Starting phenix.real_space_refine on Sun Sep 13 12:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvw_12615/09_2026/7nvw_12615.map" } resolution = 4.3 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= -0.005 sd= 0.935 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 42 5.49 5 S 146 5.16 5 C 14958 2.51 5 N 4090 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23647 Number of models: 1 Model: "" Number of chains: 17 Chain: "0" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5751 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 32, 'TRANS': 681} Chain breaks: 1 Chain: "1" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2167 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 5 Chain: "2" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3158 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 369} Chain breaks: 4 Chain: "3" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "4" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "6" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 2 Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "N" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 440 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1541 SG CYS 0 190 75.340 144.411 46.359 1.00 69.78 S ATOM 943 SG CYS 0 116 73.226 140.912 51.549 1.00 63.31 S ATOM 1083 SG CYS 0 134 69.263 142.212 46.760 1.00 62.63 S ATOM 1252 SG CYS 0 155 71.742 147.057 50.379 1.00 65.39 S ATOM 11119 SG CYS 3 6 21.528 128.473 50.992 1.00 78.91 S ATOM 11143 SG CYS 3 9 19.239 125.716 52.096 1.00 83.27 S ATOM 11315 SG CYS 3 31 21.257 125.412 48.868 1.00 78.66 S ATOM 11336 SG CYS 3 34 18.016 128.180 49.221 1.00 76.83 S ATOM 11280 SG CYS 3 26 21.468 138.116 43.515 1.00 67.16 S ATOM 11423 SG CYS 3 46 18.915 136.141 45.901 1.00 76.84 S ATOM 11445 SG CYS 3 49 20.544 139.337 46.828 1.00 73.51 S ATOM 14188 SG CYS 4 268 125.424 109.723 78.770 1.00 27.11 S ATOM 14207 SG CYS 4 271 128.436 109.399 76.466 1.00 26.62 S ATOM 14292 SG CYS 4 282 128.051 112.519 79.248 1.00 49.53 S ATOM 14312 SG CYS 4 285 125.795 112.326 75.828 1.00 42.84 S ATOM 14080 SG CYS 4 255 136.863 107.356 87.615 1.00 36.25 S ATOM 14097 SG CYS 4 257 136.672 110.832 85.593 1.00 44.83 S ATOM 14246 SG CYS 4 276 135.853 110.519 89.756 1.00 44.04 S ATOM 17300 SG CYS 6 345 131.198 81.512 56.444 1.00 29.82 S ATOM 17322 SG CYS 6 348 130.130 78.460 58.511 1.00 18.10 S ATOM 17479 SG CYS 6 368 127.545 80.464 56.746 1.00 32.98 S ATOM 17500 SG CYS 6 371 129.267 81.894 59.716 1.00 27.07 S ATOM 17420 SG CYS 6 360 132.513 93.203 58.511 1.00 43.10 S ATOM 17438 SG CYS 6 363 135.874 91.607 58.318 1.00 45.55 S ATOM 17587 SG CYS 6 382 133.129 90.690 61.023 1.00 25.70 S ATOM 17604 SG CYS 6 385 135.466 94.540 61.162 1.00 35.79 S ATOM 16864 SG CYS 6 291 122.118 100.777 98.628 1.00 34.40 S ATOM 16886 SG CYS 6 294 118.519 101.048 99.911 1.00 36.86 S ATOM 16975 SG CYS 6 305 119.179 101.531 96.306 1.00 34.09 S ATOM 16998 SG CYS 6 308 119.903 104.032 99.110 1.00 38.36 S Time building chain proxies: 4.54, per 1000 atoms: 0.19 Number of scatterers: 23647 At special positions: 0 Unit cell: (173.25, 170.1, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 146 16.00 P 42 15.00 O 4400 8.00 N 4090 7.00 C 14958 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01000 " pdb="FE4 SF4 01000 " - pdb=" SG CYS 0 155 " pdb="FE1 SF4 01000 " - pdb=" SG CYS 0 190 " pdb="FE3 SF4 01000 " - pdb=" SG CYS 0 134 " pdb="FE2 SF4 01000 " - pdb=" SG CYS 0 116 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 400 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 6 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 31 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 34 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" NE2 HIS 3 28 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 49 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 46 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 26 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 268 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 271 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 285 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 282 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" NE2 HIS 4 258 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 276 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 255 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 257 " pdb=" ZN 6 401 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 368 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 371 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 348 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 345 " pdb=" ZN 6 402 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 360 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 382 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 385 " pdb=" ZN 6 403 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 294 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 308 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 305 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 291 " Number of angles added : 36 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5422 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 24 sheets defined 55.2% alpha, 8.2% beta 21 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 removed outlier: 3.560A pdb=" N PHE 0 22 " --> pdb=" O TYR 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 Processing helix chain '0' and resid 76 through 99 removed outlier: 3.801A pdb=" N LYS 0 82 " --> pdb=" O PRO 0 78 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL 0 83 " --> pdb=" O GLU 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 126 through 139 Processing helix chain '0' and resid 139 through 149 removed outlier: 3.589A pdb=" N HIS 0 148 " --> pdb=" O ALA 0 144 " (cutoff:3.500A) Processing helix chain '0' and resid 155 through 165 removed outlier: 3.755A pdb=" N GLU 0 159 " --> pdb=" O CYS 0 155 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 188 removed outlier: 3.668A pdb=" N ALA 0 182 " --> pdb=" O ASP 0 178 " (cutoff:3.500A) Processing helix chain '0' and resid 190 through 199 removed outlier: 3.644A pdb=" N ALA 0 195 " --> pdb=" O PRO 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 208 through 212 Processing helix chain '0' and resid 214 through 222 removed outlier: 3.782A pdb=" N ASP 0 219 " --> pdb=" O PRO 0 215 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU 0 220 " --> pdb=" O LYS 0 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL 0 221 " --> pdb=" O ILE 0 217 " (cutoff:3.500A) Processing helix chain '0' and resid 223 through 227 Processing helix chain '0' and resid 238 through 246 removed outlier: 3.535A pdb=" N VAL 0 242 " --> pdb=" O ASN 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 277 Processing helix chain '0' and resid 278 through 291 removed outlier: 4.732A pdb=" N GLU 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR 0 285 " --> pdb=" O LEU 0 281 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG 0 286 " --> pdb=" O ARG 0 282 " (cutoff:3.500A) Processing helix chain '0' and resid 325 through 346 Processing helix chain '0' and resid 353 through 366 removed outlier: 4.377A pdb=" N LEU 0 358 " --> pdb=" O PRO 0 354 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 374 removed outlier: 3.830A pdb=" N PHE 0 374 " --> pdb=" O LYS 0 370 " (cutoff:3.500A) Processing helix chain '0' and resid 374 through 386 removed outlier: 3.569A pdb=" N LEU 0 386 " --> pdb=" O LEU 0 382 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 410 removed outlier: 3.716A pdb=" N SER 0 408 " --> pdb=" O ALA 0 404 " (cutoff:3.500A) Processing helix chain '0' and resid 440 through 451 Proline residue: 0 446 - end of helix Processing helix chain '0' and resid 465 through 471 removed outlier: 4.037A pdb=" N LYS 0 469 " --> pdb=" O ASP 0 465 " (cutoff:3.500A) Processing helix chain '0' and resid 513 through 531 Processing helix chain '0' and resid 541 through 555 Processing helix chain '0' and resid 556 through 565 Processing helix chain '0' and resid 573 through 590 removed outlier: 3.636A pdb=" N GLU 0 586 " --> pdb=" O GLU 0 582 " (cutoff:3.500A) Processing helix chain '0' and resid 602 through 608 removed outlier: 3.534A pdb=" N GLU 0 606 " --> pdb=" O GLY 0 602 " (cutoff:3.500A) Processing helix chain '0' and resid 630 through 643 removed outlier: 3.910A pdb=" N LYS 0 634 " --> pdb=" O SER 0 630 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA 0 635 " --> pdb=" O ARG 0 631 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 0 640 " --> pdb=" O ARG 0 636 " (cutoff:3.500A) Processing helix chain '0' and resid 647 through 663 removed outlier: 3.694A pdb=" N HIS 0 659 " --> pdb=" O ASP 0 655 " (cutoff:3.500A) Processing helix chain '0' and resid 681 through 685 Processing helix chain '0' and resid 686 through 693 Processing helix chain '0' and resid 694 through 701 removed outlier: 3.686A pdb=" N HIS 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 710 through 726 removed outlier: 3.552A pdb=" N GLN 0 726 " --> pdb=" O ARG 0 722 " (cutoff:3.500A) Processing helix chain '1' and resid 108 through 120 removed outlier: 4.405A pdb=" N GLN 1 119 " --> pdb=" O ASN 1 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU 1 120 " --> pdb=" O ARG 1 116 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 134 removed outlier: 3.627A pdb=" N PHE 1 125 " --> pdb=" O ASP 1 121 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL 1 132 " --> pdb=" O TYR 1 128 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER 1 134 " --> pdb=" O ASP 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 146 removed outlier: 4.073A pdb=" N TRP 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 1 146 " --> pdb=" O PHE 1 142 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 200 Processing helix chain '1' and resid 200 through 210 Processing helix chain '1' and resid 216 through 226 removed outlier: 3.604A pdb=" N PHE 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE 1 225 " --> pdb=" O TRP 1 221 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 1 226 " --> pdb=" O THR 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 318 removed outlier: 3.507A pdb=" N ALA 1 302 " --> pdb=" O ASN 1 298 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 1 303 " --> pdb=" O SER 1 299 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE 1 304 " --> pdb=" O ASN 1 300 " (cutoff:3.500A) Processing helix chain '1' and resid 379 through 384 removed outlier: 3.953A pdb=" N TYR 1 383 " --> pdb=" O SER 1 379 " (cutoff:3.500A) Processing helix chain '1' and resid 397 through 409 removed outlier: 3.633A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 410 through 413 removed outlier: 4.440A pdb=" N ALA 1 413 " --> pdb=" O GLU 1 410 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 410 through 413' Processing helix chain '1' and resid 423 through 435 Processing helix chain '1' and resid 455 through 478 removed outlier: 3.877A pdb=" N SER 1 459 " --> pdb=" O ASN 1 455 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU 1 460 " --> pdb=" O ASP 1 456 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS 1 474 " --> pdb=" O GLU 1 470 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N CYS 1 478 " --> pdb=" O HIS 1 474 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 515 removed outlier: 4.148A pdb=" N VAL 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS 1 492 " --> pdb=" O GLU 1 488 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 1 500 " --> pdb=" O ASN 1 496 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 1 505 " --> pdb=" O GLN 1 501 " (cutoff:3.500A) Proline residue: 1 507 - end of helix Processing helix chain '1' and resid 523 through 547 removed outlier: 3.574A pdb=" N GLU 1 527 " --> pdb=" O SER 1 523 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET 1 528 " --> pdb=" O HIS 1 524 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 1 529 " --> pdb=" O ILE 1 525 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 25 Processing helix chain '2' and resid 27 through 35 removed outlier: 3.677A pdb=" N ARG 2 33 " --> pdb=" O GLY 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 39 through 48 removed outlier: 3.909A pdb=" N PHE 2 45 " --> pdb=" O CYS 2 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 2 48 " --> pdb=" O VAL 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 51 through 59 Processing helix chain '2' and resid 67 through 73 removed outlier: 4.134A pdb=" N VAL 2 71 " --> pdb=" O PRO 2 67 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 94 removed outlier: 4.023A pdb=" N GLN 2 83 " --> pdb=" O PHE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 122 Processing helix chain '2' and resid 146 through 164 removed outlier: 3.561A pdb=" N LYS 2 150 " --> pdb=" O PRO 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 182 Processing helix chain '2' and resid 197 through 206 removed outlier: 3.587A pdb=" N PHE 2 201 " --> pdb=" O THR 2 197 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 2 206 " --> pdb=" O GLN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 227 removed outlier: 3.664A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 229 through 241 removed outlier: 3.699A pdb=" N ILE 2 233 " --> pdb=" O ASP 2 229 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE 2 236 " --> pdb=" O GLU 2 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU 2 237 " --> pdb=" O ILE 2 233 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE 2 238 " --> pdb=" O LEU 2 234 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 2 241 " --> pdb=" O LEU 2 237 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 269 Processing helix chain '2' and resid 284 through 289 removed outlier: 3.747A pdb=" N ILE 2 288 " --> pdb=" O THR 2 284 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN 2 289 " --> pdb=" O ARG 2 285 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 284 through 289' Processing helix chain '2' and resid 321 through 330 removed outlier: 3.687A pdb=" N ILE 2 325 " --> pdb=" O SER 2 321 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 358 Processing helix chain '2' and resid 360 through 371 removed outlier: 3.844A pdb=" N ILE 2 364 " --> pdb=" O THR 2 360 " (cutoff:3.500A) Processing helix chain '2' and resid 373 through 378 removed outlier: 3.844A pdb=" N LYS 2 378 " --> pdb=" O VAL 2 375 " (cutoff:3.500A) Processing helix chain '2' and resid 384 through 399 removed outlier: 3.616A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP 2 399 " --> pdb=" O GLU 2 395 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 429 removed outlier: 3.502A pdb=" N PHE 2 418 " --> pdb=" O SER 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 444 through 458 removed outlier: 3.815A pdb=" N SER 2 449 " --> pdb=" O PRO 2 445 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP 2 450 " --> pdb=" O ALA 2 446 " (cutoff:3.500A) Processing helix chain '3' and resid 11 through 16 Processing helix chain '3' and resid 31 through 41 removed outlier: 3.949A pdb=" N LEU 3 37 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG 3 41 " --> pdb=" O LEU 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 80 removed outlier: 3.764A pdb=" N LYS 3 80 " --> pdb=" O LYS 3 76 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 89 Processing helix chain '3' and resid 93 through 111 removed outlier: 4.004A pdb=" N PHE 3 98 " --> pdb=" O GLU 3 94 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU 3 99 " --> pdb=" O TYR 3 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN 3 111 " --> pdb=" O PHE 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 129 removed outlier: 3.744A pdb=" N LYS 3 127 " --> pdb=" O GLU 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 149 removed outlier: 4.120A pdb=" N THR 3 141 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG 3 142 " --> pdb=" O LEU 3 138 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 3 149 " --> pdb=" O GLU 3 145 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 29 Processing helix chain '4' and resid 33 through 52 removed outlier: 4.088A pdb=" N ASN 4 52 " --> pdb=" O HIS 4 48 " (cutoff:3.500A) Processing helix chain '4' and resid 101 through 121 Processing helix chain '4' and resid 133 through 151 Processing helix chain '4' and resid 170 through 172 No H-bonds generated for 'chain '4' and resid 170 through 172' Processing helix chain '4' and resid 173 through 188 Processing helix chain '4' and resid 200 through 211 removed outlier: 3.608A pdb=" N ILE 4 209 " --> pdb=" O GLN 4 205 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR 4 210 " --> pdb=" O ALA 4 206 " (cutoff:3.500A) Processing helix chain '4' and resid 219 through 221 No H-bonds generated for 'chain '4' and resid 219 through 221' Processing helix chain '4' and resid 222 through 230 removed outlier: 4.035A pdb=" N TYR 4 226 " --> pdb=" O SER 4 222 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU 4 227 " --> pdb=" O LEU 4 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP 4 229 " --> pdb=" O GLN 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 234 through 239 removed outlier: 4.202A pdb=" N SER 4 239 " --> pdb=" O GLN 4 235 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 49 through 64 Processing helix chain '6' and resid 9 through 14 removed outlier: 3.731A pdb=" N GLY 6 13 " --> pdb=" O LYS 6 9 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY 6 14 " --> pdb=" O ARG 6 10 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 9 through 14' Processing helix chain '6' and resid 17 through 21 removed outlier: 3.695A pdb=" N ILE 6 21 " --> pdb=" O THR 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 68 through 73 Processing helix chain '6' and resid 79 through 98 removed outlier: 3.649A pdb=" N TYR 6 90 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 135 removed outlier: 3.538A pdb=" N HIS 6 127 " --> pdb=" O ASN 6 123 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 158 removed outlier: 4.187A pdb=" N HIS 6 158 " --> pdb=" O GLN 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 193 removed outlier: 3.985A pdb=" N LEU 6 185 " --> pdb=" O ASN 6 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 6 187 " --> pdb=" O TYR 6 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR 6 188 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 205 through 216 Processing helix chain '6' and resid 224 through 237 removed outlier: 3.624A pdb=" N GLU 6 230 " --> pdb=" O SER 6 226 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER 6 237 " --> pdb=" O THR 6 233 " (cutoff:3.500A) Processing helix chain '6' and resid 314 through 320 removed outlier: 3.624A pdb=" N LEU 6 318 " --> pdb=" O SER 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 321 through 326 removed outlier: 4.167A pdb=" N LEU 6 325 " --> pdb=" O SER 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 378 Processing helix chain '6' and resid 382 through 387 removed outlier: 4.123A pdb=" N HIS 6 387 " --> pdb=" O PRO 6 383 " (cutoff:3.500A) Processing helix chain '7' and resid 92 through 104 Processing helix chain '7' and resid 119 through 129 Processing helix chain '7' and resid 132 through 144 removed outlier: 4.395A pdb=" N TYR 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 162 Processing helix chain '7' and resid 181 through 189 removed outlier: 4.555A pdb=" N ILE 7 185 " --> pdb=" O HIS 7 181 " (cutoff:3.500A) Processing helix chain '7' and resid 192 through 198 Processing helix chain '7' and resid 276 through 287 removed outlier: 3.609A pdb=" N HIS 7 286 " --> pdb=" O LYS 7 282 " (cutoff:3.500A) Processing helix chain '7' and resid 317 through 328 Processing helix chain '7' and resid 341 through 344 Processing helix chain '7' and resid 345 through 358 Processing helix chain '7' and resid 367 through 382 Processing helix chain '7' and resid 385 through 387 No H-bonds generated for 'chain '7' and resid 385 through 387' Processing helix chain '7' and resid 410 through 414 Processing helix chain '7' and resid 420 through 433 Processing helix chain '7' and resid 443 through 446 Processing helix chain '7' and resid 448 through 458 removed outlier: 3.726A pdb=" N VAL 7 454 " --> pdb=" O MET 7 450 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU 7 455 " --> pdb=" O PHE 7 451 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR 7 456 " --> pdb=" O ARG 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 478 through 484 removed outlier: 4.219A pdb=" N PHE 7 482 " --> pdb=" O VAL 7 478 " (cutoff:3.500A) Processing helix chain '7' and resid 492 through 499 Processing helix chain '7' and resid 515 through 525 Processing helix chain '7' and resid 529 through 535 removed outlier: 3.616A pdb=" N THR 7 535 " --> pdb=" O ILE 7 531 " (cutoff:3.500A) Processing helix chain '7' and resid 537 through 553 Processing helix chain '7' and resid 564 through 576 Processing helix chain '7' and resid 585 through 599 Processing helix chain '7' and resid 609 through 614 removed outlier: 3.586A pdb=" N THR 7 613 " --> pdb=" O LYS 7 609 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER 7 614 " --> pdb=" O VAL 7 610 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 609 through 614' Processing helix chain '7' and resid 632 through 641 Processing helix chain '7' and resid 667 through 677 removed outlier: 4.147A pdb=" N ALA 7 671 " --> pdb=" O THR 7 667 " (cutoff:3.500A) Processing helix chain '7' and resid 677 through 684 Processing helix chain '7' and resid 705 through 720 removed outlier: 3.606A pdb=" N GLN 7 709 " --> pdb=" O THR 7 705 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR 7 720 " --> pdb=" O VAL 7 716 " (cutoff:3.500A) Processing helix chain 'W' and resid 278 through 283 Processing helix chain 'Z' and resid 7 through 11 removed outlier: 4.145A pdb=" N UNK Z 11 " --> pdb=" O UNK Z 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain '0' and resid 38 through 41 removed outlier: 3.527A pdb=" N LEU 0 40 " --> pdb=" O ILE 0 456 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL 0 231 " --> pdb=" O ILE 0 455 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR 0 457 " --> pdb=" O VAL 0 231 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE 0 233 " --> pdb=" O THR 0 457 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE 0 71 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP 0 234 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS 0 73 " --> pdb=" O ASP 0 234 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU 0 70 " --> pdb=" O VAL 0 205 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA 0 108 " --> pdb=" O TYR 0 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 252 removed outlier: 3.578A pdb=" N GLN 0 351 " --> pdb=" O ILE 0 418 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 566 through 569 removed outlier: 6.324A pdb=" N VAL 0 536 " --> pdb=" O ILE 0 619 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE 0 621 " --> pdb=" O VAL 0 536 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE 0 538 " --> pdb=" O PHE 0 621 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL 0 618 " --> pdb=" O VAL 0 678 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA 0 680 " --> pdb=" O VAL 0 618 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET 0 620 " --> pdb=" O ALA 0 680 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE 0 494 " --> pdb=" O LEU 0 708 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 185 through 186 removed outlier: 3.878A pdb=" N LYS 2 186 " --> pdb=" O CYS 2 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 271 through 272 removed outlier: 3.738A pdb=" N PHE 2 272 " --> pdb=" O TYR 2 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR 2 282 " --> pdb=" O PHE 2 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 307 through 309 removed outlier: 6.477A pdb=" N MET 2 341 " --> pdb=" O ARG 2 337 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG 2 337 " --> pdb=" O MET 2 341 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL 2 343 " --> pdb=" O LEU 2 335 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS 7 59 " --> pdb=" O GLU 2 333 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU 2 335 " --> pdb=" O LYS 7 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 402 through 405 removed outlier: 6.907A pdb=" N PHE 5 44 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP 5 37 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 431 through 435 removed outlier: 3.727A pdb=" N PHE 2 433 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET 2 441 " --> pdb=" O TYR 2 409 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR 2 409 " --> pdb=" O MET 2 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 21 through 23 removed outlier: 3.650A pdb=" N ARG 3 59 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 69 through 71 removed outlier: 5.849A pdb=" N VAL 4 59 " --> pdb=" O LEU 4 70 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE 4 60 " --> pdb=" O LEU 4 11 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 4 13 " --> pdb=" O ILE 4 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 264 through 267 removed outlier: 3.517A pdb=" N VAL 4 267 " --> pdb=" O ILE 6 250 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR 6 311 " --> pdb=" O ARG 6 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 113 through 121 removed outlier: 6.635A pdb=" N ILE 6 106 " --> pdb=" O LEU 6 117 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU 6 119 " --> pdb=" O ILE 6 104 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE 6 104 " --> pdb=" O GLU 6 119 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN 6 103 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE 6 107 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS 6 60 " --> pdb=" O GLU 6 166 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU 6 168 " --> pdb=" O HIS 6 60 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR 6 62 " --> pdb=" O LEU 6 168 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE 6 170 " --> pdb=" O TYR 6 62 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL 6 64 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 199 through 200 Processing sheet with id=AB6, first strand: chain '6' and resid 332 through 333 removed outlier: 3.754A pdb=" N GLN 6 332 " --> pdb=" O VAL 6 359 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL 6 359 " --> pdb=" O GLN 6 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '7' and resid 83 through 87 removed outlier: 6.144A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 271 through 272 removed outlier: 4.301A pdb=" N TYR 7 175 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 268 through 269 Processing sheet with id=AC1, first strand: chain '7' and resid 440 through 441 removed outlier: 6.080A pdb=" N LEU 7 440 " --> pdb=" O LEU 7 466 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR 7 467 " --> pdb=" O ILE 7 338 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL 7 337 " --> pdb=" O LYS 7 487 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR 7 489 " --> pdb=" O VAL 7 337 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 362 through 365 removed outlier: 6.536A pdb=" N CYS 7 390 " --> pdb=" O ILE 7 407 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR 7 409 " --> pdb=" O CYS 7 390 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 435 through 437 removed outlier: 8.692A pdb=" N TRP 7 435 " --> pdb=" O HIS 7 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '7' and resid 624 through 625 removed outlier: 3.898A pdb=" N PHE 7 659 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL 7 510 " --> pdb=" O SER 7 661 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 624 through 625 removed outlier: 3.898A pdb=" N PHE 7 659 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL 7 510 " --> pdb=" O SER 7 661 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 558 through 561 removed outlier: 6.817A pdb=" N ILE 7 558 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE 7 607 " --> pdb=" O ILE 7 558 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL 7 560 " --> pdb=" O ILE 7 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1033 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10129 1.43 - 1.64: 13855 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24210 Sorted by residual: bond pdb=" C3' DT N 36 " pdb=" C2' DT N 36 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.36e+00 bond pdb=" C3' DC N 48 " pdb=" C2' DC N 48 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.04e+00 bond pdb=" C3' DT N 39 " pdb=" C2' DT N 39 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.66e+00 bond pdb=" C3' DC T -47 " pdb=" C2' DC T -47 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.18e+00 bond pdb=" C3' DT N 38 " pdb=" C2' DT N 38 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.15e+00 ... (remaining 24205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 31675 1.05 - 2.11: 966 2.11 - 3.16: 177 3.16 - 4.22: 93 4.22 - 5.27: 4 Bond angle restraints: 32915 Sorted by residual: angle pdb=" N3 DT N 45 " pdb=" C4 DT N 45 " pdb=" O4 DT N 45 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT T -44 " pdb=" C4 DT T -44 " pdb=" O4 DT T -44 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" O4' DG T -46 " pdb=" C4' DG T -46 " pdb=" C3' DG T -46 " ideal model delta sigma weight residual 106.00 103.51 2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT N 49 " pdb=" C4 DT N 49 " pdb=" O4 DT N 49 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT N 53 " pdb=" C4 DT N 53 " pdb=" O4 DT N 53 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 32910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 14169 34.97 - 69.93: 387 69.93 - 104.90: 26 104.90 - 139.86: 0 139.86 - 174.83: 1 Dihedral angle restraints: 14583 sinusoidal: 6239 harmonic: 8344 Sorted by residual: dihedral pdb=" CA GLY 3 27 " pdb=" C GLY 3 27 " pdb=" N HIS 3 28 " pdb=" CA HIS 3 28 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER 0 462 " pdb=" C SER 0 462 " pdb=" N PRO 0 463 " pdb=" CA PRO 0 463 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C4' DC N 52 " pdb=" C3' DC N 52 " pdb=" O3' DC N 52 " pdb=" P DT N 53 " ideal model delta sinusoidal sigma weight residual 220.00 45.17 174.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2759 0.033 - 0.066: 586 0.066 - 0.098: 212 0.098 - 0.131: 114 0.131 - 0.164: 40 Chirality restraints: 3711 Sorted by residual: chirality pdb=" C3' DA T -45 " pdb=" C4' DA T -45 " pdb=" O3' DA T -45 " pdb=" C2' DA T -45 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" C3' DC N 41 " pdb=" C4' DC N 41 " pdb=" O3' DC N 41 " pdb=" C2' DC N 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" C3' DC N 43 " pdb=" C4' DC N 43 " pdb=" O3' DC N 43 " pdb=" C2' DC N 43 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 3708 not shown) Planarity restraints: 4050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 0 462 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO 0 463 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO 0 463 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 0 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 211 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO 1 212 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO 1 212 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 1 212 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 7 582 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO 7 583 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO 7 583 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO 7 583 " -0.017 5.00e-02 4.00e+02 ... (remaining 4047 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 232 2.56 - 3.14: 20286 3.14 - 3.73: 37884 3.73 - 4.31: 50448 4.31 - 4.90: 83256 Nonbonded interactions: 192106 Sorted by model distance: nonbonded pdb=" OG SER 7 394 " pdb=" OP2 DG T -41 " model vdw 1.971 3.040 nonbonded pdb=" O SER 1 195 " pdb=" OG1 THR 1 199 " model vdw 2.000 3.040 nonbonded pdb=" OG1 THR 0 571 " pdb=" OD1 ASP 0 573 " model vdw 2.009 3.040 nonbonded pdb=" OG SER 4 62 " pdb=" O LEU 4 132 " model vdw 2.023 3.040 nonbonded pdb=" OG SER 0 44 " pdb=" O THR 0 46 " model vdw 2.034 3.040 ... (remaining 192101 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 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 : 0.005 0.363 24242 Z= 0.235 Angle : 0.510 14.514 32963 Z= 0.310 Chirality : 0.038 0.164 3711 Planarity : 0.002 0.059 4050 Dihedral : 15.515 174.826 9161 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.80 (0.17), residues: 2768 helix: 2.02 (0.15), residues: 1307 sheet: -1.53 (0.31), residues: 307 loop : -0.60 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 58 TYR 0.010 0.001 TYR 7 534 PHE 0.011 0.001 PHE 4 69 TRP 0.011 0.001 TRP 2 96 HIS 0.007 0.001 HIS 4 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.17 (24210) covalent geometry : angle 0.47314 / 0.31 (32915) hydrogen bonds : bond 0.25203 / 17.03 ( 1083) hydrogen bonds : angle 7.33583 / 5.27 ( 3087) metal coordination : bond 0.12554 / 7.22 ( 32) metal coordination : angle 5.03534 / 3.45 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 853 time to evaluate : 0.859 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: 0 438 MET cc_start: 0.7072 (ptp) cc_final: 0.4975 (ptp) REVERT: 0 439 ASP cc_start: 0.7386 (p0) cc_final: 0.6744 (t0) REVERT: 0 466 ILE cc_start: 0.7567 (mt) cc_final: 0.7295 (mm) REVERT: 0 545 MET cc_start: 0.8190 (ttp) cc_final: 0.7779 (ttm) REVERT: 0 719 TYR cc_start: 0.7466 (t80) cc_final: 0.7037 (t80) REVERT: 2 73 LEU cc_start: 0.8043 (pp) cc_final: 0.7495 (tt) REVERT: 2 313 TYR cc_start: 0.8229 (m-80) cc_final: 0.7859 (m-80) REVERT: 2 373 HIS cc_start: 0.7793 (t-90) cc_final: 0.7218 (t-90) REVERT: 2 408 LEU cc_start: 0.7104 (tp) cc_final: 0.6838 (tp) REVERT: 2 448 HIS cc_start: 0.7124 (t-90) cc_final: 0.6597 (t-90) REVERT: 3 74 ILE cc_start: 0.8226 (mt) cc_final: 0.8015 (mt) REVERT: 3 99 LEU cc_start: 0.8069 (mp) cc_final: 0.7722 (mp) REVERT: 4 63 HIS cc_start: 0.6521 (m90) cc_final: 0.5877 (m-70) REVERT: 4 224 LEU cc_start: 0.9009 (tp) cc_final: 0.8529 (tp) REVERT: 5 22 TYR cc_start: 0.7247 (t80) cc_final: 0.6964 (t80) REVERT: 5 44 PHE cc_start: 0.6521 (t80) cc_final: 0.6235 (t80) REVERT: 5 62 ASP cc_start: 0.7751 (m-30) cc_final: 0.7463 (m-30) REVERT: 6 79 ASN cc_start: 0.7612 (t0) cc_final: 0.7272 (t0) REVERT: 6 104 ILE cc_start: 0.8956 (tt) cc_final: 0.8657 (tt) REVERT: 6 171 PHE cc_start: 0.8301 (t80) cc_final: 0.8050 (t80) REVERT: 6 184 ASP cc_start: 0.4074 (t0) cc_final: 0.3048 (t0) REVERT: 7 86 LEU cc_start: 0.7726 (tp) cc_final: 0.7357 (tt) REVERT: 7 289 TYR cc_start: 0.4748 (m-80) cc_final: 0.4473 (m-80) REVERT: 7 473 GLU cc_start: 0.6541 (mp0) cc_final: 0.6131 (mm-30) REVERT: 7 483 LEU cc_start: 0.8670 (mt) cc_final: 0.8351 (tt) REVERT: 7 525 ILE cc_start: 0.8601 (pt) cc_final: 0.8251 (pt) REVERT: 7 662 LEU cc_start: 0.8305 (mp) cc_final: 0.8077 (mt) REVERT: W 284 SER cc_start: 0.8689 (t) cc_final: 0.8364 (p) outliers start: 0 outliers final: 0 residues processed: 853 average time/residue: 0.1727 time to fit residues: 221.5267 Evaluate side-chains 464 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 114 ASN ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 262 ASN 0 363 GLN 2 181 GLN 2 264 HIS 2 366 HIS 3 57 ASN ** 4 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 148 ASN ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 235 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 349 GLN 6 387 HIS 7 173 ASN 7 373 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.147369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129692 restraints weight = 56681.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.129192 restraints weight = 83737.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129694 restraints weight = 81068.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130431 restraints weight = 57494.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130474 restraints weight = 58254.124| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24242 Z= 0.200 Angle : 0.765 19.605 32963 Z= 0.383 Chirality : 0.045 0.261 3711 Planarity : 0.005 0.061 4050 Dihedral : 11.701 173.472 3539 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.32 % Allowed : 6.39 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.00 (0.16), residues: 2768 helix: 1.11 (0.14), residues: 1382 sheet: -1.50 (0.30), residues: 301 loop : -0.94 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG 2 226 TYR 0.025 0.002 TYR 7 121 PHE 0.031 0.002 PHE 4 50 TRP 0.013 0.002 TRP 0 696 HIS 0.010 0.002 HIS 4 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (24210) covalent geometry : angle 0.72305 / 0.38 (32915) hydrogen bonds : bond 0.06493 / 4.34 ( 1083) hydrogen bonds : angle 5.51922 / 3.91 ( 3087) metal coordination : bond 0.01674 / 0.94 ( 32) metal coordination : angle 6.61345 / 4.20 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 587 time to evaluate : 0.863 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 133 LYS cc_start: 0.8104 (mptt) cc_final: 0.7529 (tppt) REVERT: 0 264 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6834 (mt-10) REVERT: 0 345 ARG cc_start: 0.7097 (ptp-110) cc_final: 0.5881 (ttp-170) REVERT: 0 488 VAL cc_start: 0.7533 (p) cc_final: 0.7236 (p) REVERT: 0 545 MET cc_start: 0.7933 (ttp) cc_final: 0.7732 (ttm) REVERT: 0 596 LEU cc_start: 0.9230 (tp) cc_final: 0.8866 (tt) REVERT: 0 719 TYR cc_start: 0.7434 (t80) cc_final: 0.7088 (t80) REVERT: 1 308 ASN cc_start: 0.8016 (m-40) cc_final: 0.7792 (m110) REVERT: 1 411 MET cc_start: 0.6532 (pmm) cc_final: 0.6229 (pmm) REVERT: 2 73 LEU cc_start: 0.8053 (pp) cc_final: 0.7742 (tt) REVERT: 2 212 LEU cc_start: 0.8770 (tp) cc_final: 0.8548 (tp) REVERT: 2 313 TYR cc_start: 0.8339 (m-80) cc_final: 0.7765 (m-80) REVERT: 2 365 ILE cc_start: 0.8487 (pt) cc_final: 0.7951 (tp) REVERT: 2 408 LEU cc_start: 0.7374 (tp) cc_final: 0.7087 (tp) REVERT: 2 418 PHE cc_start: 0.5277 (t80) cc_final: 0.4999 (t80) REVERT: 2 443 VAL cc_start: 0.7390 (m) cc_final: 0.7126 (m) REVERT: 2 448 HIS cc_start: 0.6799 (t-90) cc_final: 0.6359 (t-170) REVERT: 3 68 VAL cc_start: 0.8010 (p) cc_final: 0.7782 (p) REVERT: 3 99 LEU cc_start: 0.8001 (mp) cc_final: 0.7609 (mp) REVERT: 5 6 LYS cc_start: 0.5020 (tppt) cc_final: 0.4780 (tppt) REVERT: 5 22 TYR cc_start: 0.7239 (t80) cc_final: 0.6741 (t80) REVERT: 5 34 ILE cc_start: 0.6899 (mt) cc_final: 0.6644 (mt) REVERT: 5 44 PHE cc_start: 0.6209 (t80) cc_final: 0.5445 (t80) REVERT: 5 51 ASN cc_start: 0.6749 (p0) cc_final: 0.6287 (t0) REVERT: 5 62 ASP cc_start: 0.7816 (m-30) cc_final: 0.7510 (m-30) REVERT: 6 66 ASP cc_start: 0.8731 (p0) cc_final: 0.8285 (p0) REVERT: 6 137 MET cc_start: 0.6488 (tpp) cc_final: 0.5745 (tpt) REVERT: 6 222 ILE cc_start: 0.8352 (mm) cc_final: 0.8105 (tp) REVERT: 7 419 ARG cc_start: 0.5604 (tpm170) cc_final: 0.5281 (mmt90) REVERT: 7 442 GLU cc_start: 0.7085 (mp0) cc_final: 0.6804 (mp0) REVERT: 7 483 LEU cc_start: 0.8632 (mt) cc_final: 0.8129 (tt) REVERT: 7 494 MET cc_start: 0.6637 (mmp) cc_final: 0.5893 (mmt) REVERT: 7 505 VAL cc_start: 0.8518 (t) cc_final: 0.8184 (t) outliers start: 8 outliers final: 0 residues processed: 593 average time/residue: 0.1539 time to fit residues: 143.0495 Evaluate side-chains 405 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 156 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 256 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 148 HIS ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 698 GLN 0 715 GLN 2 181 GLN 2 289 ASN 2 345 GLN 2 366 HIS 3 57 ASN 3 144 GLN 4 63 HIS ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 187 GLN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 545 GLN 7 594 GLN 7 598 HIS 7 709 GLN 7 711 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.147179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129988 restraints weight = 56872.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129018 restraints weight = 83017.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129491 restraints weight = 82331.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130596 restraints weight = 59071.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.130554 restraints weight = 48686.855| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24242 Z= 0.185 Angle : 0.733 20.120 32963 Z= 0.361 Chirality : 0.044 0.208 3711 Planarity : 0.005 0.098 4050 Dihedral : 11.842 173.319 3539 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.28 % Allowed : 4.75 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.32 (0.16), residues: 2768 helix: 0.83 (0.14), residues: 1385 sheet: -1.54 (0.30), residues: 290 loop : -1.13 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 2 58 TYR 0.040 0.002 TYR 7 295 PHE 0.034 0.002 PHE 2 45 TRP 0.051 0.002 TRP 4 229 HIS 0.012 0.001 HIS 4 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (24210) covalent geometry : angle 0.68702 / 0.36 (32915) hydrogen bonds : bond 0.05716 / 3.83 ( 1083) hydrogen bonds : angle 5.26802 / 3.70 ( 3087) metal coordination : bond 0.01281 / 0.66 ( 32) metal coordination : angle 6.75369 / 4.25 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 534 time to evaluate : 0.845 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 48 LYS cc_start: 0.7360 (ptmt) cc_final: 0.6795 (ptmt) REVERT: 0 264 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6919 (mt-10) REVERT: 0 345 ARG cc_start: 0.6571 (ptp-110) cc_final: 0.6088 (ttp-170) REVERT: 0 457 THR cc_start: 0.7977 (m) cc_final: 0.7740 (m) REVERT: 0 596 LEU cc_start: 0.9188 (tp) cc_final: 0.8911 (tt) REVERT: 0 659 HIS cc_start: 0.7061 (t70) cc_final: 0.6684 (t70) REVERT: 1 499 ARG cc_start: 0.5869 (mtt180) cc_final: 0.5481 (mtt180) REVERT: 2 73 LEU cc_start: 0.7984 (pp) cc_final: 0.7671 (tt) REVERT: 2 313 TYR cc_start: 0.8193 (m-80) cc_final: 0.7755 (m-80) REVERT: 2 336 TYR cc_start: 0.5997 (m-10) cc_final: 0.5714 (m-10) REVERT: 2 365 ILE cc_start: 0.8309 (pt) cc_final: 0.8086 (tp) REVERT: 2 373 HIS cc_start: 0.7999 (t-90) cc_final: 0.7715 (t-90) REVERT: 2 408 LEU cc_start: 0.7402 (tp) cc_final: 0.7168 (tp) REVERT: 2 443 VAL cc_start: 0.7386 (m) cc_final: 0.6947 (m) REVERT: 2 448 HIS cc_start: 0.6875 (t-90) cc_final: 0.6450 (t-170) REVERT: 3 21 LEU cc_start: 0.6555 (tp) cc_final: 0.5532 (tp) REVERT: 5 20 LEU cc_start: 0.8171 (mt) cc_final: 0.7786 (mt) REVERT: 5 34 ILE cc_start: 0.6940 (mt) cc_final: 0.6646 (mt) REVERT: 5 44 PHE cc_start: 0.6188 (t80) cc_final: 0.5639 (t80) REVERT: 5 51 ASN cc_start: 0.6855 (p0) cc_final: 0.6059 (t0) REVERT: 5 62 ASP cc_start: 0.7894 (m-30) cc_final: 0.7602 (m-30) REVERT: 7 412 MET cc_start: 0.7614 (tpp) cc_final: 0.6292 (tpp) REVERT: 7 419 ARG cc_start: 0.5913 (tpm170) cc_final: 0.5338 (mmt90) REVERT: 7 483 LEU cc_start: 0.8807 (mt) cc_final: 0.8384 (tt) REVERT: 7 494 MET cc_start: 0.6696 (mmp) cc_final: 0.6062 (mmt) REVERT: 7 696 MET cc_start: 0.5843 (tmm) cc_final: 0.5550 (tmm) outliers start: 7 outliers final: 0 residues processed: 540 average time/residue: 0.1433 time to fit residues: 123.3263 Evaluate side-chains 386 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 262 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 124 optimal weight: 0.4980 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 221 optimal weight: 0.0770 chunk 100 optimal weight: 2.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 145 GLN ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 368 GLN ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 715 GLN 2 181 GLN 2 264 HIS 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN 3 144 GLN 4 63 HIS 4 173 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 340 ASN 7 112 HIS ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 499 ASN 7 598 HIS 7 711 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.148190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129919 restraints weight = 57253.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.129001 restraints weight = 89379.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.129691 restraints weight = 91030.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.130354 restraints weight = 60827.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.130645 restraints weight = 55770.188| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24242 Z= 0.159 Angle : 0.711 20.633 32963 Z= 0.347 Chirality : 0.044 0.281 3711 Planarity : 0.005 0.114 4050 Dihedral : 11.922 172.903 3539 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.24 % Allowed : 4.31 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.16), residues: 2768 helix: 0.73 (0.14), residues: 1398 sheet: -1.62 (0.29), residues: 294 loop : -1.12 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG 7 520 TYR 0.051 0.002 TYR 3 125 PHE 0.032 0.002 PHE 3 58 TRP 0.054 0.002 TRP 1 221 HIS 0.022 0.001 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (24210) covalent geometry : angle 0.65746 / 0.34 (32915) hydrogen bonds : bond 0.04956 / 3.33 ( 1083) hydrogen bonds : angle 5.05025 / 3.54 ( 3087) metal coordination : bond 0.02165 / 0.90 ( 32) metal coordination : angle 7.14555 / 4.42 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 533 time to evaluate : 0.819 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 264 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7025 (mt-10) REVERT: 0 457 THR cc_start: 0.7877 (m) cc_final: 0.7675 (m) REVERT: 0 488 VAL cc_start: 0.7427 (p) cc_final: 0.7084 (p) REVERT: 0 596 LEU cc_start: 0.9199 (tp) cc_final: 0.8920 (tt) REVERT: 1 499 ARG cc_start: 0.5819 (mtt180) cc_final: 0.5376 (mtt180) REVERT: 2 73 LEU cc_start: 0.7947 (pp) cc_final: 0.7578 (tt) REVERT: 2 286 LEU cc_start: 0.8552 (mt) cc_final: 0.8304 (mt) REVERT: 2 313 TYR cc_start: 0.8247 (m-80) cc_final: 0.7839 (m-80) REVERT: 2 314 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8263 (ttt90) REVERT: 2 323 LEU cc_start: 0.8844 (tp) cc_final: 0.8614 (tp) REVERT: 2 365 ILE cc_start: 0.8307 (pt) cc_final: 0.8089 (tp) REVERT: 2 408 LEU cc_start: 0.7405 (tp) cc_final: 0.7155 (tp) REVERT: 2 448 HIS cc_start: 0.6975 (t-90) cc_final: 0.6505 (t-170) REVERT: 5 34 ILE cc_start: 0.6905 (mt) cc_final: 0.6656 (mt) REVERT: 5 44 PHE cc_start: 0.6216 (t80) cc_final: 0.5638 (t80) REVERT: 5 51 ASN cc_start: 0.6994 (p0) cc_final: 0.6205 (t0) REVERT: 6 101 ILE cc_start: 0.7892 (pt) cc_final: 0.7678 (pt) REVERT: 7 118 LEU cc_start: 0.7440 (mp) cc_final: 0.7103 (mp) REVERT: 7 483 LEU cc_start: 0.8648 (mt) cc_final: 0.8224 (tt) REVERT: 7 494 MET cc_start: 0.6747 (mmp) cc_final: 0.6238 (mmt) REVERT: 7 499 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6332 (m-40) REVERT: 7 525 ILE cc_start: 0.8385 (pt) cc_final: 0.7681 (mt) REVERT: 7 644 LEU cc_start: 0.9125 (mt) cc_final: 0.8905 (mt) REVERT: W 283 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6135 (mm-30) outliers start: 6 outliers final: 0 residues processed: 537 average time/residue: 0.1514 time to fit residues: 129.1019 Evaluate side-chains 386 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 35 optimal weight: 0.0980 chunk 168 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 276 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 715 GLN ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 181 GLN 2 211 GLN 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN 3 144 GLN 4 205 GLN 4 240 GLN 5 64 ASN ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 711 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.147103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128909 restraints weight = 57019.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127722 restraints weight = 91253.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128082 restraints weight = 85634.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129325 restraints weight = 65381.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129350 restraints weight = 52287.302| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24242 Z= 0.170 Angle : 0.723 21.100 32963 Z= 0.350 Chirality : 0.044 0.282 3711 Planarity : 0.005 0.092 4050 Dihedral : 12.013 173.225 3539 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.55 (0.16), residues: 2768 helix: 0.60 (0.14), residues: 1400 sheet: -1.55 (0.29), residues: 302 loop : -1.22 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG W 282 TYR 0.051 0.002 TYR 3 125 PHE 0.038 0.002 PHE 7 392 TRP 0.020 0.002 TRP 0 696 HIS 0.018 0.001 HIS 7 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (24210) covalent geometry : angle 0.66690 / 0.35 (32915) hydrogen bonds : bond 0.04670 / 3.14 ( 1083) hydrogen bonds : angle 5.02549 / 3.53 ( 3087) metal coordination : bond 0.01910 / 1.03 ( 32) metal coordination : angle 7.35158 / 4.60 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 499 time to evaluate : 0.952 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 264 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7173 (mt-10) REVERT: 0 438 MET cc_start: 0.6998 (ptm) cc_final: 0.6379 (ptt) REVERT: 0 457 THR cc_start: 0.8259 (m) cc_final: 0.7934 (m) REVERT: 0 596 LEU cc_start: 0.9239 (tp) cc_final: 0.8917 (tt) REVERT: 0 636 ARG cc_start: 0.7741 (tpt90) cc_final: 0.7445 (tpt90) REVERT: 1 117 MET cc_start: 0.5402 (ppp) cc_final: 0.3582 (tpt) REVERT: 1 461 LEU cc_start: 0.8115 (mt) cc_final: 0.7226 (pp) REVERT: 1 465 TYR cc_start: 0.6590 (m-80) cc_final: 0.6283 (m-80) REVERT: 2 73 LEU cc_start: 0.8044 (pp) cc_final: 0.7670 (tt) REVERT: 2 313 TYR cc_start: 0.8219 (m-80) cc_final: 0.7757 (m-80) REVERT: 2 408 LEU cc_start: 0.7533 (tp) cc_final: 0.7303 (tp) REVERT: 2 448 HIS cc_start: 0.7057 (t-90) cc_final: 0.6564 (t-170) REVERT: 3 21 LEU cc_start: 0.5737 (tp) cc_final: 0.5530 (tp) REVERT: 4 105 THR cc_start: 0.8685 (m) cc_final: 0.8194 (m) REVERT: 4 178 MET cc_start: 0.7865 (tpp) cc_final: 0.7601 (tpp) REVERT: 5 22 TYR cc_start: 0.7408 (t80) cc_final: 0.7183 (t80) REVERT: 5 44 PHE cc_start: 0.6359 (t80) cc_final: 0.5860 (t80) REVERT: 5 51 ASN cc_start: 0.7185 (p0) cc_final: 0.6410 (t0) REVERT: 6 101 ILE cc_start: 0.8091 (pt) cc_final: 0.7842 (pt) REVERT: 7 118 LEU cc_start: 0.7393 (mp) cc_final: 0.7119 (mp) REVERT: 7 412 MET cc_start: 0.7060 (tpp) cc_final: 0.5682 (tpp) REVERT: 7 483 LEU cc_start: 0.8615 (mt) cc_final: 0.8187 (tt) REVERT: 7 494 MET cc_start: 0.6676 (mmp) cc_final: 0.6332 (mmt) REVERT: 7 644 LEU cc_start: 0.9110 (mt) cc_final: 0.8904 (mt) REVERT: W 283 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6626 (mm-30) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.1498 time to fit residues: 120.3181 Evaluate side-chains 362 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 148 HIS ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 700 HIS 0 715 GLN 1 474 HIS ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 64 GLN 2 181 GLN ** 2 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN 3 144 GLN 4 65 GLN 4 187 GLN 4 205 GLN 4 237 GLN 5 64 ASN 6 227 HIS ** 6 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS 7 274 GLN 7 415 HIS 7 625 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122977 restraints weight = 58058.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123459 restraints weight = 101664.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123701 restraints weight = 88166.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.123674 restraints weight = 66176.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123903 restraints weight = 63124.700| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 24242 Z= 0.301 Angle : 0.866 23.103 32963 Z= 0.422 Chirality : 0.048 0.217 3711 Planarity : 0.006 0.071 4050 Dihedral : 12.244 174.428 3539 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.98 (0.15), residues: 2768 helix: 0.25 (0.14), residues: 1389 sheet: -1.89 (0.28), residues: 300 loop : -1.36 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG 6 165 TYR 0.030 0.003 TYR 4 71 PHE 0.032 0.003 PHE 7 659 TRP 0.025 0.003 TRP 2 74 HIS 0.017 0.002 HIS 1 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (24210) covalent geometry : angle 0.80665 / 0.42 (32915) hydrogen bonds : bond 0.05162 / 3.48 ( 1083) hydrogen bonds : angle 5.26809 / 3.70 ( 3087) metal coordination : bond 0.01330 / 0.81 ( 32) metal coordination : angle 8.28419 / 5.09 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 457 time to evaluate : 0.750 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 264 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6971 (mt-10) REVERT: 0 342 TRP cc_start: 0.5944 (t60) cc_final: 0.5617 (t60) REVERT: 0 490 LEU cc_start: 0.8819 (pp) cc_final: 0.8598 (pp) REVERT: 0 596 LEU cc_start: 0.9336 (tp) cc_final: 0.9030 (tt) REVERT: 0 657 MET cc_start: 0.8896 (mmp) cc_final: 0.7384 (tmm) REVERT: 1 117 MET cc_start: 0.5188 (ppp) cc_final: 0.3827 (tpt) REVERT: 1 499 ARG cc_start: 0.5660 (mtt180) cc_final: 0.5144 (mtt180) REVERT: 2 73 LEU cc_start: 0.8323 (pp) cc_final: 0.7814 (tt) REVERT: 2 313 TYR cc_start: 0.8459 (m-80) cc_final: 0.8077 (m-80) REVERT: 2 323 LEU cc_start: 0.8972 (tp) cc_final: 0.8731 (tp) REVERT: 2 376 MET cc_start: 0.8993 (mtt) cc_final: 0.8734 (mtm) REVERT: 2 408 LEU cc_start: 0.7627 (tp) cc_final: 0.7332 (tp) REVERT: 2 448 HIS cc_start: 0.6928 (t-90) cc_final: 0.6509 (t-170) REVERT: 3 21 LEU cc_start: 0.5711 (tp) cc_final: 0.5507 (tp) REVERT: 4 229 TRP cc_start: 0.8107 (t-100) cc_final: 0.7862 (t-100) REVERT: 5 44 PHE cc_start: 0.6313 (t80) cc_final: 0.5999 (t80) REVERT: 5 51 ASN cc_start: 0.7097 (p0) cc_final: 0.6324 (t0) REVERT: 6 101 ILE cc_start: 0.8257 (pt) cc_final: 0.8041 (pt) REVERT: 7 86 LEU cc_start: 0.7987 (tp) cc_final: 0.7727 (tt) REVERT: 7 412 MET cc_start: 0.7442 (tpp) cc_final: 0.6793 (tpp) REVERT: 7 442 GLU cc_start: 0.7782 (mp0) cc_final: 0.7432 (mp0) REVERT: 7 483 LEU cc_start: 0.8724 (mt) cc_final: 0.8330 (tt) REVERT: 7 494 MET cc_start: 0.6568 (mmp) cc_final: 0.6117 (mmm) REVERT: 7 525 ILE cc_start: 0.8467 (pt) cc_final: 0.7923 (mt) REVERT: 7 644 LEU cc_start: 0.9078 (mt) cc_final: 0.8870 (mt) REVERT: W 283 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6709 (mm-30) outliers start: 2 outliers final: 0 residues processed: 459 average time/residue: 0.1455 time to fit residues: 106.8040 Evaluate side-chains 345 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 132 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 153 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 274 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 700 HIS 0 715 GLN 2 64 GLN 2 181 GLN ** 2 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN 7 415 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.144069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126260 restraints weight = 56834.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125099 restraints weight = 88602.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125540 restraints weight = 89026.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125866 restraints weight = 60084.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126040 restraints weight = 55788.154| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24242 Z= 0.179 Angle : 0.771 23.853 32963 Z= 0.363 Chirality : 0.045 0.237 3711 Planarity : 0.005 0.078 4050 Dihedral : 12.181 172.797 3539 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.86 (0.15), residues: 2768 helix: 0.33 (0.14), residues: 1394 sheet: -1.68 (0.28), residues: 310 loop : -1.33 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 0 334 TYR 0.051 0.002 TYR 3 125 PHE 0.052 0.002 PHE 3 39 TRP 0.043 0.002 TRP 2 96 HIS 0.014 0.001 HIS 4 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (24210) covalent geometry : angle 0.69411 / 0.36 (32915) hydrogen bonds : bond 0.04506 / 3.04 ( 1083) hydrogen bonds : angle 5.03287 / 3.53 ( 3087) metal coordination : bond 0.01684 / 0.92 ( 32) metal coordination : angle 8.85148 / 5.58 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.915 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 264 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7055 (mt-10) REVERT: 0 338 GLU cc_start: 0.7609 (tp30) cc_final: 0.7397 (tp30) REVERT: 0 342 TRP cc_start: 0.5909 (t60) cc_final: 0.5224 (t60) REVERT: 0 345 ARG cc_start: 0.6560 (ptp-110) cc_final: 0.5229 (ttm170) REVERT: 0 488 VAL cc_start: 0.7546 (p) cc_final: 0.7329 (p) REVERT: 0 596 LEU cc_start: 0.9260 (tp) cc_final: 0.8929 (tt) REVERT: 1 117 MET cc_start: 0.5371 (ppp) cc_final: 0.3860 (tpt) REVERT: 1 499 ARG cc_start: 0.5297 (mtt180) cc_final: 0.4534 (mtt180) REVERT: 2 41 CYS cc_start: 0.8287 (m) cc_final: 0.7049 (p) REVERT: 2 73 LEU cc_start: 0.8181 (pp) cc_final: 0.7763 (tt) REVERT: 2 118 LEU cc_start: 0.8885 (tt) cc_final: 0.8640 (tt) REVERT: 2 313 TYR cc_start: 0.8377 (m-80) cc_final: 0.7935 (m-80) REVERT: 2 323 LEU cc_start: 0.8937 (tp) cc_final: 0.8718 (tp) REVERT: 2 376 MET cc_start: 0.8930 (mtt) cc_final: 0.8602 (mtm) REVERT: 2 448 HIS cc_start: 0.7080 (t-90) cc_final: 0.6613 (t-170) REVERT: 5 20 LEU cc_start: 0.8107 (mt) cc_final: 0.7842 (mt) REVERT: 5 21 LEU cc_start: 0.7851 (mt) cc_final: 0.7106 (mp) REVERT: 5 44 PHE cc_start: 0.6677 (t80) cc_final: 0.6199 (t80) REVERT: 5 51 ASN cc_start: 0.7156 (p0) cc_final: 0.6243 (t0) REVERT: 6 71 MET cc_start: 0.7441 (tpt) cc_final: 0.7185 (tpp) REVERT: 6 129 THR cc_start: 0.7849 (p) cc_final: 0.7623 (t) REVERT: 7 118 LEU cc_start: 0.7501 (mp) cc_final: 0.7205 (mp) REVERT: 7 412 MET cc_start: 0.7296 (tpp) cc_final: 0.6286 (tpp) REVERT: 7 442 GLU cc_start: 0.7819 (mp0) cc_final: 0.7466 (mp0) REVERT: 7 446 ILE cc_start: 0.8732 (mm) cc_final: 0.8531 (mm) REVERT: 7 483 LEU cc_start: 0.8561 (mt) cc_final: 0.8210 (tt) REVERT: 7 494 MET cc_start: 0.6470 (mmp) cc_final: 0.6110 (mmm) REVERT: 7 504 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7932 (mttt) REVERT: 7 571 TYR cc_start: 0.5069 (m-80) cc_final: 0.4649 (m-10) REVERT: 7 644 LEU cc_start: 0.9032 (mt) cc_final: 0.8794 (mt) REVERT: W 283 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6827 (mm-30) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1479 time to fit residues: 111.5119 Evaluate side-chains 351 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 64 GLN 2 116 GLN 2 181 GLN ** 2 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN 4 205 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125800 restraints weight = 56798.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.124901 restraints weight = 89506.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.125447 restraints weight = 92324.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125977 restraints weight = 59952.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.126164 restraints weight = 55714.200| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 24242 Z= 0.183 Angle : 0.788 25.127 32963 Z= 0.369 Chirality : 0.046 0.362 3711 Planarity : 0.005 0.071 4050 Dihedral : 12.205 173.056 3539 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.88 (0.15), residues: 2768 helix: 0.31 (0.14), residues: 1397 sheet: -1.67 (0.29), residues: 304 loop : -1.34 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 251 TYR 0.051 0.002 TYR 3 125 PHE 0.034 0.002 PHE 3 58 TRP 0.031 0.002 TRP 2 96 HIS 0.011 0.001 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (24210) covalent geometry : angle 0.70836 / 0.37 (32915) hydrogen bonds : bond 0.04461 / 3.02 ( 1083) hydrogen bonds : angle 5.00089 / 3.52 ( 3087) metal coordination : bond 0.02752 / 1.12 ( 32) metal coordination : angle 9.07733 / 5.82 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 0.904 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: symmetry clash REVERT: 0 342 TRP cc_start: 0.5960 (t60) cc_final: 0.5397 (t60) REVERT: 0 345 ARG cc_start: 0.6644 (ptp-110) cc_final: 0.5666 (ttm-80) REVERT: 0 457 THR cc_start: 0.8454 (m) cc_final: 0.8140 (m) REVERT: 0 488 VAL cc_start: 0.7405 (p) cc_final: 0.7060 (p) REVERT: 0 596 LEU cc_start: 0.9316 (tp) cc_final: 0.9091 (tt) REVERT: 0 657 MET cc_start: 0.8574 (mmp) cc_final: 0.7929 (tpp) REVERT: 1 117 MET cc_start: 0.5435 (ppp) cc_final: 0.3863 (tpt) REVERT: 1 499 ARG cc_start: 0.5432 (mtt180) cc_final: 0.4491 (mtt180) REVERT: 1 510 GLU cc_start: 0.7233 (pm20) cc_final: 0.6718 (pp20) REVERT: 2 41 CYS cc_start: 0.8454 (m) cc_final: 0.7104 (p) REVERT: 2 73 LEU cc_start: 0.8202 (pp) cc_final: 0.7775 (tt) REVERT: 2 118 LEU cc_start: 0.8892 (tt) cc_final: 0.8595 (tt) REVERT: 2 313 TYR cc_start: 0.8436 (m-80) cc_final: 0.7963 (m-80) REVERT: 2 323 LEU cc_start: 0.8899 (tp) cc_final: 0.8664 (tp) REVERT: 2 376 MET cc_start: 0.8851 (mtp) cc_final: 0.8532 (mtm) REVERT: 2 408 LEU cc_start: 0.7659 (tp) cc_final: 0.7365 (tp) REVERT: 2 448 HIS cc_start: 0.7079 (t-90) cc_final: 0.6620 (t-170) REVERT: 5 44 PHE cc_start: 0.6711 (t80) cc_final: 0.6224 (t80) REVERT: 5 51 ASN cc_start: 0.7050 (p0) cc_final: 0.6277 (t0) REVERT: 6 129 THR cc_start: 0.7845 (p) cc_final: 0.7568 (t) REVERT: 7 118 LEU cc_start: 0.7445 (mp) cc_final: 0.7198 (mp) REVERT: 7 340 LEU cc_start: 0.8383 (mm) cc_final: 0.7964 (mm) REVERT: 7 412 MET cc_start: 0.7283 (tpp) cc_final: 0.6447 (tpp) REVERT: 7 442 GLU cc_start: 0.7837 (mp0) cc_final: 0.7473 (mp0) REVERT: 7 483 LEU cc_start: 0.8522 (mt) cc_final: 0.8225 (tt) REVERT: 7 494 MET cc_start: 0.6404 (mmp) cc_final: 0.6000 (mmm) REVERT: 7 504 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7802 (mtpp) REVERT: 7 571 TYR cc_start: 0.4998 (m-80) cc_final: 0.4625 (m-10) REVERT: W 283 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6774 (mm-30) outliers start: 1 outliers final: 1 residues processed: 462 average time/residue: 0.1552 time to fit residues: 114.4309 Evaluate side-chains 347 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 14 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 116 GLN 2 181 GLN 2 263 GLN 2 366 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 576 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.142665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123503 restraints weight = 57044.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122905 restraints weight = 96711.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123725 restraints weight = 96384.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.124303 restraints weight = 61495.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124598 restraints weight = 57290.914| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 24242 Z= 0.227 Angle : 0.819 24.663 32963 Z= 0.388 Chirality : 0.046 0.316 3711 Planarity : 0.005 0.069 4050 Dihedral : 12.290 173.712 3539 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.06 (0.15), residues: 2768 helix: 0.17 (0.14), residues: 1395 sheet: -1.77 (0.29), residues: 304 loop : -1.44 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 7 195 TYR 0.049 0.002 TYR 3 125 PHE 0.044 0.003 PHE 3 58 TRP 0.036 0.002 TRP 2 96 HIS 0.015 0.002 HIS 0 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (24210) covalent geometry : angle 0.74263 / 0.38 (32915) hydrogen bonds : bond 0.04627 / 3.16 ( 1083) hydrogen bonds : angle 5.12669 / 3.62 ( 3087) metal coordination : bond 0.02081 / 0.89 ( 32) metal coordination : angle 9.06117 / 5.68 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.866 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: 0 264 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7386 (mt-10) REVERT: 0 342 TRP cc_start: 0.5977 (t60) cc_final: 0.5350 (t60) REVERT: 0 345 ARG cc_start: 0.6756 (ptp-110) cc_final: 0.5575 (ttm-80) REVERT: 0 571 THR cc_start: 0.6593 (p) cc_final: 0.6389 (p) REVERT: 0 657 MET cc_start: 0.8645 (mmp) cc_final: 0.7883 (tpp) REVERT: 1 117 MET cc_start: 0.5414 (ppp) cc_final: 0.3837 (tpt) REVERT: 1 499 ARG cc_start: 0.5534 (mtt180) cc_final: 0.5037 (mtt180) REVERT: 2 41 CYS cc_start: 0.8479 (m) cc_final: 0.7275 (p) REVERT: 2 73 LEU cc_start: 0.8276 (pp) cc_final: 0.7817 (tp) REVERT: 2 313 TYR cc_start: 0.8385 (m-80) cc_final: 0.7965 (m-80) REVERT: 2 408 LEU cc_start: 0.7666 (tp) cc_final: 0.7404 (tp) REVERT: 2 448 HIS cc_start: 0.7122 (t-90) cc_final: 0.6739 (t-170) REVERT: 3 99 LEU cc_start: 0.8323 (mp) cc_final: 0.7838 (mp) REVERT: 5 44 PHE cc_start: 0.6734 (t80) cc_final: 0.6206 (t80) REVERT: 5 51 ASN cc_start: 0.7129 (p0) cc_final: 0.6371 (t0) REVERT: 6 101 ILE cc_start: 0.8180 (pt) cc_final: 0.7917 (pt) REVERT: 6 129 THR cc_start: 0.7942 (p) cc_final: 0.7635 (t) REVERT: 7 118 LEU cc_start: 0.7509 (mp) cc_final: 0.7244 (mp) REVERT: 7 378 PHE cc_start: 0.6656 (m-80) cc_final: 0.6435 (m-80) REVERT: 7 412 MET cc_start: 0.7353 (tpp) cc_final: 0.6632 (tpp) REVERT: 7 442 GLU cc_start: 0.7866 (mp0) cc_final: 0.7445 (mp0) REVERT: 7 483 LEU cc_start: 0.8625 (mt) cc_final: 0.8248 (tt) REVERT: 7 494 MET cc_start: 0.6365 (mmp) cc_final: 0.5993 (mmm) REVERT: 7 504 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7416 (mtpp) REVERT: 7 571 TYR cc_start: 0.5190 (m-80) cc_final: 0.4754 (m-10) REVERT: W 283 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6884 (mm-30) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1595 time to fit residues: 113.4699 Evaluate side-chains 341 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 220 optimal weight: 0.6980 chunk 157 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 245 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 221 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 64 GLN 2 116 GLN 2 181 GLN 2 366 HIS 3 57 ASN ** 3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.144739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126205 restraints weight = 56776.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126351 restraints weight = 90548.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126740 restraints weight = 86124.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.128013 restraints weight = 60114.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.127926 restraints weight = 48854.108| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24242 Z= 0.158 Angle : 0.791 24.466 32963 Z= 0.370 Chirality : 0.045 0.299 3711 Planarity : 0.005 0.070 4050 Dihedral : 12.272 172.773 3539 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.08 % Allowed : 0.56 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.93 (0.16), residues: 2768 helix: 0.28 (0.14), residues: 1400 sheet: -1.68 (0.30), residues: 291 loop : -1.40 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 62 TYR 0.046 0.002 TYR 3 125 PHE 0.034 0.002 PHE 3 58 TRP 0.034 0.002 TRP 0 696 HIS 0.013 0.001 HIS 0 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (24210) covalent geometry : angle 0.71073 / 0.37 (32915) hydrogen bonds : bond 0.04272 / 2.88 ( 1083) hydrogen bonds : angle 4.93157 / 3.47 ( 3087) metal coordination : bond 0.02202 / 0.95 ( 32) metal coordination : angle 9.13300 / 5.60 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 1 MET cc_start: 0.4477 (ptp) cc_final: 0.4253 (ptm) REVERT: 0 264 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7185 (mt-10) REVERT: 0 342 TRP cc_start: 0.5824 (t60) cc_final: 0.5313 (t60) REVERT: 0 345 ARG cc_start: 0.6513 (ptp-110) cc_final: 0.5605 (ttm170) REVERT: 0 374 PHE cc_start: 0.6880 (m-10) cc_final: 0.6654 (m-10) REVERT: 0 571 THR cc_start: 0.7022 (p) cc_final: 0.6731 (p) REVERT: 1 117 MET cc_start: 0.5180 (ppp) cc_final: 0.3719 (tpt) REVERT: 1 499 ARG cc_start: 0.5439 (mtt180) cc_final: 0.4617 (mtt180) REVERT: 2 40 THR cc_start: 0.8102 (t) cc_final: 0.7884 (t) REVERT: 2 41 CYS cc_start: 0.8355 (m) cc_final: 0.7204 (p) REVERT: 2 73 LEU cc_start: 0.8162 (pp) cc_final: 0.7725 (tp) REVERT: 2 118 LEU cc_start: 0.8833 (tt) cc_final: 0.8607 (tt) REVERT: 2 313 TYR cc_start: 0.8327 (m-80) cc_final: 0.7880 (m-80) REVERT: 2 323 LEU cc_start: 0.8959 (tp) cc_final: 0.8717 (tp) REVERT: 2 448 HIS cc_start: 0.6968 (t-90) cc_final: 0.6623 (t-170) REVERT: 3 99 LEU cc_start: 0.8176 (mp) cc_final: 0.7757 (mp) REVERT: 4 228 LEU cc_start: 0.9565 (mt) cc_final: 0.9356 (mp) REVERT: 5 20 LEU cc_start: 0.8080 (mt) cc_final: 0.7875 (mt) REVERT: 5 44 PHE cc_start: 0.6562 (t80) cc_final: 0.6127 (t80) REVERT: 5 51 ASN cc_start: 0.7104 (p0) cc_final: 0.6363 (t0) REVERT: 7 118 LEU cc_start: 0.7378 (mp) cc_final: 0.7106 (mp) REVERT: 7 412 MET cc_start: 0.7356 (tpp) cc_final: 0.6569 (tpp) REVERT: 7 442 GLU cc_start: 0.7860 (mp0) cc_final: 0.7487 (mp0) REVERT: 7 483 LEU cc_start: 0.8509 (mt) cc_final: 0.8201 (tt) REVERT: 7 494 MET cc_start: 0.6422 (mmp) cc_final: 0.6071 (mmm) REVERT: 7 504 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7827 (mtpp) REVERT: 7 571 TYR cc_start: 0.5053 (m-80) cc_final: 0.4712 (m-10) REVERT: W 283 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6911 (mm-30) outliers start: 2 outliers final: 1 residues processed: 464 average time/residue: 0.1554 time to fit residues: 115.2880 Evaluate side-chains 354 residues out of total 2503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 118 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 272 optimal weight: 0.3980 chunk 275 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 157 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 307 ASN ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 116 GLN 2 181 GLN ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 240 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.145090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126284 restraints weight = 56656.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125670 restraints weight = 94904.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126218 restraints weight = 88084.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127197 restraints weight = 63935.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127244 restraints weight = 61288.362| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 24242 Z= 0.156 Angle : 0.772 24.688 32963 Z= 0.363 Chirality : 0.045 0.274 3711 Planarity : 0.005 0.067 4050 Dihedral : 12.276 173.178 3539 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.86 (0.16), residues: 2768 helix: 0.31 (0.14), residues: 1401 sheet: -1.64 (0.29), residues: 304 loop : -1.34 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 0 253 TYR 0.046 0.002 TYR 3 125 PHE 0.040 0.002 PHE 7 518 TRP 0.035 0.002 TRP 0 696 HIS 0.010 0.001 HIS 0 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (24210) covalent geometry : angle 0.69634 / 0.36 (32915) hydrogen bonds : bond 0.04179 / 2.83 ( 1083) hydrogen bonds : angle 4.90908 / 3.46 ( 3087) metal coordination : bond 0.03139 / 1.33 ( 32) metal coordination : angle 8.78491 / 5.36 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.62 seconds wall clock time: 65 minutes 52.05 seconds (3952.05 seconds total)