Starting phenix.real_space_refine on Sun Aug 24 12:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092.map" model { file = "/net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i02_35092/08_2025/8i02_35092_neut.cif" } resolution = 2.9 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= -0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 S 103 5.16 5 C 12702 2.51 5 N 3377 2.21 5 O 3686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 250 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19876 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1702 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 19, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 7173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7173 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 36, 'TRANS': 827} Chain breaks: 6 Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2957 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 15, 'TRANS': 353} Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 1 Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1378 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1337 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Chain: "G" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2275 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" 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 171 SG CYS F 137 57.666 35.100 80.932 1.00 77.48 S ATOM 353 SG CYS F 160 56.585 38.764 77.543 1.00 79.66 S ATOM 60 SG CYS F 120 49.847 28.802 79.913 1.00 75.07 S ATOM 218 SG CYS F 143 45.468 30.262 78.727 1.00 76.69 S ATOM 17635 SG CYS G 266 80.671 67.521 131.409 1.00 58.13 S ATOM 17652 SG CYS G 269 77.934 69.167 129.364 1.00 51.87 S ATOM 17798 SG CYS G 289 76.676 68.440 132.695 1.00 51.11 S ATOM 18455 SG CYS G 409 58.407 95.813 97.741 1.00 15.88 S ATOM 18483 SG CYS G 412 57.406 99.479 97.015 1.00 14.69 S ATOM 18673 SG CYS G 436 56.697 98.367 100.584 1.00 17.31 S ATOM 18576 SG CYS G 425 61.214 84.100 100.203 1.00 16.98 S ATOM 18809 SG CYS G 453 57.664 85.341 99.638 1.00 18.08 S Time building chain proxies: 4.51, per 1000 atoms: 0.23 Number of scatterers: 19876 At special positions: 0 Unit cell: (108.7, 148.919, 191.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 103 16.00 O 3686 8.00 N 3377 7.00 C 12702 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: 1.70 Conformation dependent library (CDL) restraints added in 733.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 175 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 160 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 137 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 140 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 120 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 143 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 266 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 269 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 701 " - pdb=" ND1 HIS G 286 " pdb=" ZN G 702 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 436 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 412 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 409 " pdb=" ZN G 703 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 453 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 425 " pdb="ZN ZN G 703 " - pdb=" NE2 HIS G 456 " Number of angles added : 3 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 20 sheets defined 43.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.888A pdb=" N ASN F 152 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 153 " --> pdb=" O PRO F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 153' Processing helix chain 'F' and resid 160 through 165 Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.550A pdb=" N GLN F 188 " --> pdb=" O TRP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 201 removed outlier: 3.612A pdb=" N HIS F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 343 through 371 removed outlier: 3.564A pdb=" N ASN F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 403 removed outlier: 3.692A pdb=" N ALA F 394 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG F 396 " --> pdb=" O PRO F 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.872A pdb=" N TYR A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.781A pdb=" N THR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.797A pdb=" N SER A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.136A pdb=" N THR A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.845A pdb=" N GLN A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.053A pdb=" N PHE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 removed outlier: 3.646A pdb=" N HIS A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.521A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.653A pdb=" N LEU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.745A pdb=" N ASN A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 425 removed outlier: 3.586A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.590A pdb=" N TYR A 435 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 4.218A pdb=" N TYR A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 453 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 removed outlier: 4.218A pdb=" N MET A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 497 removed outlier: 4.180A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.815A pdb=" N LYS A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 514 removed outlier: 3.670A pdb=" N LEU A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 514' Processing helix chain 'A' and resid 516 through 529 removed outlier: 3.872A pdb=" N TYR A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 removed outlier: 3.734A pdb=" N LEU A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 removed outlier: 3.869A pdb=" N ASP A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 582 " --> pdb=" O THR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 4.640A pdb=" N LEU A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.183A pdb=" N PHE A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 746 through 770 removed outlier: 3.698A pdb=" N PHE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 807 through 822 removed outlier: 3.590A pdb=" N ASN A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 838 removed outlier: 3.532A pdb=" N TYR A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.647A pdb=" N VAL A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 removed outlier: 4.206A pdb=" N VAL A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.539A pdb=" N ARG A 989 " --> pdb=" O THR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 removed outlier: 3.637A pdb=" N LEU A1026 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.598A pdb=" N ASP A1033 " --> pdb=" O THR A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 removed outlier: 4.164A pdb=" N GLY B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.772A pdb=" N PHE B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.639A pdb=" N LYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.608A pdb=" N PHE B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.202A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.606A pdb=" N GLU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.605A pdb=" N GLU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 274 through 286 removed outlier: 4.969A pdb=" N CYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 282 " --> pdb=" O HIS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.675A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.943A pdb=" N GLY B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 369 removed outlier: 3.573A pdb=" N ASN B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 40 Proline residue: C 38 - end of helix Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 355 through 358 removed outlier: 3.727A pdb=" N ILE C 358 " --> pdb=" O LEU C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.778A pdb=" N TRP C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 205 through 216 removed outlier: 4.172A pdb=" N PHE D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 296 through 314 removed outlier: 3.518A pdb=" N TYR D 304 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 335 removed outlier: 4.259A pdb=" N SER D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 178 No H-bonds generated for 'chain 'E' and resid 177 through 178' Processing helix chain 'E' and resid 180 through 180 No H-bonds generated for 'chain 'E' and resid 180 through 180' Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.788A pdb=" N ILE E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.506A pdb=" N ALA E 209 " --> pdb=" O ARG E 205 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 244 removed outlier: 3.603A pdb=" N VAL E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY E 244 " --> pdb=" O ASN E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.601A pdb=" N GLN E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 removed outlier: 3.816A pdb=" N LEU E 271 " --> pdb=" O MET E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 294 through 315 Processing helix chain 'G' and resid 334 through 345 removed outlier: 3.666A pdb=" N TRP G 338 " --> pdb=" O MET G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 361 removed outlier: 3.511A pdb=" N SER G 360 " --> pdb=" O PRO G 356 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 361 " --> pdb=" O HIS G 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 356 through 361' Processing helix chain 'G' and resid 518 through 545 removed outlier: 3.639A pdb=" N ILE G 542 " --> pdb=" O GLU G 538 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU G 543 " --> pdb=" O GLN G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 568 removed outlier: 3.691A pdb=" N THR G 553 " --> pdb=" O ASP G 549 " (cutoff:3.500A) Proline residue: G 559 - end of helix Processing helix chain 'G' and resid 575 through 587 removed outlier: 3.688A pdb=" N ALA G 579 " --> pdb=" O ASP G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 605 Processing sheet with id=AA1, first strand: chain 'F' and resid 254 through 256 Processing sheet with id=AA2, first strand: chain 'G' and resid 472 through 474 removed outlier: 6.642A pdb=" N LEU F 339 " --> pdb=" O ILE G 473 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR F 340 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 743 through 745 removed outlier: 4.020A pdb=" N GLY A 918 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 removed outlier: 6.705A pdb=" N LEU A 905 " --> pdb=" O MET A 922 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 992 through 995 removed outlier: 3.840A pdb=" N LEU C 43 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 407 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 387 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.142A pdb=" N TYR B 10 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER B 9 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 254 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL B 295 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 256 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 168 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN B 257 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 170 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL B 221 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 192 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 223 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER B 194 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 225 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS B 196 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 82 removed outlier: 3.854A pdb=" N VAL C 79 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 87 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 88 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 90 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 148 Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.027A pdb=" N GLY C 203 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 190 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 201 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 241 removed outlier: 4.128A pdb=" N ASP C 239 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 287 removed outlier: 7.138A pdb=" N CYS C 300 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL C 287 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 308 " --> pdb=" O HIS C 319 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS C 319 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 333 removed outlier: 3.913A pdb=" N LEU C 341 " --> pdb=" O TRP C 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AB9, first strand: chain 'G' and resid 276 through 277 Processing sheet with id=AC1, first strand: chain 'G' and resid 367 through 368 Processing sheet with id=AC2, first strand: chain 'G' and resid 423 through 424 715 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 22 1.17 - 1.33: 5661 1.33 - 1.49: 6677 1.49 - 1.66: 7868 1.66 - 1.82: 139 Bond restraints: 20367 Sorted by residual: bond pdb=" C CYS A 337 " pdb=" O CYS A 337 " ideal model delta sigma weight residual 1.235 1.010 0.226 1.26e-02 6.30e+03 3.21e+02 bond pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 1.469 1.696 -0.228 1.28e-02 6.10e+03 3.17e+02 bond pdb=" C PHE A 359 " pdb=" O PHE A 359 " ideal model delta sigma weight residual 1.236 1.086 0.150 1.15e-02 7.56e+03 1.70e+02 bond pdb=" C SER A 370 " pdb=" O SER A 370 " ideal model delta sigma weight residual 1.234 1.076 0.158 1.28e-02 6.10e+03 1.52e+02 bond pdb=" C SER A 352 " pdb=" O SER A 352 " ideal model delta sigma weight residual 1.236 1.093 0.143 1.19e-02 7.06e+03 1.44e+02 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 27244 3.56 - 7.11: 312 7.11 - 10.67: 42 10.67 - 14.22: 11 14.22 - 17.78: 4 Bond angle restraints: 27613 Sorted by residual: angle pdb=" C HIS A 371 " pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 119.84 137.62 -17.78 1.25e+00 6.40e-01 2.02e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" C GLU A 378 " ideal model delta sigma weight residual 112.72 127.03 -14.31 1.14e+00 7.69e-01 1.58e+02 angle pdb=" O VAL A 369 " pdb=" C VAL A 369 " pdb=" N SER A 370 " ideal model delta sigma weight residual 122.69 110.83 11.86 1.14e+00 7.69e-01 1.08e+02 angle pdb=" C ASN A 365 " pdb=" CA ASN A 365 " pdb=" CB ASN A 365 " ideal model delta sigma weight residual 110.26 95.25 15.01 1.50e+00 4.44e-01 1.00e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" CB GLU A 378 " ideal model delta sigma weight residual 110.70 97.65 13.05 1.49e+00 4.50e-01 7.67e+01 ... (remaining 27608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10511 17.95 - 35.90: 1230 35.90 - 53.85: 338 53.85 - 71.80: 90 71.80 - 89.74: 35 Dihedral angle restraints: 12204 sinusoidal: 4947 harmonic: 7257 Sorted by residual: dihedral pdb=" CA ASN G 438 " pdb=" C ASN G 438 " pdb=" N PRO G 439 " pdb=" CA PRO G 439 " ideal model delta harmonic sigma weight residual 180.00 99.24 80.76 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N PRO F 146 " pdb=" CA PRO F 146 " ideal model delta harmonic sigma weight residual 180.00 121.06 58.94 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual 180.00 122.23 57.77 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2962 0.181 - 0.361: 19 0.361 - 0.542: 4 0.542 - 0.723: 1 0.723 - 0.904: 2 Chirality restraints: 2988 Sorted by residual: chirality pdb=" CA SER A 376 " pdb=" N SER A 376 " pdb=" C SER A 376 " pdb=" CB SER A 376 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLU A 377 " pdb=" N GLU A 377 " pdb=" C GLU A 377 " pdb=" CB GLU A 377 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2985 not shown) Planarity restraints: 3562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 336 " 0.036 2.00e-02 2.50e+03 7.52e-02 5.66e+01 pdb=" C GLU A 336 " -0.130 2.00e-02 2.50e+03 pdb=" O GLU A 336 " 0.050 2.00e-02 2.50e+03 pdb=" N CYS A 337 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 373 " -0.030 2.00e-02 2.50e+03 6.08e-02 3.69e+01 pdb=" C THR A 373 " 0.105 2.00e-02 2.50e+03 pdb=" O THR A 373 " -0.040 2.00e-02 2.50e+03 pdb=" N TRP A 374 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 247 " 0.024 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C GLN C 247 " -0.087 2.00e-02 2.50e+03 pdb=" O GLN C 247 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP C 248 " 0.030 2.00e-02 2.50e+03 ... (remaining 3559 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 45 2.27 - 2.99: 10466 2.99 - 3.70: 33105 3.70 - 4.42: 54880 4.42 - 5.14: 94177 Nonbonded interactions: 192673 Sorted by model distance: nonbonded pdb=" OG SER A 354 " pdb=" OD2 ASP B 67 " model vdw 1.549 3.040 nonbonded pdb=" OD2 ASP B 173 " pdb="ZN ZN B 501 " model vdw 1.810 2.230 nonbonded pdb=" NH1 ARG A 80 " pdb=" O ASN A 234 " model vdw 2.053 3.120 nonbonded pdb=" OG SER A 306 " pdb=" NH1 ARG A 310 " model vdw 2.058 3.120 nonbonded pdb=" OH TYR A1018 " pdb=" OD1 ASP A1020 " model vdw 2.075 3.040 ... (remaining 192668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 170 through 178 or resid 180 through 329)) selection = (chain 'E' and (resid 170 through 290 or resid 294 through 329)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.013 0.623 20383 Z= 0.582 Angle : 1.043 20.521 27616 Z= 0.605 Chirality : 0.062 0.904 2988 Planarity : 0.007 0.080 3562 Dihedral : 17.701 89.744 7500 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.80 % Favored : 87.54 % Rotamer: Outliers : 9.99 % Allowed : 20.53 % Favored : 69.48 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.22 % 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 aren not related in a simple way. whole: -4.49 (0.14), residues: 2415 helix: -2.31 (0.13), residues: 973 sheet: -2.91 (0.32), residues: 209 loop : -3.66 (0.14), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 356 TYR 0.027 0.003 TYR A 891 PHE 0.078 0.003 PHE A 381 TRP 0.053 0.004 TRP A 361 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00984 (20367) covalent geometry : angle 1.02985 (27613) hydrogen bonds : bond 0.17381 ( 711) hydrogen bonds : angle 7.11389 ( 2013) metal coordination : bond 0.29140 ( 16) metal coordination : angle 15.60505 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 427 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 142 SER cc_start: 0.5542 (OUTLIER) cc_final: 0.5184 (p) REVERT: F 360 LYS cc_start: 0.7392 (ttpp) cc_final: 0.6888 (mtmp) REVERT: F 361 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7230 (mttp) REVERT: F 368 LYS cc_start: 0.7420 (ptpp) cc_final: 0.6945 (tptt) REVERT: A 40 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7341 (mptt) REVERT: A 79 GLU cc_start: 0.7897 (pt0) cc_final: 0.7460 (mt-10) REVERT: A 346 VAL cc_start: 0.6422 (t) cc_final: 0.6161 (m) REVERT: A 374 TRP cc_start: 0.4310 (OUTLIER) cc_final: 0.3771 (t60) REVERT: A 381 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: A 439 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: A 446 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7028 (ptmm) REVERT: A 527 LYS cc_start: 0.6888 (tptt) cc_final: 0.5916 (mppt) REVERT: A 603 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 742 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: A 887 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: A 992 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: B 45 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5939 (p90) REVERT: B 57 THR cc_start: 0.8363 (p) cc_final: 0.8010 (m) REVERT: B 191 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8174 (ttp) REVERT: B 275 MET cc_start: 0.8696 (ttp) cc_final: 0.7881 (mtp) REVERT: C 75 MET cc_start: 0.7304 (pp-130) cc_final: 0.6724 (ptp) REVERT: C 79 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7564 (t) REVERT: C 83 VAL cc_start: 0.6940 (t) cc_final: 0.6513 (t) REVERT: C 197 LYS cc_start: 0.6837 (tmtt) cc_final: 0.6444 (ttpt) REVERT: C 214 LEU cc_start: 0.6968 (mt) cc_final: 0.6729 (mt) REVERT: C 248 ASP cc_start: 0.2278 (OUTLIER) cc_final: 0.1564 (t0) REVERT: C 306 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7169 (pt) REVERT: D 261 GLN cc_start: 0.7061 (mt0) cc_final: 0.6818 (mm-40) REVERT: E 204 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6968 (t) REVERT: E 237 ILE cc_start: 0.8341 (mt) cc_final: 0.8068 (mp) REVERT: G 438 ASN cc_start: 0.7211 (t0) cc_final: 0.6948 (t0) REVERT: G 550 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6846 (p90) REVERT: G 565 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6215 (m-30) outliers start: 219 outliers final: 55 residues processed: 600 average time/residue: 0.5050 time to fit residues: 346.8356 Evaluate side-chains 341 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 268 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 372 PRO Chi-restraints excluded: chain A residue 374 TRP Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 792 TRP Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 173 HIS F 364 ASN F 390 ASN A 52 HIS A 109 ASN A 159 ASN A 175 ASN A 234 ASN A 241 GLN A 286 GLN A 371 HIS A 421 GLN A 583 ASN A 597 ASN A 777 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN A 912 ASN A 998 GLN A1040 GLN B 37 ASN B 41 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 125 ASN B 138 HIS B 247 GLN B 332 GLN B 350 HIS B 351 ASN C 21 ASN C 22 GLN C 193 ASN C 236 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN D 230 GLN E 221 ASN E 261 GLN E 303 ASN G 447 ASN G 459 HIS G 526 ASN G 529 ASN G 593 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.201634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149149 restraints weight = 21665.032| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.76 r_work: 0.3581 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20383 Z= 0.149 Angle : 0.718 9.844 27616 Z= 0.376 Chirality : 0.045 0.218 2988 Planarity : 0.006 0.071 3562 Dihedral : 9.214 71.254 2805 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 6.34 % Allowed : 24.86 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.22 % 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 aren not related in a simple way. whole: -3.06 (0.15), residues: 2415 helix: -0.75 (0.16), residues: 977 sheet: -2.41 (0.33), residues: 207 loop : -3.15 (0.15), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 75 TYR 0.036 0.002 TYR C 70 PHE 0.023 0.002 PHE E 239 TRP 0.013 0.001 TRP A 792 HIS 0.005 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00336 (20367) covalent geometry : angle 0.71692 (27613) hydrogen bonds : bond 0.05145 ( 711) hydrogen bonds : angle 5.00933 ( 2013) metal coordination : bond 0.01794 ( 16) metal coordination : angle 3.74769 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 317 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7867 (t) REVERT: F 220 GLU cc_start: 0.5432 (pm20) cc_final: 0.4779 (pm20) REVERT: F 360 LYS cc_start: 0.7452 (ttpp) cc_final: 0.6745 (mtmt) REVERT: F 361 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7192 (mttp) REVERT: F 368 LYS cc_start: 0.7639 (ptpp) cc_final: 0.6815 (tptt) REVERT: F 373 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6542 (p) REVERT: A 182 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: A 226 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: A 351 ILE cc_start: 0.7532 (mm) cc_final: 0.7234 (tt) REVERT: A 374 TRP cc_start: 0.4093 (OUTLIER) cc_final: 0.3591 (t60) REVERT: A 439 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5131 (tp30) REVERT: A 496 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6962 (mtm-85) REVERT: A 527 LYS cc_start: 0.6926 (tptt) cc_final: 0.5773 (mppt) REVERT: A 619 ARG cc_start: 0.5393 (ptp-110) cc_final: 0.4798 (mtm-85) REVERT: A 795 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7518 (mtp85) REVERT: A 989 ARG cc_start: 0.8101 (mmt90) cc_final: 0.7673 (mtm180) REVERT: B 57 THR cc_start: 0.8327 (p) cc_final: 0.7886 (m) REVERT: B 75 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7779 (mtm110) REVERT: C 75 MET cc_start: 0.7674 (pp-130) cc_final: 0.6675 (ptp) REVERT: C 86 TYR cc_start: 0.7734 (m-80) cc_final: 0.7413 (m-80) REVERT: C 175 LYS cc_start: 0.7506 (pptt) cc_final: 0.6570 (tppt) REVERT: C 197 LYS cc_start: 0.6917 (tmtt) cc_final: 0.6112 (ttpt) REVERT: C 268 ASP cc_start: 0.7399 (t0) cc_final: 0.7166 (t0) REVERT: C 306 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6833 (pp) REVERT: D 215 LYS cc_start: 0.6210 (tptt) cc_final: 0.5936 (tmtm) REVERT: D 241 LYS cc_start: 0.6336 (mtmm) cc_final: 0.5986 (mtmt) REVERT: D 246 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7181 (pmt) REVERT: D 261 GLN cc_start: 0.6655 (mt0) cc_final: 0.6239 (mm-40) REVERT: D 266 THR cc_start: 0.6118 (OUTLIER) cc_final: 0.5750 (t) REVERT: D 319 TYR cc_start: 0.6823 (m-10) cc_final: 0.6425 (m-10) REVERT: E 169 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7084 (mttp) REVERT: E 216 ILE cc_start: 0.7635 (tt) cc_final: 0.7426 (pp) REVERT: E 237 ILE cc_start: 0.7548 (mt) cc_final: 0.7344 (mp) REVERT: G 344 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.4949 (t80) REVERT: G 438 ASN cc_start: 0.7361 (t0) cc_final: 0.7123 (t0) REVERT: G 535 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6969 (mt-10) REVERT: G 550 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6980 (p90) REVERT: G 565 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6170 (m-30) outliers start: 139 outliers final: 52 residues processed: 423 average time/residue: 0.5737 time to fit residues: 277.4719 Evaluate side-chains 322 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 374 TRP Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 597 ASN A 757 ASN A 783 ASN A 808 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 37 ASN B 345 ASN C 152 HIS C 193 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.198051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144986 restraints weight = 21504.378| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.87 r_work: 0.3523 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20383 Z= 0.161 Angle : 0.699 9.965 27616 Z= 0.363 Chirality : 0.045 0.214 2988 Planarity : 0.006 0.070 3562 Dihedral : 8.252 72.189 2737 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.90 % Favored : 90.85 % Rotamer: Outliers : 6.11 % Allowed : 24.73 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.43 (0.16), residues: 2415 helix: -0.26 (0.16), residues: 985 sheet: -1.97 (0.35), residues: 210 loop : -2.79 (0.15), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 366 TYR 0.031 0.002 TYR D 272 PHE 0.018 0.002 PHE A1031 TRP 0.011 0.001 TRP A 792 HIS 0.006 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00380 (20367) covalent geometry : angle 0.69872 (27613) hydrogen bonds : bond 0.05241 ( 711) hydrogen bonds : angle 4.84707 ( 2013) metal coordination : bond 0.00654 ( 16) metal coordination : angle 2.02841 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 290 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 220 GLU cc_start: 0.5258 (pm20) cc_final: 0.4700 (pm20) REVERT: F 360 LYS cc_start: 0.7557 (ttpp) cc_final: 0.6715 (mtmt) REVERT: F 361 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7320 (ttmm) REVERT: F 367 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7667 (tppt) REVERT: F 368 LYS cc_start: 0.7642 (ptpp) cc_final: 0.6974 (tptt) REVERT: F 373 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6804 (p) REVERT: A 182 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6663 (tm-30) REVERT: A 226 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8723 (mt0) REVERT: A 342 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6786 (mtt90) REVERT: A 423 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6632 (ptt-90) REVERT: A 439 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5009 (tp30) REVERT: A 496 ARG cc_start: 0.7302 (mtt180) cc_final: 0.7033 (mtm-85) REVERT: A 527 LYS cc_start: 0.6880 (tptt) cc_final: 0.5772 (mppt) REVERT: A 859 HIS cc_start: 0.7483 (t-90) cc_final: 0.6901 (m90) REVERT: A 903 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5616 (mm-30) REVERT: A 970 ILE cc_start: 0.8278 (pt) cc_final: 0.8002 (pt) REVERT: A 982 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7199 (tpp-160) REVERT: A 989 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: B 45 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6347 (p90) REVERT: B 57 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7911 (m) REVERT: B 74 TRP cc_start: 0.8475 (t60) cc_final: 0.8102 (t-100) REVERT: B 75 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7927 (mtp-110) REVERT: B 88 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: B 323 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: C 75 MET cc_start: 0.7635 (pp-130) cc_final: 0.6965 (ptp) REVERT: C 86 TYR cc_start: 0.7799 (m-80) cc_final: 0.7507 (m-80) REVERT: C 164 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: C 197 LYS cc_start: 0.6897 (tmtt) cc_final: 0.6252 (ttpt) REVERT: C 306 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7359 (pp) REVERT: C 407 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8001 (tt) REVERT: D 214 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7076 (p) REVERT: D 241 LYS cc_start: 0.6441 (mtmm) cc_final: 0.5947 (mtmt) REVERT: D 261 GLN cc_start: 0.6833 (mt0) cc_final: 0.6232 (mm-40) REVERT: D 272 TYR cc_start: 0.7397 (m-80) cc_final: 0.7087 (m-10) REVERT: D 319 TYR cc_start: 0.7302 (m-80) cc_final: 0.6878 (m-10) REVERT: D 325 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: E 169 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7170 (mttm) REVERT: E 216 ILE cc_start: 0.7473 (tt) cc_final: 0.7133 (pp) REVERT: E 224 ASP cc_start: 0.7032 (m-30) cc_final: 0.6784 (m-30) REVERT: E 237 ILE cc_start: 0.7646 (mt) cc_final: 0.7356 (mp) REVERT: E 246 MET cc_start: 0.7393 (mtm) cc_final: 0.4923 (pp-130) REVERT: E 307 GLU cc_start: 0.7118 (tp30) cc_final: 0.6876 (mt-10) REVERT: G 438 ASN cc_start: 0.7755 (t0) cc_final: 0.7385 (t0) REVERT: G 449 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.6885 (ttm110) REVERT: G 535 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6979 (mt-10) REVERT: G 550 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6875 (p90) REVERT: G 565 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6291 (m-30) outliers start: 134 outliers final: 58 residues processed: 386 average time/residue: 0.5636 time to fit residues: 246.8036 Evaluate side-chains 331 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 989 ARG Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 20 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN A 159 ASN A 593 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 85 GLN B 87 HIS B 125 ASN C 152 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS D 303 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.198174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146020 restraints weight = 21595.037| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.83 r_work: 0.3520 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20383 Z= 0.153 Angle : 0.674 9.005 27616 Z= 0.350 Chirality : 0.044 0.251 2988 Planarity : 0.006 0.071 3562 Dihedral : 7.981 70.510 2727 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.16 % Favored : 91.64 % Rotamer: Outliers : 5.98 % Allowed : 25.41 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.09 (0.16), residues: 2415 helix: 0.02 (0.16), residues: 991 sheet: -1.81 (0.34), residues: 224 loop : -2.62 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 366 TYR 0.036 0.002 TYR C 70 PHE 0.021 0.002 PHE A1031 TRP 0.012 0.001 TRP A 792 HIS 0.005 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00364 (20367) covalent geometry : angle 0.67416 (27613) hydrogen bonds : bond 0.04910 ( 711) hydrogen bonds : angle 4.67174 ( 2013) metal coordination : bond 0.00673 ( 16) metal coordination : angle 1.70889 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 273 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 208 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7387 (ttm-80) REVERT: F 220 GLU cc_start: 0.5432 (pm20) cc_final: 0.4834 (pm20) REVERT: F 361 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7637 (ttmm) REVERT: F 367 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7669 (tppt) REVERT: F 368 LYS cc_start: 0.7636 (ptpp) cc_final: 0.7171 (pptt) REVERT: F 373 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6955 (p) REVERT: A 181 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 182 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: A 226 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: A 342 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6827 (mtt90) REVERT: A 423 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6556 (ptt-90) REVERT: A 439 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5098 (tp30) REVERT: A 496 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7022 (mtm-85) REVERT: A 527 LYS cc_start: 0.6756 (tptt) cc_final: 0.5714 (mppt) REVERT: A 554 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.7043 (ptt90) REVERT: A 859 HIS cc_start: 0.7412 (t-90) cc_final: 0.6938 (m90) REVERT: A 903 GLU cc_start: 0.5839 (mm-30) cc_final: 0.4909 (mm-30) REVERT: A 970 ILE cc_start: 0.8169 (pt) cc_final: 0.7912 (pt) REVERT: A 982 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7145 (tpp-160) REVERT: A 989 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7583 (mtm180) REVERT: B 45 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6381 (p90) REVERT: B 74 TRP cc_start: 0.8517 (t60) cc_final: 0.8135 (t-100) REVERT: B 88 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 323 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: C 64 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7535 (tt) REVERT: C 68 HIS cc_start: 0.6554 (m-70) cc_final: 0.5565 (t-90) REVERT: C 75 MET cc_start: 0.7578 (pp-130) cc_final: 0.6965 (ptp) REVERT: C 86 TYR cc_start: 0.7627 (m-80) cc_final: 0.7366 (m-80) REVERT: C 164 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: C 197 LYS cc_start: 0.6942 (tmtt) cc_final: 0.6313 (ttpt) REVERT: C 388 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7912 (ppp) REVERT: C 407 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8037 (tt) REVERT: D 241 LYS cc_start: 0.6692 (mtmm) cc_final: 0.6171 (mtmt) REVERT: D 266 THR cc_start: 0.6213 (OUTLIER) cc_final: 0.5984 (t) REVERT: D 304 TYR cc_start: 0.7276 (m-10) cc_final: 0.7030 (m-10) REVERT: D 325 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7107 (tp40) REVERT: E 169 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7085 (mttm) REVERT: E 237 ILE cc_start: 0.7571 (mt) cc_final: 0.7176 (mp) REVERT: E 241 LYS cc_start: 0.6665 (ptpt) cc_final: 0.5609 (ttpt) REVERT: E 246 MET cc_start: 0.7245 (mtm) cc_final: 0.4938 (pp-130) REVERT: G 294 ILE cc_start: 0.3123 (OUTLIER) cc_final: 0.2705 (mp) REVERT: G 334 MET cc_start: 0.6976 (mpp) cc_final: 0.6763 (mpt) REVERT: G 341 LEU cc_start: 0.3868 (OUTLIER) cc_final: 0.3488 (mt) REVERT: G 371 MET cc_start: 0.7210 (ptm) cc_final: 0.6926 (ptm) REVERT: G 397 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (tp) REVERT: G 400 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7342 (ptmt) REVERT: G 438 ASN cc_start: 0.7709 (t0) cc_final: 0.7420 (t0) REVERT: G 449 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.6953 (ttm110) REVERT: G 535 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6968 (mt-10) REVERT: G 550 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6944 (p90) REVERT: G 565 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6289 (m-30) outliers start: 131 outliers final: 64 residues processed: 374 average time/residue: 0.5684 time to fit residues: 241.5941 Evaluate side-chains 339 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 253 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 137 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 177 optimal weight: 0.3980 chunk 95 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 593 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 85 GLN B 87 HIS B 125 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS E 201 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 357 HIS G 483 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.198619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146267 restraints weight = 21445.584| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.79 r_work: 0.3524 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20383 Z= 0.135 Angle : 0.646 9.189 27616 Z= 0.335 Chirality : 0.043 0.281 2988 Planarity : 0.005 0.072 3562 Dihedral : 7.668 67.934 2725 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 5.47 % Allowed : 26.64 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.84 (0.16), residues: 2415 helix: 0.23 (0.16), residues: 993 sheet: -1.62 (0.35), residues: 219 loop : -2.48 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 366 TYR 0.024 0.002 TYR C 151 PHE 0.021 0.001 PHE B 249 TRP 0.011 0.001 TRP A 792 HIS 0.007 0.001 HIS G 357 Details of bonding type rmsd covalent geometry : bond 0.00317 (20367) covalent geometry : angle 0.64631 (27613) hydrogen bonds : bond 0.04471 ( 711) hydrogen bonds : angle 4.50876 ( 2013) metal coordination : bond 0.00472 ( 16) metal coordination : angle 1.13372 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 273 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 208 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7359 (ttm-80) REVERT: F 220 GLU cc_start: 0.5355 (pm20) cc_final: 0.4747 (pm20) REVERT: F 361 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7697 (ttmm) REVERT: F 367 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7671 (tppt) REVERT: F 368 LYS cc_start: 0.7640 (ptpp) cc_final: 0.6873 (tptt) REVERT: F 373 VAL cc_start: 0.7155 (OUTLIER) cc_final: 0.6927 (p) REVERT: A 44 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 181 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8192 (m) REVERT: A 182 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: A 226 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8709 (mt0) REVERT: A 342 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6775 (mtt90) REVERT: A 423 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6660 (ptt-90) REVERT: A 439 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.4971 (tp30) REVERT: A 496 ARG cc_start: 0.7256 (mtt180) cc_final: 0.7012 (mtm-85) REVERT: A 527 LYS cc_start: 0.6829 (tptt) cc_final: 0.5853 (mppt) REVERT: A 552 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8064 (ptp90) REVERT: A 554 ARG cc_start: 0.7348 (ptm-80) cc_final: 0.6908 (ptt90) REVERT: A 859 HIS cc_start: 0.7330 (t-90) cc_final: 0.6870 (m90) REVERT: A 903 GLU cc_start: 0.5818 (mm-30) cc_final: 0.4826 (mm-30) REVERT: A 982 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7091 (tpp-160) REVERT: A 989 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7513 (mtm180) REVERT: A 1013 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6413 (tpm170) REVERT: B 45 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6333 (p90) REVERT: B 51 ILE cc_start: 0.8530 (mt) cc_final: 0.8323 (mt) REVERT: B 63 ARG cc_start: 0.7308 (ttm170) cc_final: 0.6722 (mtp85) REVERT: B 74 TRP cc_start: 0.8470 (t60) cc_final: 0.8048 (t-100) REVERT: C 64 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7519 (tt) REVERT: C 68 HIS cc_start: 0.6539 (m-70) cc_final: 0.5587 (t-90) REVERT: C 75 MET cc_start: 0.7500 (pp-130) cc_final: 0.6972 (ptp) REVERT: C 86 TYR cc_start: 0.7661 (m-80) cc_final: 0.7358 (m-80) REVERT: C 197 LYS cc_start: 0.6994 (tmtt) cc_final: 0.6401 (ttpt) REVERT: C 306 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7329 (pt) REVERT: C 388 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7869 (ppp) REVERT: C 407 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8038 (tt) REVERT: D 241 LYS cc_start: 0.6691 (mtmm) cc_final: 0.6089 (ptpt) REVERT: D 304 TYR cc_start: 0.7304 (m-10) cc_final: 0.7066 (m-10) REVERT: D 325 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7103 (tp40) REVERT: E 237 ILE cc_start: 0.7539 (mt) cc_final: 0.7224 (mp) REVERT: E 246 MET cc_start: 0.7297 (mtm) cc_final: 0.4898 (pp-130) REVERT: G 294 ILE cc_start: 0.3005 (OUTLIER) cc_final: 0.2788 (mp) REVERT: G 352 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: G 397 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8241 (tp) REVERT: G 400 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7445 (ptmt) REVERT: G 438 ASN cc_start: 0.7711 (t0) cc_final: 0.7464 (t0) REVERT: G 449 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.6991 (ttm110) REVERT: G 535 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6911 (mt-10) REVERT: G 550 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6948 (p90) REVERT: G 565 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6290 (m-30) outliers start: 120 outliers final: 58 residues processed: 361 average time/residue: 0.6182 time to fit residues: 252.2514 Evaluate side-chains 324 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 109 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 593 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 85 GLN B 87 HIS B 88 GLN B 125 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.197700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145891 restraints weight = 21428.829| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.85 r_work: 0.3519 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20383 Z= 0.149 Angle : 0.661 9.426 27616 Z= 0.340 Chirality : 0.044 0.244 2988 Planarity : 0.005 0.069 3562 Dihedral : 7.498 68.635 2719 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 5.38 % Allowed : 26.87 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.70 (0.17), residues: 2415 helix: 0.28 (0.16), residues: 1000 sheet: -1.45 (0.34), residues: 219 loop : -2.38 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 366 TYR 0.032 0.002 TYR C 70 PHE 0.022 0.002 PHE B 249 TRP 0.010 0.001 TRP A 792 HIS 0.006 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00358 (20367) covalent geometry : angle 0.66116 (27613) hydrogen bonds : bond 0.04679 ( 711) hydrogen bonds : angle 4.50854 ( 2013) metal coordination : bond 0.00454 ( 16) metal coordination : angle 0.99532 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 259 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.8014 (t) REVERT: F 208 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7238 (ttm-80) REVERT: F 215 LYS cc_start: 0.5156 (mmmm) cc_final: 0.4804 (mmmm) REVERT: F 220 GLU cc_start: 0.5422 (pm20) cc_final: 0.4862 (pm20) REVERT: F 361 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7771 (ttmm) REVERT: F 367 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7657 (tppt) REVERT: F 368 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7168 (pptt) REVERT: A 44 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 182 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: A 226 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8756 (mt0) REVERT: A 342 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6777 (mtt90) REVERT: A 439 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5049 (tp30) REVERT: A 496 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6974 (mtm-85) REVERT: A 527 LYS cc_start: 0.6867 (tptt) cc_final: 0.5879 (mppt) REVERT: A 554 ARG cc_start: 0.7310 (ptm-80) cc_final: 0.6831 (ptt90) REVERT: A 566 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 859 HIS cc_start: 0.7404 (t-90) cc_final: 0.6935 (m90) REVERT: A 896 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: A 903 GLU cc_start: 0.5943 (mm-30) cc_final: 0.5666 (mm-30) REVERT: A 982 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7099 (tpp-160) REVERT: A 989 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7597 (mtm180) REVERT: A 1013 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6313 (tpm170) REVERT: B 45 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6374 (p90) REVERT: B 51 ILE cc_start: 0.8553 (mt) cc_final: 0.8344 (mt) REVERT: B 57 THR cc_start: 0.8233 (p) cc_final: 0.7788 (m) REVERT: B 63 ARG cc_start: 0.7309 (ttm170) cc_final: 0.6710 (mtp85) REVERT: B 74 TRP cc_start: 0.8489 (t60) cc_final: 0.8048 (t-100) REVERT: B 92 ASN cc_start: 0.8262 (t0) cc_final: 0.7858 (t0) REVERT: C 64 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7526 (tt) REVERT: C 68 HIS cc_start: 0.6413 (m-70) cc_final: 0.5494 (t-90) REVERT: C 75 MET cc_start: 0.7449 (pp-130) cc_final: 0.6971 (ptp) REVERT: C 86 TYR cc_start: 0.7633 (m-80) cc_final: 0.7380 (m-80) REVERT: C 164 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: C 178 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5763 (p90) REVERT: C 197 LYS cc_start: 0.7092 (tmtt) cc_final: 0.6514 (ttpt) REVERT: C 306 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7286 (pt) REVERT: C 388 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7813 (ppp) REVERT: C 407 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 304 TYR cc_start: 0.7301 (m-10) cc_final: 0.7084 (m-10) REVERT: D 325 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7162 (tp40) REVERT: E 169 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7212 (mttm) REVERT: E 216 ILE cc_start: 0.7420 (pp) cc_final: 0.6945 (mm) REVERT: E 221 ASN cc_start: 0.8429 (p0) cc_final: 0.8048 (p0) REVERT: E 237 ILE cc_start: 0.7365 (mt) cc_final: 0.7037 (mp) REVERT: E 246 MET cc_start: 0.7332 (mtm) cc_final: 0.4909 (pp-130) REVERT: G 397 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8211 (tp) REVERT: G 400 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7465 (ptmt) REVERT: G 438 ASN cc_start: 0.7765 (t0) cc_final: 0.7508 (t0) REVERT: G 449 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.6983 (ttm110) REVERT: G 535 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6919 (mt-10) REVERT: G 550 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6879 (p90) REVERT: G 565 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6324 (m-30) outliers start: 118 outliers final: 66 residues processed: 345 average time/residue: 0.5551 time to fit residues: 217.3843 Evaluate side-chains 328 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 76 optimal weight: 0.0670 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 177 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 593 HIS A 998 GLN B 24 GLN B 85 GLN B 87 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.199396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147696 restraints weight = 21342.835| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.85 r_work: 0.3538 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20383 Z= 0.125 Angle : 0.631 9.494 27616 Z= 0.324 Chirality : 0.042 0.201 2988 Planarity : 0.005 0.069 3562 Dihedral : 7.220 66.060 2719 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.12 % Favored : 91.76 % Rotamer: Outliers : 5.25 % Allowed : 27.10 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.47 (0.17), residues: 2415 helix: 0.53 (0.17), residues: 992 sheet: -1.31 (0.35), residues: 219 loop : -2.30 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 366 TYR 0.027 0.001 TYR C 70 PHE 0.022 0.001 PHE A1031 TRP 0.009 0.001 TRP C 212 HIS 0.005 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00295 (20367) covalent geometry : angle 0.63069 (27613) hydrogen bonds : bond 0.04150 ( 711) hydrogen bonds : angle 4.39971 ( 2013) metal coordination : bond 0.00401 ( 16) metal coordination : angle 0.87746 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 260 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6152 (OUTLIER) cc_final: 0.5843 (t) REVERT: F 207 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.8083 (t) REVERT: F 215 LYS cc_start: 0.5096 (mmmm) cc_final: 0.4776 (mmmm) REVERT: F 220 GLU cc_start: 0.5439 (pm20) cc_final: 0.4801 (pm20) REVERT: F 361 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7664 (ttmm) REVERT: F 367 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7641 (tppt) REVERT: F 368 LYS cc_start: 0.7673 (ptpp) cc_final: 0.7107 (pptt) REVERT: A 44 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: A 182 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: A 226 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: A 342 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6711 (mtt90) REVERT: A 423 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6690 (ptt-90) REVERT: A 439 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5043 (tp30) REVERT: A 496 ARG cc_start: 0.7233 (mtt180) cc_final: 0.7003 (mtm-85) REVERT: A 552 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7656 (ptp90) REVERT: A 554 ARG cc_start: 0.7203 (ptm-80) cc_final: 0.6870 (ptt90) REVERT: A 566 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 791 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5242 (tt) REVERT: A 896 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: A 903 GLU cc_start: 0.5764 (mm-30) cc_final: 0.4826 (mm-30) REVERT: A 982 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7064 (tpp-160) REVERT: A 989 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7500 (mtm180) REVERT: A 1013 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6189 (tpm170) REVERT: B 45 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6318 (p90) REVERT: B 51 ILE cc_start: 0.8507 (mt) cc_final: 0.8299 (mt) REVERT: B 57 THR cc_start: 0.8216 (p) cc_final: 0.7776 (m) REVERT: B 63 ARG cc_start: 0.7227 (ttm170) cc_final: 0.6614 (mtp85) REVERT: B 74 TRP cc_start: 0.8464 (t60) cc_final: 0.8091 (t-100) REVERT: B 92 ASN cc_start: 0.8150 (t0) cc_final: 0.7823 (t0) REVERT: B 323 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6927 (tp30) REVERT: C 68 HIS cc_start: 0.6374 (m-70) cc_final: 0.5565 (t-90) REVERT: C 75 MET cc_start: 0.7379 (pp-130) cc_final: 0.6945 (ptp) REVERT: C 86 TYR cc_start: 0.7602 (m-80) cc_final: 0.7342 (m-80) REVERT: C 164 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: C 197 LYS cc_start: 0.7177 (tmtt) cc_final: 0.6554 (ttpt) REVERT: C 238 SER cc_start: 0.6786 (OUTLIER) cc_final: 0.6502 (m) REVERT: C 280 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.5580 (t-90) REVERT: C 306 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7347 (pt) REVERT: C 407 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7990 (tt) REVERT: D 304 TYR cc_start: 0.7252 (m-10) cc_final: 0.7017 (m-10) REVERT: D 319 TYR cc_start: 0.7453 (m-80) cc_final: 0.7211 (m-10) REVERT: E 169 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7282 (mttm) REVERT: E 237 ILE cc_start: 0.7276 (mt) cc_final: 0.6936 (mp) REVERT: E 246 MET cc_start: 0.7221 (mtm) cc_final: 0.4843 (pp-130) REVERT: G 397 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8175 (tp) REVERT: G 400 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7451 (ptmt) REVERT: G 438 ASN cc_start: 0.7604 (t0) cc_final: 0.7376 (t0) REVERT: G 449 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.6958 (ttm110) REVERT: G 535 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6792 (mt-10) REVERT: G 550 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7081 (p90) REVERT: G 565 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6381 (m-30) outliers start: 115 outliers final: 57 residues processed: 345 average time/residue: 0.6096 time to fit residues: 238.5876 Evaluate side-chains 318 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 238 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 118 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN A 159 ASN A 593 HIS A 777 GLN A 998 GLN B 85 GLN B 87 HIS B 369 ASN C 63 GLN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.193709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139516 restraints weight = 21313.418| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.93 r_work: 0.3445 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20383 Z= 0.252 Angle : 0.776 11.340 27616 Z= 0.398 Chirality : 0.049 0.262 2988 Planarity : 0.006 0.070 3562 Dihedral : 7.579 75.825 2712 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.32 % Favored : 90.52 % Rotamer: Outliers : 5.52 % Allowed : 27.33 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.81 (0.16), residues: 2415 helix: 0.06 (0.16), residues: 1002 sheet: -1.49 (0.35), residues: 221 loop : -2.33 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 75 TYR 0.033 0.003 TYR B 300 PHE 0.039 0.003 PHE A 381 TRP 0.017 0.002 TRP A 792 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00624 (20367) covalent geometry : angle 0.77599 (27613) hydrogen bonds : bond 0.06260 ( 711) hydrogen bonds : angle 4.81354 ( 2013) metal coordination : bond 0.00706 ( 16) metal coordination : angle 1.41658 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 262 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5844 (t) REVERT: F 215 LYS cc_start: 0.5466 (mmmm) cc_final: 0.5128 (mmmm) REVERT: F 220 GLU cc_start: 0.5549 (pm20) cc_final: 0.4876 (pm20) REVERT: F 358 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: F 361 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7648 (ttmm) REVERT: F 367 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7683 (tppt) REVERT: A 182 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 342 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6721 (mtt90) REVERT: A 351 ILE cc_start: 0.7460 (mm) cc_final: 0.7259 (tt) REVERT: A 423 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6881 (ptt-90) REVERT: A 443 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6352 (mt) REVERT: A 527 LYS cc_start: 0.6884 (tptt) cc_final: 0.5862 (mppt) REVERT: A 566 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 801 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7715 (t0) REVERT: A 859 HIS cc_start: 0.7590 (t-90) cc_final: 0.7137 (m90) REVERT: A 982 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7242 (tpp-160) REVERT: A 989 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (mtm180) REVERT: A 1013 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6299 (tpm170) REVERT: B 45 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6366 (p90) REVERT: B 57 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7848 (m) REVERT: B 63 ARG cc_start: 0.7645 (ttm170) cc_final: 0.6954 (mtp180) REVERT: B 74 TRP cc_start: 0.8482 (t60) cc_final: 0.8014 (t-100) REVERT: B 92 ASN cc_start: 0.8582 (t0) cc_final: 0.8143 (t0) REVERT: B 323 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: C 64 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7486 (tt) REVERT: C 68 HIS cc_start: 0.6331 (m-70) cc_final: 0.5580 (t-90) REVERT: C 75 MET cc_start: 0.7758 (pp-130) cc_final: 0.7034 (ptp) REVERT: C 164 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: C 197 LYS cc_start: 0.7376 (tmtt) cc_final: 0.6668 (ttpt) REVERT: C 388 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7898 (ppp) REVERT: D 241 LYS cc_start: 0.7271 (mtmm) cc_final: 0.6453 (tmtt) REVERT: D 261 GLN cc_start: 0.7270 (mt0) cc_final: 0.7010 (mt0) REVERT: E 169 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7233 (mttm) REVERT: E 216 ILE cc_start: 0.7263 (pp) cc_final: 0.6835 (mm) REVERT: E 246 MET cc_start: 0.7329 (mtm) cc_final: 0.4783 (pp-130) REVERT: E 286 GLU cc_start: 0.7389 (tp30) cc_final: 0.7076 (tp30) REVERT: G 371 MET cc_start: 0.7208 (ptm) cc_final: 0.6989 (ptm) REVERT: G 397 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8277 (tp) REVERT: G 400 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7497 (ptmt) REVERT: G 438 ASN cc_start: 0.7976 (t0) cc_final: 0.7688 (t0) REVERT: G 449 ARG cc_start: 0.7746 (mtp-110) cc_final: 0.7078 (ttm110) REVERT: G 535 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7113 (mt-10) REVERT: G 565 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6520 (m-30) outliers start: 121 outliers final: 68 residues processed: 353 average time/residue: 0.6441 time to fit residues: 256.4411 Evaluate side-chains 330 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 989 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 226 GLN A 461 HIS A 593 HIS A 998 GLN B 85 GLN B 87 HIS C 183 HIS G 352 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.196805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144694 restraints weight = 21177.254| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.86 r_work: 0.3500 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20383 Z= 0.150 Angle : 0.682 9.359 27616 Z= 0.352 Chirality : 0.045 0.414 2988 Planarity : 0.006 0.076 3562 Dihedral : 7.193 69.731 2709 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.74 % Favored : 92.13 % Rotamer: Outliers : 4.52 % Allowed : 28.51 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.55 (0.17), residues: 2415 helix: 0.39 (0.16), residues: 999 sheet: -1.39 (0.35), residues: 219 loop : -2.26 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 366 TYR 0.024 0.002 TYR C 178 PHE 0.030 0.002 PHE B 249 TRP 0.012 0.001 TRP A 412 HIS 0.018 0.001 HIS A 461 Details of bonding type rmsd covalent geometry : bond 0.00363 (20367) covalent geometry : angle 0.68226 (27613) hydrogen bonds : bond 0.04741 ( 711) hydrogen bonds : angle 4.56300 ( 2013) metal coordination : bond 0.00537 ( 16) metal coordination : angle 0.93512 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 261 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6001 (OUTLIER) cc_final: 0.5772 (t) REVERT: F 208 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7524 (mtm-85) REVERT: F 215 LYS cc_start: 0.5489 (mmmm) cc_final: 0.5166 (mmmm) REVERT: F 220 GLU cc_start: 0.5423 (pm20) cc_final: 0.4839 (pm20) REVERT: F 361 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7555 (ttmm) REVERT: F 367 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7732 (tppt) REVERT: F 368 LYS cc_start: 0.7523 (ptpp) cc_final: 0.6704 (tptt) REVERT: A 44 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 182 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 342 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6676 (mtt90) REVERT: A 423 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6760 (ptt-90) REVERT: A 443 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6455 (mt) REVERT: A 554 ARG cc_start: 0.7383 (ptm-80) cc_final: 0.6893 (ptt90) REVERT: A 566 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 801 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7692 (t0) REVERT: A 859 HIS cc_start: 0.7487 (t-90) cc_final: 0.7034 (m90) REVERT: A 982 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7116 (tpp-160) REVERT: A 989 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7523 (mtm180) REVERT: B 45 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6259 (p90) REVERT: B 51 ILE cc_start: 0.8568 (mt) cc_final: 0.8250 (mt) REVERT: B 57 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7798 (m) REVERT: B 63 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6710 (mtp180) REVERT: B 74 TRP cc_start: 0.8439 (t60) cc_final: 0.8073 (t-100) REVERT: B 75 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7027 (ptt180) REVERT: B 92 ASN cc_start: 0.8505 (t0) cc_final: 0.8123 (t0) REVERT: B 323 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: B 329 ASP cc_start: 0.8672 (m-30) cc_final: 0.8461 (m-30) REVERT: C 68 HIS cc_start: 0.6276 (m-70) cc_final: 0.5560 (t-90) REVERT: C 75 MET cc_start: 0.7702 (pp-130) cc_final: 0.7018 (ptp) REVERT: C 197 LYS cc_start: 0.7307 (tmtt) cc_final: 0.6663 (ttpt) REVERT: C 306 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7221 (pt) REVERT: C 394 TYR cc_start: 0.6325 (m-10) cc_final: 0.6115 (m-10) REVERT: C 407 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8048 (tt) REVERT: D 241 LYS cc_start: 0.7411 (mtmm) cc_final: 0.6693 (tmtt) REVERT: D 261 GLN cc_start: 0.7249 (mt0) cc_final: 0.6984 (mt0) REVERT: E 169 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7248 (mttm) REVERT: E 216 ILE cc_start: 0.7117 (pp) cc_final: 0.6697 (mm) REVERT: E 237 ILE cc_start: 0.7360 (mt) cc_final: 0.7038 (mm) REVERT: E 246 MET cc_start: 0.7182 (mtm) cc_final: 0.4806 (pp-130) REVERT: E 270 ASP cc_start: 0.4131 (OUTLIER) cc_final: 0.2477 (p0) REVERT: G 397 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8256 (tp) REVERT: G 400 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7524 (ptmt) REVERT: G 438 ASN cc_start: 0.7776 (t0) cc_final: 0.7544 (t0) REVERT: G 449 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7039 (ttm110) REVERT: G 535 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7051 (mt-10) REVERT: G 540 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7612 (tp) REVERT: G 550 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.6685 (p90) REVERT: G 565 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6460 (m-30) outliers start: 99 outliers final: 57 residues processed: 334 average time/residue: 0.6092 time to fit residues: 231.0683 Evaluate side-chains 329 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 92 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 183 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 226 GLN A 461 HIS A 593 HIS ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 87 HIS C 183 HIS G 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.195570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143581 restraints weight = 21215.561| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.85 r_work: 0.3479 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20383 Z= 0.181 Angle : 0.716 10.046 27616 Z= 0.369 Chirality : 0.046 0.445 2988 Planarity : 0.006 0.077 3562 Dihedral : 7.201 71.870 2708 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.85 % Rotamer: Outliers : 4.29 % Allowed : 28.60 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.55 (0.17), residues: 2415 helix: 0.36 (0.16), residues: 994 sheet: -1.35 (0.36), residues: 220 loop : -2.24 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 366 TYR 0.025 0.002 TYR B 300 PHE 0.034 0.002 PHE B 249 TRP 0.015 0.002 TRP A 412 HIS 0.010 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00443 (20367) covalent geometry : angle 0.71545 (27613) hydrogen bonds : bond 0.05264 ( 711) hydrogen bonds : angle 4.63484 ( 2013) metal coordination : bond 0.00627 ( 16) metal coordination : angle 1.28684 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.5923 (OUTLIER) cc_final: 0.5723 (t) REVERT: F 208 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7593 (mtm-85) REVERT: F 215 LYS cc_start: 0.5889 (mmmm) cc_final: 0.5576 (mmmm) REVERT: F 220 GLU cc_start: 0.5414 (pm20) cc_final: 0.4844 (pm20) REVERT: F 361 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7560 (ttmm) REVERT: F 367 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7720 (tppt) REVERT: F 368 LYS cc_start: 0.7502 (ptpp) cc_final: 0.6638 (tptt) REVERT: A 44 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 182 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: A 342 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6675 (mtt90) REVERT: A 423 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6818 (ptt-90) REVERT: A 443 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6456 (mt) REVERT: A 554 ARG cc_start: 0.7382 (ptm-80) cc_final: 0.6882 (ptt90) REVERT: A 566 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 801 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7719 (t0) REVERT: A 859 HIS cc_start: 0.7580 (t-90) cc_final: 0.7109 (m90) REVERT: A 903 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5862 (mm-30) REVERT: A 982 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7133 (tpp-160) REVERT: A 989 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7618 (mtm180) REVERT: B 45 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.6273 (p90) REVERT: B 57 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7804 (m) REVERT: B 63 ARG cc_start: 0.7556 (ttm170) cc_final: 0.6889 (mtp180) REVERT: B 74 TRP cc_start: 0.8440 (t60) cc_final: 0.8078 (t-100) REVERT: B 75 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7106 (ptt180) REVERT: B 92 ASN cc_start: 0.8490 (t0) cc_final: 0.8102 (t0) REVERT: B 323 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7015 (tp30) REVERT: B 329 ASP cc_start: 0.8671 (m-30) cc_final: 0.8461 (m-30) REVERT: C 64 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7489 (tt) REVERT: C 68 HIS cc_start: 0.6336 (m-70) cc_final: 0.5611 (t-90) REVERT: C 75 MET cc_start: 0.7716 (pp-130) cc_final: 0.6986 (ptp) REVERT: C 197 LYS cc_start: 0.7392 (tmtt) cc_final: 0.6701 (ttpt) REVERT: C 306 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7126 (pt) REVERT: D 241 LYS cc_start: 0.7528 (mtmm) cc_final: 0.6781 (tmtt) REVERT: D 261 GLN cc_start: 0.7277 (mt0) cc_final: 0.6996 (mt0) REVERT: E 169 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7462 (mttm) REVERT: E 216 ILE cc_start: 0.7160 (pp) cc_final: 0.6728 (mm) REVERT: E 246 MET cc_start: 0.7284 (mtm) cc_final: 0.4895 (pp-130) REVERT: E 270 ASP cc_start: 0.4417 (OUTLIER) cc_final: 0.2643 (p0) REVERT: E 286 GLU cc_start: 0.7324 (tp30) cc_final: 0.6966 (tp30) REVERT: G 397 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8271 (tp) REVERT: G 400 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7516 (ptmt) REVERT: G 438 ASN cc_start: 0.7831 (t0) cc_final: 0.7589 (t0) REVERT: G 449 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7032 (ttm110) REVERT: G 535 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7024 (mt-10) REVERT: G 540 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7703 (tp) REVERT: G 550 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6630 (p90) REVERT: G 565 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6486 (m-30) outliers start: 94 outliers final: 65 residues processed: 328 average time/residue: 0.6047 time to fit residues: 225.2730 Evaluate side-chains 334 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 251 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 132 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN A 461 HIS A 593 HIS A 998 GLN B 87 HIS C 183 HIS ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145215 restraints weight = 21230.272| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.83 r_work: 0.3514 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20383 Z= 0.144 Angle : 0.667 10.477 27616 Z= 0.344 Chirality : 0.044 0.435 2988 Planarity : 0.006 0.076 3562 Dihedral : 7.001 68.706 2708 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.03 % Favored : 91.84 % Rotamer: Outliers : 3.83 % Allowed : 29.11 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.35 (0.17), residues: 2415 helix: 0.59 (0.17), residues: 982 sheet: -1.16 (0.37), residues: 207 loop : -2.18 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 366 TYR 0.027 0.002 TYR A 574 PHE 0.035 0.002 PHE A 889 TRP 0.017 0.002 TRP A1042 HIS 0.011 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00346 (20367) covalent geometry : angle 0.66652 (27613) hydrogen bonds : bond 0.04546 ( 711) hydrogen bonds : angle 4.51309 ( 2013) metal coordination : bond 0.00581 ( 16) metal coordination : angle 1.09143 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8870.60 seconds wall clock time: 151 minutes 27.28 seconds (9087.28 seconds total)