 560 MET cc_start: 0.4689 (tmm) cc_final: 0.2930 (ttm) REVERT: E 256 MET cc_start: 0.4095 (ttp) cc_final: 0.3209 (mtt) outliers start: 48 outliers final: 20 residues processed: 250 average time/residue: 0.2315 time to fit residues: 87.8849 Evaluate side-chains 205 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 268 GLN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 545 ASN E 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13720 Z= 0.193 Angle : 0.563 8.605 18494 Z= 0.298 Chirality : 0.041 0.180 1998 Planarity : 0.004 0.065 2351 Dihedral : 4.427 35.543 1773 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.92 % Allowed : 18.59 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.15 (0.21), residues: 1604 helix: 1.41 (0.18), residues: 819 sheet: -0.24 (0.51), residues: 100 loop : -1.53 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 719 HIS 0.010 0.001 HIS A 785 PHE 0.027 0.002 PHE E 289 TYR 0.017 0.002 TYR B 347 ARG 0.005 0.001 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 1.467 Fit side-chains REVERT: A 764 PHE cc_start: 0.4923 (OUTLIER) cc_final: 0.3850 (t80) REVERT: B 288 MET cc_start: 0.8401 (ttp) cc_final: 0.8071 (ttm) REVERT: D 438 MET cc_start: 0.6936 (mtp) cc_final: 0.6497 (mtp) REVERT: D 470 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6914 (p) REVERT: F 316 MET cc_start: 0.3185 (mpm) cc_final: 0.2184 (ptt) REVERT: F 560 MET cc_start: 0.4672 (tmm) cc_final: 0.2834 (ttm) REVERT: E 256 MET cc_start: 0.3927 (ttp) cc_final: 0.2841 (mtt) REVERT: E 347 MET cc_start: 0.6001 (ttp) cc_final: 0.5672 (mtp) REVERT: E 368 MET cc_start: 0.3204 (ttp) cc_final: 0.1843 (tpt) outliers start: 44 outliers final: 22 residues processed: 239 average time/residue: 0.2349 time to fit residues: 83.3737 Evaluate side-chains 185 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13720 Z= 0.172 Angle : 0.525 7.354 18494 Z= 0.279 Chirality : 0.041 0.184 1998 Planarity : 0.004 0.067 2351 Dihedral : 4.298 35.173 1771 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.25 % Allowed : 19.39 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1604 helix: 1.55 (0.18), residues: 820 sheet: 0.11 (0.56), residues: 84 loop : -1.52 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 719 HIS 0.010 0.001 HIS A 785 PHE 0.022 0.001 PHE B 160 TYR 0.017 0.001 TYR D 549 ARG 0.010 0.001 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.3809 (t80) REVERT: A 986 TYR cc_start: 0.6928 (m-10) cc_final: 0.6499 (m-80) REVERT: B 53 MET cc_start: 0.8091 (mmm) cc_final: 0.7802 (mmm) REVERT: B 117 TYR cc_start: 0.8000 (t80) cc_final: 0.7787 (t80) REVERT: B 313 TYR cc_start: 0.6402 (m-80) cc_final: 0.5985 (m-10) REVERT: F 332 ASN cc_start: 0.5656 (t0) cc_final: 0.5197 (p0) REVERT: F 552 PHE cc_start: 0.4029 (OUTLIER) cc_final: 0.3348 (m-80) REVERT: F 560 MET cc_start: 0.4479 (tmm) cc_final: 0.2732 (ttm) REVERT: E 256 MET cc_start: 0.4039 (ttp) cc_final: 0.3279 (mtt) REVERT: E 368 MET cc_start: 0.3327 (ttp) cc_final: 0.2455 (tpt) outliers start: 49 outliers final: 26 residues processed: 220 average time/residue: 0.2413 time to fit residues: 79.4233 Evaluate side-chains 180 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN A1150 HIS ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13720 Z= 0.207 Angle : 0.558 8.908 18494 Z= 0.296 Chirality : 0.042 0.186 1998 Planarity : 0.004 0.067 2351 Dihedral : 4.404 24.010 1769 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.25 % Allowed : 20.32 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1604 helix: 1.49 (0.18), residues: 827 sheet: -0.18 (0.55), residues: 89 loop : -1.42 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 912 HIS 0.009 0.001 HIS A 785 PHE 0.027 0.002 PHE F 326 TYR 0.012 0.001 TYR B 347 ARG 0.007 0.001 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 178 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 LYS cc_start: 0.4760 (ttmt) cc_final: 0.4383 (mmtt) REVERT: A 986 TYR cc_start: 0.7004 (m-10) cc_final: 0.6597 (m-80) REVERT: A 1021 PHE cc_start: 0.8192 (t80) cc_final: 0.7855 (t80) REVERT: A 1300 MET cc_start: 0.7230 (ttp) cc_final: 0.7011 (ttm) REVERT: B 53 MET cc_start: 0.8366 (mmm) cc_final: 0.8132 (mmm) REVERT: D 438 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6451 (mtp) REVERT: D 553 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5975 (m-30) REVERT: F 332 ASN cc_start: 0.6355 (t0) cc_final: 0.5725 (p0) REVERT: F 552 PHE cc_start: 0.4099 (OUTLIER) cc_final: 0.3151 (m-80) REVERT: F 560 MET cc_start: 0.4497 (tmm) cc_final: 0.2661 (ttm) REVERT: E 256 MET cc_start: 0.4000 (ttp) cc_final: 0.3074 (mtt) REVERT: E 309 LEU cc_start: -0.3342 (OUTLIER) cc_final: -0.3698 (mt) REVERT: E 368 MET cc_start: 0.2788 (ttp) cc_final: 0.1292 (tpt) outliers start: 49 outliers final: 31 residues processed: 217 average time/residue: 0.2518 time to fit residues: 80.4129 Evaluate side-chains 197 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 345 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 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 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13720 Z= 0.160 Angle : 0.522 10.590 18494 Z= 0.274 Chirality : 0.041 0.189 1998 Planarity : 0.004 0.066 2351 Dihedral : 4.217 22.556 1769 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.19 % Allowed : 20.85 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.49 (0.21), residues: 1604 helix: 1.69 (0.19), residues: 816 sheet: -0.18 (0.56), residues: 88 loop : -1.32 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 719 HIS 0.010 0.001 HIS A 785 PHE 0.014 0.001 PHE E 289 TYR 0.018 0.001 TYR A 675 ARG 0.008 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.3622 (t80) REVERT: A 986 TYR cc_start: 0.7003 (m-10) cc_final: 0.6664 (m-80) REVERT: A 1021 PHE cc_start: 0.8008 (t80) cc_final: 0.7663 (t80) REVERT: A 1135 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7157 (mp) REVERT: A 1170 LYS cc_start: 0.7415 (mtpt) cc_final: 0.7193 (mtpt) REVERT: A 1304 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 438 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6352 (mtp) REVERT: F 276 ASP cc_start: -0.0024 (OUTLIER) cc_final: -0.0356 (t70) REVERT: F 332 ASN cc_start: 0.6545 (t0) cc_final: 0.5787 (p0) REVERT: F 552 PHE cc_start: 0.4064 (OUTLIER) cc_final: 0.3322 (m-80) REVERT: F 560 MET cc_start: 0.4418 (tmm) cc_final: 0.2745 (ttm) REVERT: E 256 MET cc_start: 0.3948 (ttp) cc_final: 0.3216 (mtt) REVERT: E 309 LEU cc_start: -0.3415 (OUTLIER) cc_final: -0.3832 (mt) REVERT: E 368 MET cc_start: 0.2441 (ttp) cc_final: 0.1225 (tpt) outliers start: 48 outliers final: 31 residues processed: 213 average time/residue: 0.2383 time to fit residues: 76.1274 Evaluate side-chains 198 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 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 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13720 Z= 0.165 Angle : 0.520 12.258 18494 Z= 0.275 Chirality : 0.040 0.196 1998 Planarity : 0.004 0.071 2351 Dihedral : 4.164 22.756 1769 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.19 % Allowed : 21.25 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 (0.22), residues: 1604 helix: 1.77 (0.19), residues: 815 sheet: -0.38 (0.53), residues: 103 loop : -1.24 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 905 HIS 0.009 0.001 HIS A 785 PHE 0.024 0.001 PHE A1305 TYR 0.014 0.001 TYR A 675 ARG 0.010 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 PHE cc_start: 0.4964 (OUTLIER) cc_final: 0.3631 (t80) REVERT: A 986 TYR cc_start: 0.7025 (m-10) cc_final: 0.6701 (m-80) REVERT: A 1135 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 1304 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 53 MET cc_start: 0.8236 (mmm) cc_final: 0.7915 (mmm) REVERT: D 438 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6343 (mtp) REVERT: D 549 TYR cc_start: 0.6570 (m-80) cc_final: 0.6345 (m-80) REVERT: F 552 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.3273 (m-80) REVERT: F 560 MET cc_start: 0.4406 (tmm) cc_final: 0.2711 (ttm) REVERT: E 256 MET cc_start: 0.3805 (ttp) cc_final: 0.3138 (mtt) REVERT: E 309 LEU cc_start: -0.3412 (OUTLIER) cc_final: -0.3785 (mt) REVERT: E 368 MET cc_start: 0.2537 (ttp) cc_final: 0.1156 (tpt) outliers start: 48 outliers final: 33 residues processed: 204 average time/residue: 0.2432 time to fit residues: 74.1760 Evaluate side-chains 194 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13720 Z= 0.204 Angle : 0.556 12.833 18494 Z= 0.292 Chirality : 0.041 0.195 1998 Planarity : 0.004 0.071 2351 Dihedral : 4.336 23.279 1769 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.25 % Allowed : 21.78 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.54 (0.22), residues: 1604 helix: 1.73 (0.19), residues: 812 sheet: -0.25 (0.56), residues: 93 loop : -1.25 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1151 HIS 0.009 0.001 HIS A 785 PHE 0.017 0.001 PHE A1021 TYR 0.012 0.001 TYR D 372 ARG 0.009 0.001 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 791 GLU cc_start: 0.5910 (mp0) cc_final: 0.5479 (mt-10) REVERT: A 986 TYR cc_start: 0.7125 (m-10) cc_final: 0.6720 (m-80) REVERT: A 1135 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 1304 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 59 LYS cc_start: 0.6692 (pttt) cc_final: 0.6486 (pttt) REVERT: D 438 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6416 (mtp) REVERT: D 549 TYR cc_start: 0.6675 (m-80) cc_final: 0.6415 (m-80) REVERT: F 552 PHE cc_start: 0.4063 (OUTLIER) cc_final: 0.3172 (m-80) REVERT: E 256 MET cc_start: 0.3870 (ttp) cc_final: 0.3197 (mtt) REVERT: E 301 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5753 (pt) REVERT: E 309 LEU cc_start: -0.3316 (OUTLIER) cc_final: -0.3734 (mt) REVERT: E 368 MET cc_start: 0.2473 (ttp) cc_final: 0.1151 (tpt) outliers start: 49 outliers final: 36 residues processed: 204 average time/residue: 0.2423 time to fit residues: 73.9659 Evaluate side-chains 198 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.0010 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13720 Z= 0.163 Angle : 0.524 13.620 18494 Z= 0.275 Chirality : 0.040 0.199 1998 Planarity : 0.004 0.074 2351 Dihedral : 4.193 22.994 1769 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.59 % Allowed : 22.71 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.66 (0.22), residues: 1604 helix: 1.81 (0.19), residues: 815 sheet: -0.30 (0.54), residues: 103 loop : -1.17 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1151 HIS 0.009 0.001 HIS A 785 PHE 0.023 0.001 PHE A1305 TYR 0.012 0.001 TYR A 675 ARG 0.009 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 791 GLU cc_start: 0.5967 (mp0) cc_final: 0.5515 (mt-10) REVERT: A 986 TYR cc_start: 0.7076 (m-10) cc_final: 0.6693 (m-80) REVERT: A 1135 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 1136 PHE cc_start: 0.6970 (m-80) cc_final: 0.6725 (m-80) REVERT: A 1304 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 438 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6241 (mtp) REVERT: D 549 TYR cc_start: 0.6653 (m-80) cc_final: 0.6442 (m-80) REVERT: F 552 PHE cc_start: 0.3964 (OUTLIER) cc_final: 0.3212 (m-80) REVERT: E 256 MET cc_start: 0.4180 (ttp) cc_final: 0.3617 (mtt) REVERT: E 301 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5633 (pt) REVERT: E 309 LEU cc_start: -0.3349 (OUTLIER) cc_final: -0.3749 (mt) REVERT: E 368 MET cc_start: 0.2381 (ttp) cc_final: 0.1081 (tpt) outliers start: 39 outliers final: 31 residues processed: 194 average time/residue: 0.2487 time to fit residues: 71.1560 Evaluate side-chains 190 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 102 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13720 Z= 0.170 Angle : 0.535 13.837 18494 Z= 0.280 Chirality : 0.041 0.210 1998 Planarity : 0.004 0.072 2351 Dihedral : 4.220 23.319 1769 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.52 % Allowed : 23.17 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.71 (0.22), residues: 1604 helix: 1.81 (0.19), residues: 815 sheet: -0.10 (0.56), residues: 100 loop : -1.13 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1151 HIS 0.009 0.001 HIS A 785 PHE 0.018 0.001 PHE A1021 TYR 0.012 0.001 TYR B 176 ARG 0.008 0.000 ARG C 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: A 791 GLU cc_start: 0.6018 (mp0) cc_final: 0.5547 (mt-10) REVERT: A 874 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4332 (pt0) REVERT: A 986 TYR cc_start: 0.7090 (m-10) cc_final: 0.6709 (m-80) REVERT: A 1135 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 1175 ARG cc_start: 0.7402 (ttm170) cc_final: 0.7187 (mtt-85) REVERT: A 1304 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 316 MET cc_start: 0.3242 (tmm) cc_final: 0.3002 (tmm) REVERT: D 549 TYR cc_start: 0.6735 (m-80) cc_final: 0.6515 (m-80) REVERT: F 552 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.3241 (m-80) REVERT: E 256 MET cc_start: 0.4080 (ttp) cc_final: 0.3485 (mtt) REVERT: E 301 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5742 (pt) REVERT: E 309 LEU cc_start: -0.3321 (OUTLIER) cc_final: -0.3726 (mt) REVERT: E 368 MET cc_start: 0.2014 (ttp) cc_final: 0.0831 (tpt) outliers start: 38 outliers final: 31 residues processed: 191 average time/residue: 0.2320 time to fit residues: 66.6296 Evaluate side-chains 189 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1135 ILE Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain F residue 552 PHE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 0.0010 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 0.0020 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN D 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.214705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.171143 restraints weight = 16763.414| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.20 r_work: 0.3851 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13720 Z= 0.131 Angle : 0.501 11.834 18494 Z= 0.263 Chirality : 0.040 0.215 1998 Planarity : 0.004 0.070 2351 Dihedral : 3.973 22.313 1769 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.26 % Allowed : 23.37 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.81 (0.22), residues: 1604 helix: 1.91 (0.19), residues: 816 sheet: 0.04 (0.57), residues: 101 loop : -1.11 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1151 HIS 0.007 0.001 HIS A 785 PHE 0.013 0.001 PHE E 289 TYR 0.019 0.001 TYR D 506 ARG 0.009 0.000 ARG C 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.90 seconds wall clock time: 57 minutes 55.37 seconds (3475.37 seconds total)