Starting phenix.real_space_refine on Thu Feb 5 19:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j64_61162/02_2026/9j64_61162.map" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3824 atoms to isotropic. 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 131 5.16 5 C 10372 2.51 5 N 2804 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16354 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4558 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 543} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5213 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 601 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 1 Chain: "F" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 685 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain breaks: 2 Chain: "H" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Chain: "I" Number of atoms: 3822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 480, 3811 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 13, 'TRANS': 466} Conformer: "B" Number of residues, atoms: 480, 3811 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 13, 'TRANS': 466} bond proxies already assigned to first conformer: 3866 Chain: "J" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 165 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9928 SG CYS E 42 77.934 37.666 64.407 1.00225.72 S ATOM 9947 SG CYS E 45 78.369 33.895 63.758 1.00229.95 S ATOM 10173 SG CYS E 83 81.401 35.902 64.991 1.00252.78 S ATOM 10102 SG CYS E 75 76.842 50.225 68.582 1.00284.61 S ATOM 10269 SG CYS E 94 78.758 48.962 64.763 1.00250.55 S ATOM 10014 SG CYS E 53 83.002 31.797 66.801 1.00307.00 S ATOM 10037 SG CYS E 56 83.856 29.631 69.880 1.00270.98 S ATOM 10052 SG CYS E 68 81.541 32.673 70.265 1.00283.48 S ATOM 11928 SG CYS H 42 62.923 39.488 50.988 1.00496.87 S ATOM 11947 SG CYS H 45 60.257 36.449 50.157 1.00500.78 S ATOM 12078 SG CYS H 75 60.233 49.750 59.592 1.00514.80 S ATOM 12245 SG CYS H 94 57.530 46.367 58.375 1.00525.98 S ATOM 12014 SG CYS H 53 58.418 35.546 44.222 1.00525.55 S ATOM 12028 SG CYS H 68 60.392 38.473 43.241 1.00554.20 S ATOM 15953 SG CYS I 599 79.870 83.349 143.878 1.00 94.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG I 177 " occ=0.18 ... (20 atoms not shown) pdb=" NH2BARG I 177 " occ=0.82 Time building chain proxies: 4.47, per 1000 atoms: 0.27 Number of scatterers: 16354 At special positions: 0 Unit cell: (122.98, 163.4, 176.3, 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 131 16.00 O 3040 8.00 N 2804 7.00 C 10372 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 - 3.00 Amino acid : True - 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: 1.44 Conformation dependent library (CDL) restraints added in 776.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 68 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 53 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 42 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 80 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 75 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 94 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 53 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 82 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 68 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 565 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 627 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 599 " Number of angles added : 6 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 62.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 57 through 79 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 155 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.020A pdb=" N GLU A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 229 removed outlier: 3.500A pdb=" N PHE A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.662A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.579A pdb=" N MET A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 329 removed outlier: 3.535A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.769A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.827A pdb=" N MET A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.630A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.630A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.541A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.825A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 497 removed outlier: 3.982A pdb=" N TYR A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 3.559A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 542 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 596 through 604 removed outlier: 3.824A pdb=" N GLN A 600 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.627A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 5.436A pdb=" N ASN D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.572A pdb=" N PHE D 39 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 78 removed outlier: 3.878A pdb=" N TYR D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 105 removed outlier: 4.157A pdb=" N LYS D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR D 105 " --> pdb=" O MET D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.823A pdb=" N PHE D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 155 through 171 Processing helix chain 'D' and resid 179 through 192 removed outlier: 4.126A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.620A pdb=" N PHE D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU D 217 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 254 removed outlier: 3.949A pdb=" N LEU D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.832A pdb=" N VAL D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 removed outlier: 3.608A pdb=" N LEU D 278 " --> pdb=" O HIS D 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 281 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS D 283 " --> pdb=" O HIS D 279 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 286 " --> pdb=" O CYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 302 removed outlier: 4.009A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 306 removed outlier: 6.762A pdb=" N THR D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 306' Processing helix chain 'D' and resid 307 through 326 removed outlier: 4.134A pdb=" N MET D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 322 " --> pdb=" O HIS D 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 324 " --> pdb=" O HIS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 357 removed outlier: 3.686A pdb=" N PHE D 339 " --> pdb=" O MET D 335 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL D 340 " --> pdb=" O PRO D 336 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 351 " --> pdb=" O HIS D 347 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 354 " --> pdb=" O PHE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.738A pdb=" N MET D 365 " --> pdb=" O ASP D 361 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 369 " --> pdb=" O MET D 365 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 3.975A pdb=" N GLU D 389 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 385 through 390' Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.546A pdb=" N TYR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 423 removed outlier: 3.644A pdb=" N ILE D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR D 420 " --> pdb=" O THR D 416 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 446 removed outlier: 3.684A pdb=" N LYS D 433 " --> pdb=" O ASP D 429 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 438 " --> pdb=" O PHE D 434 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.776A pdb=" N ILE D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 497 removed outlier: 4.346A pdb=" N TYR D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR D 478 " --> pdb=" O HIS D 474 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN D 496 " --> pdb=" O ASN D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 548 removed outlier: 3.874A pdb=" N GLN D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 587 Processing helix chain 'D' and resid 596 through 604 removed outlier: 3.567A pdb=" N GLN D 600 " --> pdb=" O TYR D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 621 Processing helix chain 'E' and resid 81 through 91 Processing helix chain 'F' and resid 32 through 38 removed outlier: 3.779A pdb=" N ALA F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 47 Processing helix chain 'F' and resid 67 through 83 Processing helix chain 'F' and resid 101 through 110 removed outlier: 6.541A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'H' and resid 80 through 91 Processing helix chain 'I' and resid 156 through 165 removed outlier: 3.524A pdb=" N ILE I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR I 163 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 176 removed outlier: 3.598A pdb=" N VAL I 170 " --> pdb=" O HIS I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 198 Processing helix chain 'I' and resid 199 through 209 removed outlier: 3.977A pdb=" N GLU I 205 " --> pdb=" O ASP I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 230 Processing helix chain 'I' and resid 231 through 240 Processing helix chain 'I' and resid 245 through 262 removed outlier: 3.527A pdb=" N ARG I 249 " --> pdb=" O ASP I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 284 Processing helix chain 'I' and resid 310 through 317 Processing helix chain 'I' and resid 320 through 337 removed outlier: 3.578A pdb=" N GLY I 328 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 329 " --> pdb=" O HIS I 325 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE I 330 " --> pdb=" O MET I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 357 removed outlier: 3.888A pdb=" N ILE I 347 " --> pdb=" O VAL I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 377 removed outlier: 3.541A pdb=" N LYS I 365 " --> pdb=" O GLU I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 398 removed outlier: 3.635A pdb=" N GLN I 390 " --> pdb=" O LEU I 386 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE I 392 " --> pdb=" O PHE I 388 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN I 394 " --> pdb=" O GLN I 390 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET I 395 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 429 removed outlier: 4.052A pdb=" N GLU I 417 " --> pdb=" O CYS I 413 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE I 418 " --> pdb=" O SER I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 457 removed outlier: 4.108A pdb=" N ASP I 438 " --> pdb=" O HIS I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 477 removed outlier: 3.829A pdb=" N GLN I 464 " --> pdb=" O SER I 460 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN I 470 " --> pdb=" O LYS I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 493 Processing helix chain 'I' and resid 511 through 522 removed outlier: 4.014A pdb=" N THR I 515 " --> pdb=" O ASN I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 540 removed outlier: 3.840A pdb=" N ILE I 539 " --> pdb=" O ALA I 535 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL I 540 " --> pdb=" O LEU I 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 535 through 540' Processing helix chain 'I' and resid 548 through 561 removed outlier: 3.675A pdb=" N ILE I 556 " --> pdb=" O LEU I 552 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER I 558 " --> pdb=" O SER I 554 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 561 " --> pdb=" O ILE I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 580 Processing helix chain 'I' and resid 582 through 592 Processing helix chain 'I' and resid 597 through 602 Processing helix chain 'I' and resid 602 through 609 removed outlier: 3.980A pdb=" N ARG I 606 " --> pdb=" O ALA I 602 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 607 " --> pdb=" O ARG I 603 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 627 removed outlier: 3.886A pdb=" N VAL I 624 " --> pdb=" O LEU I 620 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 507 through 512 Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 566 removed outlier: 4.328A pdb=" N TYR A 573 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AA4, first strand: chain 'D' and resid 561 through 562 removed outlier: 3.734A pdb=" N GLY D 562 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL D 577 " --> pdb=" O GLY D 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.713A pdb=" N PHE E 79 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 3.925A pdb=" N VAL F 60 " --> pdb=" O LYS F 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 22 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 31 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU F 28 " --> pdb=" O THR G 13 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE G 15 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE F 30 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N ASP G 17 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 16 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 18 " --> pdb=" O VAL G 3 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2343 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: 1.74 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4922 1.33 - 1.45: 2489 1.45 - 1.57: 9064 1.57 - 1.69: 0 1.69 - 1.81: 206 Bond restraints: 16681 Sorted by residual: bond pdb=" N HIS A 274 " pdb=" CA HIS A 274 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.00e-02 1.00e+04 1.32e+01 bond pdb=" N ILE A 419 " pdb=" CA ILE A 419 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N LEU A 275 " pdb=" CA LEU A 275 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.62e+00 bond pdb=" N HIS A 279 " pdb=" CA HIS A 279 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.15e+00 bond pdb=" N LEU F 110 " pdb=" CA LEU F 110 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.18e-02 7.18e+03 6.76e+00 ... (remaining 16676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 21854 1.94 - 3.88: 580 3.88 - 5.82: 61 5.82 - 7.76: 17 7.76 - 9.70: 2 Bond angle restraints: 22514 Sorted by residual: angle pdb=" C THR D 520 " pdb=" CA THR D 520 " pdb=" CB THR D 520 " ideal model delta sigma weight residual 116.63 110.47 6.16 1.16e+00 7.43e-01 2.82e+01 angle pdb=" N THR D 613 " pdb=" CA THR D 613 " pdb=" C THR D 613 " ideal model delta sigma weight residual 111.36 106.24 5.12 1.09e+00 8.42e-01 2.20e+01 angle pdb=" N LYS D 615 " pdb=" CA LYS D 615 " pdb=" C LYS D 615 " ideal model delta sigma weight residual 111.82 106.65 5.17 1.16e+00 7.43e-01 1.99e+01 angle pdb=" N SER D 616 " pdb=" CA SER D 616 " pdb=" C SER D 616 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N LEU G 57 " pdb=" CA LEU G 57 " pdb=" C LEU G 57 " ideal model delta sigma weight residual 113.18 107.97 5.21 1.21e+00 6.83e-01 1.85e+01 ... (remaining 22509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 9115 17.57 - 35.14: 867 35.14 - 52.71: 117 52.71 - 70.28: 24 70.28 - 87.85: 7 Dihedral angle restraints: 10130 sinusoidal: 4162 harmonic: 5968 Sorted by residual: dihedral pdb=" CA GLU D 468 " pdb=" C GLU D 468 " pdb=" N PHE D 469 " pdb=" CA PHE D 469 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS I 565 " pdb=" C HIS I 565 " pdb=" N THR I 566 " pdb=" CA THR I 566 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LYS D 252 " pdb=" C LYS D 252 " pdb=" N TYR D 253 " pdb=" CA TYR D 253 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1899 0.045 - 0.090: 473 0.090 - 0.136: 105 0.136 - 0.181: 12 0.181 - 0.226: 3 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CB THR D 554 " pdb=" CA THR D 554 " pdb=" OG1 THR D 554 " pdb=" CG2 THR D 554 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE D 614 " pdb=" N ILE D 614 " pdb=" C ILE D 614 " pdb=" CB ILE D 614 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA LEU D 610 " pdb=" N LEU D 610 " pdb=" C LEU D 610 " pdb=" CB LEU D 610 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 2489 not shown) Planarity restraints: 2877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 255 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 256 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 414 " -0.210 9.50e-02 1.11e+02 9.42e-02 5.44e+00 pdb=" NE ARG A 414 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 414 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 414 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 414 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 105 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C MET F 105 " -0.040 2.00e-02 2.50e+03 pdb=" O MET F 105 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 106 " 0.013 2.00e-02 2.50e+03 ... (remaining 2874 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1215 2.73 - 3.27: 18306 3.27 - 3.82: 26829 3.82 - 4.36: 31924 4.36 - 4.90: 49575 Nonbonded interactions: 127849 Sorted by model distance: nonbonded pdb=" OD1 ASP H 97 " pdb="ZN ZN H 202 " model vdw 2.189 2.230 nonbonded pdb=" NH1 ARG D 32 " pdb=" O PRO F 49 " model vdw 2.221 3.120 nonbonded pdb=" O ASP D 170 " pdb=" NH2 ARG D 249 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR F 79 " pdb=" O PRO F 91 " model vdw 2.237 3.040 nonbonded pdb=" O ASN I 443 " pdb=" OG1 THR I 446 " model vdw 2.240 3.040 ... (remaining 127844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 57 through 106 or resid 136 through 646)) } ncs_group { reference = (chain 'E' and (resid 24 through 54 or resid 68 through 203)) selection = (chain 'H' and (resid 24 through 105 or resid 201 through 203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 : 0.010 0.654 16704 Z= 0.376 Angle : 0.724 9.705 22520 Z= 0.434 Chirality : 0.043 0.226 2492 Planarity : 0.004 0.094 2877 Dihedral : 13.570 87.845 6240 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 0.33 % Allowed : 0.88 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 1980 helix: 0.44 (0.15), residues: 1053 sheet: -1.28 (0.88), residues: 37 loop : -1.05 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 374 TYR 0.034 0.002 TYR D 105 PHE 0.027 0.002 PHE D 469 TRP 0.020 0.002 TRP A 147 HIS 0.011 0.001 HIS I 627 Details of bonding type rmsd covalent geometry : bond 0.00439 (16681) covalent geometry : angle 0.72364 (22514) hydrogen bonds : bond 0.26844 ( 785) hydrogen bonds : angle 7.30860 ( 2343) metal coordination : bond 0.23393 ( 23) metal coordination : angle 1.74007 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.5299 (tpt) cc_final: 0.4858 (tpt) REVERT: A 566 MET cc_start: 0.3635 (mpp) cc_final: 0.3382 (mpp) REVERT: A 582 MET cc_start: 0.7291 (mtt) cc_final: 0.6883 (mtt) REVERT: D 60 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7400 (mm-30) REVERT: D 335 MET cc_start: 0.8642 (mmt) cc_final: 0.8124 (mmm) REVERT: D 489 LYS cc_start: 0.8896 (tttm) cc_final: 0.8380 (tptp) REVERT: D 576 MET cc_start: 0.5801 (pmm) cc_final: 0.5550 (pmm) REVERT: G 1 MET cc_start: 0.1788 (ppp) cc_final: 0.1346 (ppp) REVERT: G 6 MET cc_start: 0.8302 (ttm) cc_final: 0.8042 (ttm) REVERT: I 193 PHE cc_start: 0.8451 (m-80) cc_final: 0.8162 (m-80) REVERT: I 395 MET cc_start: 0.8714 (ppp) cc_final: 0.8125 (ppp) outliers start: 6 outliers final: 1 residues processed: 224 average time/residue: 0.1274 time to fit residues: 42.6295 Evaluate side-chains 140 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 186 ASN A 225 ASN ** A 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 488 ASN D 279 HIS ** D 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 HIS I 372 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.135009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.113951 restraints weight = 90179.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.110874 restraints weight = 117059.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.108236 restraints weight = 87043.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.108359 restraints weight = 87313.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.107632 restraints weight = 66251.046| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16704 Z= 0.192 Angle : 0.669 8.180 22520 Z= 0.361 Chirality : 0.043 0.157 2492 Planarity : 0.005 0.051 2877 Dihedral : 5.267 61.678 2171 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 1980 helix: 0.34 (0.15), residues: 1144 sheet: -1.06 (0.87), residues: 42 loop : -1.46 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 606 TYR 0.047 0.002 TYR D 105 PHE 0.030 0.002 PHE I 447 TRP 0.033 0.002 TRP A 91 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00420 (16681) covalent geometry : angle 0.66765 (22514) hydrogen bonds : bond 0.06500 ( 785) hydrogen bonds : angle 5.41622 ( 2343) metal coordination : bond 0.01349 ( 23) metal coordination : angle 2.56880 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.7350 (t60) cc_final: 0.7097 (t60) REVERT: A 335 MET cc_start: 0.5264 (tpt) cc_final: 0.4765 (mmm) REVERT: A 566 MET cc_start: 0.4624 (mpp) cc_final: 0.4067 (mpp) REVERT: A 576 MET cc_start: 0.6538 (ppp) cc_final: 0.6069 (ppp) REVERT: A 582 MET cc_start: 0.7213 (mtt) cc_final: 0.6527 (mtt) REVERT: D 60 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7091 (mm-30) REVERT: D 335 MET cc_start: 0.8584 (mmt) cc_final: 0.8109 (mmm) REVERT: D 576 MET cc_start: 0.5788 (pmm) cc_final: 0.5588 (pmm) REVERT: G 1 MET cc_start: 0.1809 (ppp) cc_final: 0.1586 (ppp) outliers start: 3 outliers final: 1 residues processed: 189 average time/residue: 0.1156 time to fit residues: 33.3221 Evaluate side-chains 135 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 139 optimal weight: 0.0970 chunk 180 optimal weight: 6.9990 chunk 88 optimal weight: 0.0670 chunk 188 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN F 108 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 372 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.118317 restraints weight = 110967.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.117974 restraints weight = 144450.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.115968 restraints weight = 91920.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.115807 restraints weight = 86785.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.115126 restraints weight = 74952.606| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16704 Z= 0.130 Angle : 0.588 9.381 22520 Z= 0.312 Chirality : 0.041 0.185 2492 Planarity : 0.004 0.051 2877 Dihedral : 4.926 54.335 2171 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 1980 helix: 0.55 (0.15), residues: 1145 sheet: -1.12 (0.68), residues: 57 loop : -1.41 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 171 TYR 0.025 0.001 TYR D 105 PHE 0.030 0.002 PHE A 188 TRP 0.044 0.002 TRP I 209 HIS 0.007 0.001 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00261 (16681) covalent geometry : angle 0.58665 (22514) hydrogen bonds : bond 0.05284 ( 785) hydrogen bonds : angle 4.82991 ( 2343) metal coordination : bond 0.00637 ( 23) metal coordination : angle 2.04573 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.8641 (mmt) cc_final: 0.8429 (mmp) REVERT: A 335 MET cc_start: 0.5517 (tpt) cc_final: 0.5074 (mmm) REVERT: A 582 MET cc_start: 0.7227 (mtt) cc_final: 0.6520 (mtt) REVERT: D 60 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7175 (mm-30) REVERT: D 147 TRP cc_start: 0.8338 (t60) cc_final: 0.7337 (t60) REVERT: G 1 MET cc_start: 0.1643 (ppp) cc_final: 0.1345 (ppp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1093 time to fit residues: 30.9427 Evaluate side-chains 136 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 189 optimal weight: 0.4980 chunk 69 optimal weight: 0.4980 chunk 108 optimal weight: 0.3980 chunk 105 optimal weight: 0.0870 chunk 173 optimal weight: 10.0000 chunk 107 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 165 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN D 36 ASN D 82 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN G 42 GLN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.121204 restraints weight = 132897.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.120538 restraints weight = 151355.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.119078 restraints weight = 95129.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.119209 restraints weight = 75332.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.118772 restraints weight = 69001.563| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16704 Z= 0.118 Angle : 0.563 7.627 22520 Z= 0.295 Chirality : 0.040 0.175 2492 Planarity : 0.003 0.057 2877 Dihedral : 4.749 50.616 2171 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 1980 helix: 0.68 (0.15), residues: 1150 sheet: -1.04 (0.69), residues: 57 loop : -1.42 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 251 TYR 0.024 0.001 TYR A 298 PHE 0.030 0.001 PHE A 188 TRP 0.028 0.001 TRP I 209 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00228 (16681) covalent geometry : angle 0.56181 (22514) hydrogen bonds : bond 0.04567 ( 785) hydrogen bonds : angle 4.56392 ( 2343) metal coordination : bond 0.00468 ( 23) metal coordination : angle 1.90064 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.5498 (tpt) cc_final: 0.5031 (mmm) REVERT: A 582 MET cc_start: 0.7133 (mtt) cc_final: 0.6463 (mtt) REVERT: D 60 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7451 (mm-30) REVERT: G 1 MET cc_start: 0.1515 (ppp) cc_final: 0.1223 (ppp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1211 time to fit residues: 33.7934 Evaluate side-chains 140 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 332 GLN A 488 ASN A 508 GLN D 124 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.132949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.114593 restraints weight = 89458.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.110187 restraints weight = 100398.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.108244 restraints weight = 100454.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.108110 restraints weight = 88561.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.107773 restraints weight = 66196.478| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 16704 Z= 0.278 Angle : 0.763 15.352 22520 Z= 0.404 Chirality : 0.046 0.229 2492 Planarity : 0.005 0.062 2877 Dihedral : 5.204 50.246 2171 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.18), residues: 1980 helix: 0.35 (0.15), residues: 1156 sheet: -1.49 (0.71), residues: 47 loop : -1.59 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 43 TYR 0.067 0.003 TYR D 105 PHE 0.036 0.003 PHE D 469 TRP 0.019 0.003 TRP I 209 HIS 0.012 0.002 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00638 (16681) covalent geometry : angle 0.76127 (22514) hydrogen bonds : bond 0.06234 ( 785) hydrogen bonds : angle 5.01896 ( 2343) metal coordination : bond 0.01140 ( 23) metal coordination : angle 2.77296 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.7591 (ptp) cc_final: 0.7301 (ptp) REVERT: A 335 MET cc_start: 0.5628 (tpt) cc_final: 0.5050 (mmm) REVERT: A 508 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.6095 (mp10) REVERT: A 582 MET cc_start: 0.7253 (mtt) cc_final: 0.6532 (mtt) REVERT: D 60 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 547 HIS cc_start: 0.7612 (t70) cc_final: 0.7387 (t70) REVERT: G 1 MET cc_start: 0.1458 (ppp) cc_final: 0.1096 (ppp) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.1096 time to fit residues: 27.3898 Evaluate side-chains 128 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 71 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 162 optimal weight: 0.0270 chunk 67 optimal weight: 0.0980 chunk 161 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 508 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.126850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106299 restraints weight = 86625.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.103164 restraints weight = 123456.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101416 restraints weight = 84225.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.101555 restraints weight = 75117.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100907 restraints weight = 63279.857| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16704 Z= 0.124 Angle : 0.596 9.406 22520 Z= 0.310 Chirality : 0.041 0.254 2492 Planarity : 0.004 0.059 2877 Dihedral : 4.851 43.205 2171 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 1980 helix: 0.65 (0.15), residues: 1154 sheet: -1.08 (0.65), residues: 57 loop : -1.55 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.024 0.001 TYR D 105 PHE 0.037 0.002 PHE I 447 TRP 0.015 0.001 TRP I 209 HIS 0.006 0.001 HIS D 279 Details of bonding type rmsd covalent geometry : bond 0.00253 (16681) covalent geometry : angle 0.59530 (22514) hydrogen bonds : bond 0.04767 ( 785) hydrogen bonds : angle 4.46607 ( 2343) metal coordination : bond 0.00553 ( 23) metal coordination : angle 2.19615 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.7763 (ptp) cc_final: 0.7428 (ptp) REVERT: A 335 MET cc_start: 0.5626 (tpt) cc_final: 0.5028 (mmm) REVERT: A 582 MET cc_start: 0.7283 (mtt) cc_final: 0.6578 (mtt) REVERT: D 60 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7370 (mm-30) REVERT: D 547 HIS cc_start: 0.7665 (t70) cc_final: 0.7379 (t70) REVERT: G 1 MET cc_start: 0.1704 (ppp) cc_final: 0.1379 (ppp) REVERT: I 326 MET cc_start: 0.6064 (ptp) cc_final: 0.5263 (tpp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0995 time to fit residues: 28.1472 Evaluate side-chains 135 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.108150 restraints weight = 108901.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.103744 restraints weight = 106155.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.101559 restraints weight = 86853.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.101482 restraints weight = 82413.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.100791 restraints weight = 66612.945| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16704 Z= 0.129 Angle : 0.584 8.908 22520 Z= 0.305 Chirality : 0.041 0.201 2492 Planarity : 0.004 0.060 2877 Dihedral : 4.729 38.703 2171 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 1980 helix: 0.74 (0.15), residues: 1160 sheet: -1.23 (0.80), residues: 42 loop : -1.49 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 29 TYR 0.030 0.001 TYR D 105 PHE 0.030 0.001 PHE A 188 TRP 0.013 0.001 TRP I 209 HIS 0.014 0.001 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00277 (16681) covalent geometry : angle 0.58287 (22514) hydrogen bonds : bond 0.04503 ( 785) hydrogen bonds : angle 4.35691 ( 2343) metal coordination : bond 0.00490 ( 23) metal coordination : angle 1.87491 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.7673 (ptp) cc_final: 0.7396 (ptp) REVERT: A 335 MET cc_start: 0.5627 (tpt) cc_final: 0.5053 (mmm) REVERT: A 582 MET cc_start: 0.7241 (mtt) cc_final: 0.6544 (mtt) REVERT: D 1 MET cc_start: 0.7366 (mpp) cc_final: 0.7100 (mpt) REVERT: D 60 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7247 (mm-30) REVERT: D 438 MET cc_start: 0.9100 (mmp) cc_final: 0.8892 (mmp) REVERT: D 547 HIS cc_start: 0.7622 (t70) cc_final: 0.7352 (t70) REVERT: G 1 MET cc_start: 0.1745 (ppp) cc_final: 0.1407 (ppp) REVERT: I 326 MET cc_start: 0.5905 (ptp) cc_final: 0.5150 (tpp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1033 time to fit residues: 27.5727 Evaluate side-chains 130 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 161 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 175 optimal weight: 0.0010 chunk 130 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 189 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.139211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116728 restraints weight = 84939.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.115303 restraints weight = 131492.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.113670 restraints weight = 99711.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.113794 restraints weight = 93087.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.113915 restraints weight = 69074.880| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16704 Z= 0.113 Angle : 0.574 9.045 22520 Z= 0.296 Chirality : 0.040 0.176 2492 Planarity : 0.004 0.063 2877 Dihedral : 4.607 28.818 2171 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 1980 helix: 0.89 (0.15), residues: 1151 sheet: -0.86 (0.68), residues: 57 loop : -1.52 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 29 TYR 0.033 0.001 TYR A 219 PHE 0.028 0.001 PHE A 188 TRP 0.012 0.001 TRP D 517 HIS 0.006 0.001 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00232 (16681) covalent geometry : angle 0.57360 (22514) hydrogen bonds : bond 0.04131 ( 785) hydrogen bonds : angle 4.20810 ( 2343) metal coordination : bond 0.00373 ( 23) metal coordination : angle 1.78954 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7832 (ptm) cc_final: 0.7518 (ptm) REVERT: A 311 MET cc_start: 0.7679 (ptp) cc_final: 0.7410 (ptp) REVERT: A 335 MET cc_start: 0.5526 (tpt) cc_final: 0.5016 (mmm) REVERT: A 372 LEU cc_start: 0.8455 (mm) cc_final: 0.8200 (mm) REVERT: A 582 MET cc_start: 0.7225 (mtt) cc_final: 0.6540 (mtt) REVERT: D 1 MET cc_start: 0.7275 (mpp) cc_final: 0.7004 (mpt) REVERT: D 60 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7155 (mm-30) REVERT: D 476 MET cc_start: 0.6853 (mmm) cc_final: 0.6619 (mmm) REVERT: G 1 MET cc_start: 0.1804 (ppp) cc_final: 0.1459 (ppp) REVERT: G 88 LEU cc_start: 0.5873 (pp) cc_final: 0.4953 (mp) REVERT: I 326 MET cc_start: 0.5761 (ptp) cc_final: 0.5037 (tpp) REVERT: I 422 MET cc_start: 0.8322 (ppp) cc_final: 0.8039 (ppp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1157 time to fit residues: 31.6039 Evaluate side-chains 132 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 158 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.126572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.107501 restraints weight = 92879.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104927 restraints weight = 121030.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.103338 restraints weight = 100772.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.103090 restraints weight = 116023.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102459 restraints weight = 91142.426| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16704 Z= 0.251 Angle : 0.732 13.662 22520 Z= 0.385 Chirality : 0.046 0.254 2492 Planarity : 0.005 0.066 2877 Dihedral : 4.958 27.449 2171 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 1980 helix: 0.61 (0.15), residues: 1155 sheet: -1.10 (0.82), residues: 37 loop : -1.58 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 210 TYR 0.061 0.002 TYR D 105 PHE 0.035 0.002 PHE I 447 TRP 0.026 0.003 TRP I 209 HIS 0.009 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00575 (16681) covalent geometry : angle 0.73095 (22514) hydrogen bonds : bond 0.05676 ( 785) hydrogen bonds : angle 4.69892 ( 2343) metal coordination : bond 0.00926 ( 23) metal coordination : angle 2.48095 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7723 (ptm) cc_final: 0.7404 (ptm) REVERT: A 335 MET cc_start: 0.5402 (tpt) cc_final: 0.4960 (mmm) REVERT: A 582 MET cc_start: 0.7359 (mtt) cc_final: 0.6624 (mtt) REVERT: D 60 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 137 MET cc_start: 0.7757 (ptm) cc_final: 0.6926 (ptm) REVERT: D 335 MET cc_start: 0.8427 (mmt) cc_final: 0.7860 (mpp) REVERT: G 1 MET cc_start: 0.2120 (ppp) cc_final: 0.1645 (ppp) REVERT: G 88 LEU cc_start: 0.6019 (pp) cc_final: 0.5105 (mp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1155 time to fit residues: 29.0376 Evaluate side-chains 124 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 173 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 128 optimal weight: 0.1980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.119397 restraints weight = 120063.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.118590 restraints weight = 151313.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.116278 restraints weight = 104292.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.116181 restraints weight = 97153.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.116133 restraints weight = 72719.380| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16704 Z= 0.119 Angle : 0.599 7.569 22520 Z= 0.309 Chirality : 0.041 0.182 2492 Planarity : 0.004 0.066 2877 Dihedral : 4.667 27.749 2171 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1980 helix: 0.77 (0.15), residues: 1164 sheet: -1.25 (0.74), residues: 47 loop : -1.49 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 29 TYR 0.023 0.001 TYR A 219 PHE 0.038 0.001 PHE I 193 TRP 0.032 0.002 TRP I 209 HIS 0.009 0.001 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00246 (16681) covalent geometry : angle 0.59786 (22514) hydrogen bonds : bond 0.04334 ( 785) hydrogen bonds : angle 4.24314 ( 2343) metal coordination : bond 0.00391 ( 23) metal coordination : angle 2.02417 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7819 (ptm) cc_final: 0.7505 (ptm) REVERT: A 335 MET cc_start: 0.5552 (tpt) cc_final: 0.5073 (mmm) REVERT: A 372 LEU cc_start: 0.8400 (mm) cc_final: 0.7998 (pp) REVERT: A 582 MET cc_start: 0.7355 (mtt) cc_final: 0.6716 (mtt) REVERT: D 60 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7370 (mm-30) REVERT: D 194 TYR cc_start: 0.6869 (m-80) cc_final: 0.6375 (m-10) REVERT: D 335 MET cc_start: 0.8483 (mmt) cc_final: 0.7880 (mpp) REVERT: G 1 MET cc_start: 0.1931 (ppp) cc_final: 0.1553 (ppp) REVERT: G 88 LEU cc_start: 0.5749 (pp) cc_final: 0.4966 (mp) REVERT: I 326 MET cc_start: 0.5764 (ptp) cc_final: 0.5000 (tpp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1175 time to fit residues: 31.7222 Evaluate side-chains 133 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN D 82 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN H 48 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.134433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.114730 restraints weight = 137664.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.113686 restraints weight = 153507.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.112056 restraints weight = 87989.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.111919 restraints weight = 106091.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.111461 restraints weight = 82939.897| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16704 Z= 0.179 Angle : 0.656 9.937 22520 Z= 0.342 Chirality : 0.043 0.236 2492 Planarity : 0.004 0.066 2877 Dihedral : 4.750 26.802 2171 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1980 helix: 0.73 (0.15), residues: 1163 sheet: -1.49 (0.74), residues: 47 loop : -1.52 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 29 TYR 0.046 0.002 TYR D 105 PHE 0.031 0.002 PHE I 447 TRP 0.033 0.002 TRP I 209 HIS 0.005 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00406 (16681) covalent geometry : angle 0.65471 (22514) hydrogen bonds : bond 0.04941 ( 785) hydrogen bonds : angle 4.44585 ( 2343) metal coordination : bond 0.00669 ( 23) metal coordination : angle 2.13890 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.81 seconds wall clock time: 48 minutes 44.87 seconds (2924.87 seconds total)