Starting phenix.real_space_refine on Tue Jun 17 11:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i02_35092/06_2025/8i02_35092_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i02_35092/06_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_35092/06_2025/8i02_35092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i02_35092/06_2025/8i02_35092.map" model { file = "/net/cci-nas-00/data/ceres_data/8i02_35092/06_2025/8i02_35092_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i02_35092/06_2025/8i02_35092_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 3} 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: 12.87, per 1000 atoms: 0.65 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: 5.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.23 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: 6.30 Time building geometry restraints manager: 6.21 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.310 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.053 0.004 TRP A 361 HIS 0.009 0.002 HIS B 207 PHE 0.078 0.003 PHE A 381 TYR 0.027 0.003 TYR A 891 ARG 0.016 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.17381 ( 711) hydrogen bonds : angle 7.11389 ( 2013) metal coordination : bond 0.29140 ( 16) metal coordination : angle 15.60505 ( 3) covalent geometry : bond 0.00984 (20367) covalent geometry : angle 1.02985 (27613) *********************** 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 : 2.272 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: 0.6889 (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: 0.7461 (mt-10) REVERT: A 346 VAL cc_start: 0.6422 (t) cc_final: 0.6162 (m) REVERT: A 374 TRP cc_start: 0.4310 (OUTLIER) cc_final: 0.3769 (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: 0.5037 (tp30) REVERT: A 446 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7029 (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: 0.7177 (t80) REVERT: A 742 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (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: 0.8011 (m) 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: 0.6723 (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: 0.6514 (t) REVERT: C 197 LYS cc_start: 0.6837 (tmtt) cc_final: 0.6443 (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: 0.1565 (t0) REVERT: C 306 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7170 (pt) REVERT: D 261 GLN cc_start: 0.7061 (mt0) cc_final: 0.6820 (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: 56 residues processed: 600 average time/residue: 1.1110 time to fit residues: 764.9266 Evaluate side-chains 338 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 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 279 GLU 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 205 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 777 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS 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 188 ASN 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 = 0.4279 r_free = 0.4279 target = 0.200744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148820 restraints weight = 21597.015| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.79 r_work: 0.3569 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20383 Z= 0.158 Angle : 0.726 9.543 27616 Z= 0.380 Chirality : 0.046 0.224 2988 Planarity : 0.006 0.071 3562 Dihedral : 9.274 71.852 2805 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.53 % Favored : 91.22 % Rotamer: Outliers : 6.43 % Allowed : 24.95 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.15), residues: 2415 helix: -0.80 (0.16), residues: 980 sheet: -2.43 (0.33), residues: 207 loop : -3.15 (0.15), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 792 HIS 0.006 0.001 HIS B 36 PHE 0.023 0.002 PHE E 239 TYR 0.035 0.002 TYR C 70 ARG 0.007 0.001 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 711) hydrogen bonds : angle 5.03415 ( 2013) metal coordination : bond 0.02866 ( 16) metal coordination : angle 3.68685 ( 3) covalent geometry : bond 0.00358 (20367) covalent geometry : angle 0.72483 (27613) *********************** 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 459 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 318 time to evaluate : 5.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7906 (t) REVERT: F 220 GLU cc_start: 0.5422 (pm20) cc_final: 0.4762 (pm20) REVERT: F 360 LYS cc_start: 0.7423 (ttpp) cc_final: 0.6697 (mtmt) REVERT: F 361 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7218 (mttm) REVERT: F 368 LYS cc_start: 0.7636 (ptpp) cc_final: 0.6823 (tptt) REVERT: F 373 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6558 (p) REVERT: A 79 GLU cc_start: 0.8141 (pt0) cc_final: 0.7671 (mt-10) REVERT: A 182 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: A 226 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: A 299 PHE cc_start: 0.8342 (t80) cc_final: 0.8130 (t80) REVERT: A 351 ILE cc_start: 0.7589 (mm) cc_final: 0.7272 (tt) REVERT: A 374 TRP cc_start: 0.4102 (OUTLIER) cc_final: 0.3594 (t60) REVERT: A 386 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6227 (mtpp) REVERT: A 439 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5160 (tp30) REVERT: A 460 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6157 (tp30) REVERT: A 496 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6983 (mtm-85) REVERT: A 527 LYS cc_start: 0.6932 (tptt) cc_final: 0.5764 (mppt) REVERT: A 619 ARG cc_start: 0.5445 (ptp-110) cc_final: 0.4813 (mtm-85) REVERT: A 795 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7679 (mtp85) REVERT: A 989 ARG cc_start: 0.8092 (mmt90) cc_final: 0.7663 (mtm180) REVERT: B 57 THR cc_start: 0.8343 (p) cc_final: 0.7897 (m) REVERT: C 75 MET cc_start: 0.7681 (pp-130) cc_final: 0.6696 (ptp) REVERT: C 86 TYR cc_start: 0.7736 (m-80) cc_final: 0.7389 (m-80) REVERT: C 175 LYS cc_start: 0.7548 (pptt) cc_final: 0.6573 (tppt) REVERT: C 197 LYS cc_start: 0.6934 (tmtt) cc_final: 0.6122 (ttpt) REVERT: C 235 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6493 (ttmt) REVERT: C 306 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6885 (pp) REVERT: D 215 LYS cc_start: 0.6154 (tptt) cc_final: 0.5871 (tmtm) REVERT: D 241 LYS cc_start: 0.6330 (mtmm) cc_final: 0.5974 (mtmt) REVERT: D 246 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7230 (pmt) REVERT: D 261 GLN cc_start: 0.6545 (mt0) cc_final: 0.6147 (mm-40) REVERT: D 266 THR cc_start: 0.6102 (OUTLIER) cc_final: 0.5726 (t) REVERT: D 319 TYR cc_start: 0.6869 (m-10) cc_final: 0.6467 (m-10) REVERT: E 169 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7077 (mttp) REVERT: E 216 ILE cc_start: 0.7639 (tt) cc_final: 0.7425 (pp) REVERT: E 237 ILE cc_start: 0.7551 (mt) cc_final: 0.7342 (mp) REVERT: G 344 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.4954 (t80) REVERT: G 438 ASN cc_start: 0.7378 (t0) cc_final: 0.7086 (t0) REVERT: G 535 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6964 (mt-10) REVERT: G 550 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7077 (p90) REVERT: G 565 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6149 (m-30) outliers start: 141 outliers final: 52 residues processed: 426 average time/residue: 1.2153 time to fit residues: 593.5225 Evaluate side-chains 328 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 386 LYS Chi-restraints excluded: chain A residue 387 THR 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 37 ASN 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 235 LYS 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 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 163 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 150 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 757 ASN A 783 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145374 restraints weight = 21136.910| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.88 r_work: 0.3505 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20383 Z= 0.175 Angle : 0.712 10.018 27616 Z= 0.370 Chirality : 0.046 0.226 2988 Planarity : 0.006 0.070 3562 Dihedral : 8.363 73.076 2737 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.23 % Favored : 90.48 % Rotamer: Outliers : 6.07 % Allowed : 25.32 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2415 helix: -0.38 (0.16), residues: 984 sheet: -1.97 (0.36), residues: 209 loop : -2.84 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 792 HIS 0.007 0.001 HIS B 36 PHE 0.021 0.002 PHE A 381 TYR 0.034 0.002 TYR D 272 ARG 0.010 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05447 ( 711) hydrogen bonds : angle 4.91198 ( 2013) metal coordination : bond 0.00986 ( 16) metal coordination : angle 1.86694 ( 3) covalent geometry : bond 0.00412 (20367) covalent geometry : angle 0.71153 (27613) *********************** 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 418 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 285 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 220 GLU cc_start: 0.5238 (pm20) cc_final: 0.4702 (pm20) REVERT: F 360 LYS cc_start: 0.7563 (ttpp) cc_final: 0.6695 (mtmt) REVERT: F 361 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7279 (ttmm) REVERT: F 367 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7630 (tppt) REVERT: F 368 LYS cc_start: 0.7645 (ptpp) cc_final: 0.6964 (tptt) REVERT: F 373 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6805 (p) REVERT: A 182 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: A 226 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8728 (mt0) REVERT: A 299 PHE cc_start: 0.8442 (t80) cc_final: 0.8195 (t80) REVERT: A 342 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6676 (mtt90) REVERT: A 423 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6636 (ptt-90) REVERT: A 496 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7035 (mtm-85) REVERT: A 527 LYS cc_start: 0.6873 (tptt) cc_final: 0.5746 (mppt) REVERT: A 859 HIS cc_start: 0.7490 (t-90) cc_final: 0.6908 (m90) REVERT: A 903 GLU cc_start: 0.5941 (mm-30) cc_final: 0.5703 (mm-30) REVERT: A 970 ILE cc_start: 0.8281 (pt) cc_final: 0.8017 (pt) REVERT: A 989 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7616 (mtm180) REVERT: B 45 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6377 (p90) REVERT: B 57 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7902 (m) REVERT: B 88 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: B 323 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: C 64 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7486 (tt) REVERT: C 75 MET cc_start: 0.7668 (pp-130) cc_final: 0.6942 (ptp) REVERT: C 86 TYR cc_start: 0.7782 (m-80) cc_final: 0.7447 (m-80) REVERT: C 164 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: C 197 LYS cc_start: 0.6939 (tmtt) cc_final: 0.6272 (ttpt) REVERT: C 306 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7372 (pp) REVERT: C 407 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7957 (tt) REVERT: D 214 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.6896 (p) REVERT: D 241 LYS cc_start: 0.6401 (mtmm) cc_final: 0.5933 (mtmt) REVERT: D 261 GLN cc_start: 0.6633 (mt0) cc_final: 0.6096 (mm-40) REVERT: D 272 TYR cc_start: 0.7366 (m-80) cc_final: 0.7061 (m-10) REVERT: D 304 TYR cc_start: 0.7332 (m-10) cc_final: 0.7091 (m-10) REVERT: D 325 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7124 (tp40) REVERT: E 169 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7100 (mttm) REVERT: E 216 ILE cc_start: 0.7485 (tt) cc_final: 0.7131 (pp) REVERT: E 224 ASP cc_start: 0.6988 (m-30) cc_final: 0.6706 (m-30) REVERT: E 237 ILE cc_start: 0.7595 (mt) cc_final: 0.7337 (mp) REVERT: E 246 MET cc_start: 0.7386 (mtm) cc_final: 0.4961 (pp-130) REVERT: G 438 ASN cc_start: 0.7756 (t0) cc_final: 0.7403 (t0) REVERT: G 449 ARG cc_start: 0.7479 (mtp-110) cc_final: 0.6903 (ttm110) REVERT: G 535 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6979 (mt-10) REVERT: G 550 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.6907 (p90) REVERT: G 565 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6321 (m-30) outliers start: 133 outliers final: 59 residues processed: 386 average time/residue: 1.4099 time to fit residues: 620.2694 Evaluate side-chains 329 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 252 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 200 VAL 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 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 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 774 SER 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 989 ARG 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 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 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 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 169 LYS 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 E residue 300 CYS Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 234 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 165 optimal weight: 0.0000 chunk 101 optimal weight: 1.9990 chunk 233 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 overall best weight: 0.6344 ------------------------------------------------------------------------------- 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 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 87 HIS B 125 ASN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS D 170 HIS D 303 ASN E 201 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148015 restraints weight = 21545.431| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.84 r_work: 0.3547 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3815 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= 0.130 Angle : 0.645 9.409 27616 Z= 0.336 Chirality : 0.043 0.237 2988 Planarity : 0.005 0.071 3562 Dihedral : 7.721 68.244 2724 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.76 % Rotamer: Outliers : 5.20 % Allowed : 26.09 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2415 helix: 0.11 (0.16), residues: 988 sheet: -1.83 (0.35), residues: 212 loop : -2.62 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 74 HIS 0.004 0.001 HIS C 152 PHE 0.020 0.001 PHE A1031 TYR 0.039 0.002 TYR C 70 ARG 0.010 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 711) hydrogen bonds : angle 4.56745 ( 2013) metal coordination : bond 0.00647 ( 16) metal coordination : angle 1.64316 ( 3) covalent geometry : bond 0.00300 (20367) covalent geometry : angle 0.64506 (27613) *********************** 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 400 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 286 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 208 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7389 (ttm-80) REVERT: F 220 GLU cc_start: 0.5417 (pm20) cc_final: 0.4833 (pm20) REVERT: F 360 LYS cc_start: 0.7496 (ttpp) cc_final: 0.6638 (mtmt) REVERT: F 361 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7590 (ttmm) REVERT: F 367 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7668 (tppt) REVERT: F 368 LYS cc_start: 0.7643 (ptpp) cc_final: 0.7143 (pptt) REVERT: F 373 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6938 (p) REVERT: A 44 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 182 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: A 226 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8683 (mt0) REVERT: A 299 PHE cc_start: 0.8470 (t80) cc_final: 0.8236 (t80) REVERT: A 342 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6672 (mtt90) REVERT: A 423 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6596 (ptt-90) REVERT: A 496 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6999 (mtm-85) REVERT: A 527 LYS cc_start: 0.6743 (tptt) cc_final: 0.5678 (mppt) REVERT: A 554 ARG cc_start: 0.7339 (ptm-80) cc_final: 0.6993 (ptt90) REVERT: A 562 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 859 HIS cc_start: 0.7335 (t-90) cc_final: 0.6908 (m90) REVERT: A 903 GLU cc_start: 0.5678 (mm-30) cc_final: 0.4721 (mm-30) REVERT: A 970 ILE cc_start: 0.8122 (pt) cc_final: 0.7844 (pt) REVERT: A 989 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7625 (mtm180) REVERT: B 45 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6333 (p90) REVERT: B 63 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6625 (mtp180) REVERT: B 74 TRP cc_start: 0.8482 (t60) cc_final: 0.8110 (t-100) REVERT: C 68 HIS cc_start: 0.6533 (m-70) cc_final: 0.5548 (t-90) REVERT: C 75 MET cc_start: 0.7583 (pp-130) cc_final: 0.6959 (ptp) REVERT: C 86 TYR cc_start: 0.7615 (m-80) cc_final: 0.7287 (m-80) REVERT: C 164 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: C 197 LYS cc_start: 0.6890 (tmtt) cc_final: 0.6277 (ttpt) REVERT: C 302 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7540 (p) REVERT: C 407 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8011 (tt) REVERT: D 214 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.7076 (p) REVERT: D 215 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6165 (tmtm) REVERT: D 241 LYS cc_start: 0.6681 (mtmm) cc_final: 0.6095 (mtmt) REVERT: D 246 MET cc_start: 0.7662 (pmm) cc_final: 0.7048 (pmt) REVERT: D 266 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5997 (t) REVERT: D 304 TYR cc_start: 0.7236 (m-10) cc_final: 0.6991 (m-10) REVERT: D 325 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7118 (tp40) REVERT: E 169 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7254 (mttm) REVERT: E 237 ILE cc_start: 0.7559 (mt) cc_final: 0.7202 (mp) REVERT: E 241 LYS cc_start: 0.6704 (ptpt) cc_final: 0.5656 (ttpt) REVERT: E 246 MET cc_start: 0.7193 (mtm) cc_final: 0.4919 (pp-130) REVERT: G 294 ILE cc_start: 0.3195 (OUTLIER) cc_final: 0.2815 (mp) REVERT: G 341 LEU cc_start: 0.3820 (OUTLIER) cc_final: 0.3502 (mt) REVERT: G 352 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: G 397 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8207 (tp) REVERT: G 400 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7339 (ptmt) REVERT: G 438 ASN cc_start: 0.7596 (t0) cc_final: 0.7328 (t0) REVERT: G 449 ARG cc_start: 0.7549 (mtp-110) cc_final: 0.6956 (ttm110) REVERT: G 535 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6898 (mt-10) REVERT: G 550 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7074 (p90) REVERT: G 565 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6237 (m-30) outliers start: 114 outliers final: 53 residues processed: 369 average time/residue: 1.2929 time to fit residues: 544.9270 Evaluate side-chains 322 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR 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 391 LEU Chi-restraints excluded: chain A residue 44 GLN 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 302 LEU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 562 VAL 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 781 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 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 292 MET 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 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 302 THR 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 214 SER Chi-restraints excluded: chain D residue 215 LYS 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 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 G residue 263 ASN 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 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 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 63 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 85 GLN B 87 HIS B 88 GLN B 125 ASN C 183 HIS ** C 257 GLN ** 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 357 HIS ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.199140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147725 restraints weight = 21497.956| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.87 r_work: 0.3541 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20383 Z= 0.131 Angle : 0.645 9.200 27616 Z= 0.335 Chirality : 0.043 0.258 2988 Planarity : 0.005 0.071 3562 Dihedral : 7.456 68.153 2718 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.41 % Favored : 91.47 % Rotamer: Outliers : 5.29 % Allowed : 26.55 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2415 helix: 0.26 (0.16), residues: 997 sheet: -1.63 (0.35), residues: 217 loop : -2.47 (0.16), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.008 0.001 HIS A 461 PHE 0.019 0.001 PHE A1031 TYR 0.026 0.002 TYR C 70 ARG 0.011 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 711) hydrogen bonds : angle 4.48321 ( 2013) metal coordination : bond 0.00494 ( 16) metal coordination : angle 1.25964 ( 3) covalent geometry : bond 0.00306 (20367) covalent geometry : angle 0.64526 (27613) *********************** 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 374 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 258 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 208 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7310 (ttm-80) REVERT: F 220 GLU cc_start: 0.5325 (pm20) cc_final: 0.4753 (pm20) REVERT: F 360 LYS cc_start: 0.7467 (ttpp) cc_final: 0.6636 (mtmt) REVERT: F 361 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7546 (ttmm) REVERT: F 367 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7603 (tppt) REVERT: F 368 LYS cc_start: 0.7636 (ptpp) cc_final: 0.7039 (pptt) REVERT: F 373 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6944 (p) REVERT: A 44 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 181 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 182 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: A 226 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8687 (mt0) REVERT: A 299 PHE cc_start: 0.8437 (t80) cc_final: 0.8234 (t80) REVERT: A 342 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6788 (mtt90) REVERT: A 423 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6538 (ptt-90) REVERT: A 496 ARG cc_start: 0.7234 (mtt180) cc_final: 0.7005 (mtm-85) REVERT: A 527 LYS cc_start: 0.6797 (tptt) cc_final: 0.5750 (mppt) REVERT: A 554 ARG cc_start: 0.7326 (ptm-80) cc_final: 0.6874 (ptt90) REVERT: A 859 HIS cc_start: 0.7403 (t-90) cc_final: 0.6939 (m90) REVERT: A 903 GLU cc_start: 0.5750 (mm-30) cc_final: 0.5494 (mm-30) REVERT: A 989 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7531 (mtm180) REVERT: B 45 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6349 (p90) REVERT: B 51 ILE cc_start: 0.8500 (mt) cc_final: 0.8299 (mt) REVERT: B 63 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6623 (mtp85) REVERT: B 74 TRP cc_start: 0.8435 (t60) cc_final: 0.8107 (t-100) REVERT: C 68 HIS cc_start: 0.6581 (m-70) cc_final: 0.5579 (t-90) REVERT: C 75 MET cc_start: 0.7565 (pp-130) cc_final: 0.6957 (ptp) REVERT: C 86 TYR cc_start: 0.7613 (m-80) cc_final: 0.7299 (m-80) REVERT: C 175 LYS cc_start: 0.7270 (pptt) cc_final: 0.6229 (tppt) REVERT: C 197 LYS cc_start: 0.7079 (tmtt) cc_final: 0.6447 (ttpt) REVERT: C 407 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8009 (tt) REVERT: D 241 LYS cc_start: 0.6647 (mtmm) cc_final: 0.6015 (ptpt) REVERT: D 266 THR cc_start: 0.6151 (OUTLIER) cc_final: 0.5944 (t) REVERT: D 304 TYR cc_start: 0.7230 (m-10) cc_final: 0.6996 (m-10) REVERT: D 325 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.7067 (tp40) REVERT: E 237 ILE cc_start: 0.7481 (mt) cc_final: 0.7094 (mp) REVERT: E 241 LYS cc_start: 0.6628 (ptpt) cc_final: 0.5642 (ttpt) REVERT: E 246 MET cc_start: 0.7324 (mtm) cc_final: 0.4924 (pp-130) REVERT: G 294 ILE cc_start: 0.3045 (OUTLIER) cc_final: 0.2766 (mp) REVERT: G 371 MET cc_start: 0.7110 (ptm) cc_final: 0.6894 (ptm) REVERT: G 397 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8215 (tp) REVERT: G 400 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7314 (ptmt) REVERT: G 438 ASN cc_start: 0.7599 (t0) cc_final: 0.7324 (t0) REVERT: G 449 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.6944 (ttm110) REVERT: G 535 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6878 (mt-10) REVERT: G 550 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6973 (p90) REVERT: G 565 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6262 (m-30) outliers start: 116 outliers final: 59 residues processed: 344 average time/residue: 1.2827 time to fit residues: 501.8956 Evaluate side-chains 317 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 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 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP 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 180 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 70 TYR 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 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 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 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 170 HIS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 215 LYS 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 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 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 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 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.196016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144299 restraints weight = 21417.573| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.63 r_work: 0.3483 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20383 Z= 0.188 Angle : 0.704 10.725 27616 Z= 0.363 Chirality : 0.046 0.265 2988 Planarity : 0.006 0.070 3562 Dihedral : 7.551 71.846 2714 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.94 % Favored : 90.93 % Rotamer: Outliers : 5.57 % Allowed : 26.46 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2415 helix: 0.16 (0.16), residues: 1001 sheet: -1.60 (0.34), residues: 219 loop : -2.42 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 792 HIS 0.022 0.001 HIS A 461 PHE 0.026 0.002 PHE A 381 TYR 0.025 0.002 TYR A 574 ARG 0.007 0.001 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 711) hydrogen bonds : angle 4.63622 ( 2013) metal coordination : bond 0.00535 ( 16) metal coordination : angle 1.07429 ( 3) covalent geometry : bond 0.00457 (20367) covalent geometry : angle 0.70424 (27613) *********************** 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 386 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 264 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8078 (t) REVERT: F 215 LYS cc_start: 0.5214 (mmmm) cc_final: 0.4873 (mmmm) REVERT: F 220 GLU cc_start: 0.5360 (pm20) cc_final: 0.4747 (pm20) REVERT: F 360 LYS cc_start: 0.7653 (ttpp) cc_final: 0.6700 (mtmt) REVERT: F 361 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7724 (ttmm) REVERT: F 367 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7681 (tppt) REVERT: F 368 LYS cc_start: 0.7658 (ptpp) cc_final: 0.7223 (pptt) REVERT: F 373 VAL cc_start: 0.7188 (OUTLIER) cc_final: 0.6955 (p) REVERT: A 181 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8220 (m) REVERT: A 182 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: A 299 PHE cc_start: 0.8485 (t80) cc_final: 0.8241 (t80) REVERT: A 342 ARG cc_start: 0.7344 (mtt180) cc_final: 0.6863 (mtt90) REVERT: A 423 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6484 (ptt-90) REVERT: A 527 LYS cc_start: 0.6830 (tptt) cc_final: 0.5894 (mppt) REVERT: A 554 ARG cc_start: 0.7383 (ptm-80) cc_final: 0.6914 (ptt90) REVERT: A 741 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7796 (ptpp) REVERT: A 859 HIS cc_start: 0.7529 (t-90) cc_final: 0.7132 (m90) REVERT: A 896 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: A 989 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7659 (mtm180) REVERT: A 1013 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6352 (tpm170) REVERT: B 45 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6326 (p90) REVERT: B 57 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7856 (m) REVERT: B 74 TRP cc_start: 0.8471 (t60) cc_final: 0.8170 (t-100) REVERT: B 92 ASN cc_start: 0.8485 (t0) cc_final: 0.8104 (t0) REVERT: B 323 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: C 64 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (tt) REVERT: C 68 HIS cc_start: 0.6467 (m-70) cc_final: 0.5638 (t-90) REVERT: C 75 MET cc_start: 0.7478 (pp-130) cc_final: 0.7031 (ptp) REVERT: C 86 TYR cc_start: 0.7564 (m-80) cc_final: 0.7353 (m-80) REVERT: C 164 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6004 (mp0) REVERT: C 175 LYS cc_start: 0.7213 (pptt) cc_final: 0.6246 (tppt) REVERT: C 197 LYS cc_start: 0.7134 (tmtt) cc_final: 0.6509 (ttpt) REVERT: C 388 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7900 (ppp) REVERT: C 407 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 304 TYR cc_start: 0.7292 (m-10) cc_final: 0.7086 (m-10) REVERT: D 319 TYR cc_start: 0.7498 (m-80) cc_final: 0.7263 (m-10) REVERT: D 325 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: E 169 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7095 (mttm) REVERT: E 216 ILE cc_start: 0.7426 (pp) cc_final: 0.7020 (mm) REVERT: E 221 ASN cc_start: 0.8470 (p0) cc_final: 0.8114 (p0) REVERT: E 237 ILE cc_start: 0.7693 (mt) cc_final: 0.7393 (mp) REVERT: E 246 MET cc_start: 0.7342 (mtm) cc_final: 0.4836 (pp-130) REVERT: E 286 GLU cc_start: 0.7419 (tp30) cc_final: 0.7144 (tp30) REVERT: G 334 MET cc_start: 0.6957 (mpp) cc_final: 0.6753 (tmm) REVERT: G 371 MET cc_start: 0.7196 (ptm) cc_final: 0.6951 (ptm) REVERT: G 397 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8292 (tp) REVERT: G 400 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7505 (ptmt) REVERT: G 438 ASN cc_start: 0.7842 (t0) cc_final: 0.7566 (t0) REVERT: G 449 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7032 (ttm110) REVERT: G 535 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7089 (mt-10) REVERT: G 550 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6760 (p90) REVERT: G 565 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6372 (m-30) outliers start: 122 outliers final: 68 residues processed: 355 average time/residue: 1.2499 time to fit residues: 502.0901 Evaluate side-chains 336 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 247 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 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 78 ILE 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 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 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 741 LYS Chi-restraints excluded: chain A residue 742 GLU 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 888 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 900 ASN 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 322 ASP 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 132 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 187 CYS 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 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 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 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 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 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 16 optimal weight: 0.5980 chunk 187 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.0000 chunk 5 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 24 GLN B 85 GLN B 87 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 483 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146784 restraints weight = 21351.461| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.86 r_work: 0.3528 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4462 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 : 0.639 10.072 27616 Z= 0.329 Chirality : 0.043 0.305 2988 Planarity : 0.005 0.070 3562 Dihedral : 7.214 66.911 2714 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 5.11 % Allowed : 27.05 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2415 helix: 0.42 (0.16), residues: 1000 sheet: -1.40 (0.35), residues: 219 loop : -2.33 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 212 HIS 0.004 0.001 HIS C 280 PHE 0.021 0.001 PHE B 249 TYR 0.024 0.001 TYR C 178 ARG 0.011 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 711) hydrogen bonds : angle 4.42876 ( 2013) metal coordination : bond 0.00405 ( 16) metal coordination : angle 0.95810 ( 3) covalent geometry : bond 0.00293 (20367) covalent geometry : angle 0.63846 (27613) *********************** 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 378 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 266 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6289 (OUTLIER) cc_final: 0.5962 (t) REVERT: F 207 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8108 (t) REVERT: F 208 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7015 (ttm170) REVERT: F 215 LYS cc_start: 0.5041 (mmmm) cc_final: 0.4784 (mmmm) REVERT: F 220 GLU cc_start: 0.5453 (pm20) cc_final: 0.4795 (pm20) REVERT: F 360 LYS cc_start: 0.7541 (ttpp) cc_final: 0.6667 (mtmt) REVERT: F 361 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7717 (ttmm) REVERT: F 367 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7670 (tppt) REVERT: F 368 LYS cc_start: 0.7685 (ptpp) cc_final: 0.7172 (pptt) REVERT: A 44 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 182 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: A 299 PHE cc_start: 0.8456 (t80) cc_final: 0.8214 (t80) REVERT: A 342 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6774 (mtt90) REVERT: A 552 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7565 (ptp90) REVERT: A 554 ARG cc_start: 0.7291 (ptm-80) cc_final: 0.6959 (ptt90) REVERT: A 859 HIS cc_start: 0.7415 (t-90) cc_final: 0.6941 (m90) REVERT: A 903 GLU cc_start: 0.5938 (mm-30) cc_final: 0.5712 (mm-30) REVERT: A 989 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7573 (mtm180) REVERT: A 1013 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6213 (tpm170) REVERT: B 45 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6400 (p90) REVERT: B 51 ILE cc_start: 0.8542 (mt) cc_final: 0.8335 (mt) REVERT: B 57 THR cc_start: 0.8217 (p) cc_final: 0.7773 (m) REVERT: B 74 TRP cc_start: 0.8431 (t60) cc_final: 0.8115 (t-100) REVERT: B 92 ASN cc_start: 0.8346 (t0) cc_final: 0.8013 (t0) REVERT: B 323 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: C 68 HIS cc_start: 0.6452 (m-70) cc_final: 0.5658 (t-90) REVERT: C 75 MET cc_start: 0.7435 (pp-130) cc_final: 0.6971 (ptp) REVERT: C 164 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: C 175 LYS cc_start: 0.7166 (pptt) cc_final: 0.6294 (mppt) REVERT: C 197 LYS cc_start: 0.7157 (tmtt) cc_final: 0.6543 (ttpt) REVERT: C 407 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8025 (tt) REVERT: D 241 LYS cc_start: 0.7098 (mtmm) cc_final: 0.6409 (tmtt) REVERT: D 304 TYR cc_start: 0.7303 (m-10) cc_final: 0.7061 (m-10) REVERT: D 319 TYR cc_start: 0.7475 (m-80) cc_final: 0.7209 (m-10) REVERT: D 325 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7152 (tp40) REVERT: E 169 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7144 (mttm) REVERT: E 237 ILE cc_start: 0.7389 (mt) cc_final: 0.7062 (mp) REVERT: E 246 MET cc_start: 0.7282 (mtm) cc_final: 0.4839 (pp-130) REVERT: E 286 GLU cc_start: 0.7399 (tp30) cc_final: 0.7067 (tp30) REVERT: G 339 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2649 (mpm) REVERT: G 352 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: G 371 MET cc_start: 0.7142 (ptm) cc_final: 0.6866 (ptm) REVERT: G 397 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8252 (tp) REVERT: G 400 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7495 (ptmt) REVERT: G 438 ASN cc_start: 0.7642 (t0) cc_final: 0.7364 (t0) REVERT: G 449 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.6977 (ttm110) REVERT: G 535 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6870 (mt-10) REVERT: G 550 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7038 (p90) REVERT: G 565 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6377 (m-30) outliers start: 112 outliers final: 64 residues processed: 343 average time/residue: 1.3063 time to fit residues: 510.2026 Evaluate side-chains 332 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 208 ARG 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 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 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR 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 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 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 1004 ASP 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 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 124 ASN 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 331 ILE 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 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 215 LYS 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 339 MET 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 418 VAL Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER 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 84 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 chunk 230 optimal weight: 0.0980 chunk 189 optimal weight: 0.8980 chunk 197 optimal weight: 0.0030 chunk 179 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.2138 ------------------------------------------------------------------------------- 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 20 HIS C 183 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.202670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151757 restraints weight = 21584.941| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.83 r_work: 0.3587 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20383 Z= 0.111 Angle : 0.613 9.589 27616 Z= 0.317 Chirality : 0.041 0.272 2988 Planarity : 0.005 0.070 3562 Dihedral : 6.726 62.214 2712 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.66 % Favored : 92.22 % Rotamer: Outliers : 3.47 % Allowed : 28.97 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2415 helix: 0.80 (0.17), residues: 989 sheet: -1.14 (0.36), residues: 207 loop : -2.18 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 304 HIS 0.021 0.001 HIS A 461 PHE 0.020 0.001 PHE B 249 TYR 0.032 0.001 TYR C 70 ARG 0.014 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 711) hydrogen bonds : angle 4.27061 ( 2013) metal coordination : bond 0.00403 ( 16) metal coordination : angle 0.96866 ( 3) covalent geometry : bond 0.00252 (20367) covalent geometry : angle 0.61300 (27613) *********************** 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 352 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 276 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.5811 (OUTLIER) cc_final: 0.5554 (t) REVERT: F 207 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8056 (t) REVERT: F 208 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: F 215 LYS cc_start: 0.5270 (mmmm) cc_final: 0.4952 (mmmm) REVERT: F 220 GLU cc_start: 0.5398 (pm20) cc_final: 0.4817 (pm20) REVERT: F 360 LYS cc_start: 0.7416 (ttpp) cc_final: 0.6523 (mtmt) REVERT: F 361 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7659 (ttmm) REVERT: F 367 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7706 (tppt) REVERT: F 368 LYS cc_start: 0.7618 (ptpp) cc_final: 0.7101 (tmtp) REVERT: A 182 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: A 342 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6574 (mtt90) REVERT: A 467 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7982 (tppt) REVERT: A 552 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7118 (ptp90) REVERT: A 554 ARG cc_start: 0.7206 (ptm-80) cc_final: 0.6824 (ptt90) REVERT: A 801 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7306 (t0) REVERT: A 989 ARG cc_start: 0.7792 (mmt90) cc_final: 0.7492 (mtm180) REVERT: B 45 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 63 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6728 (mtp180) REVERT: B 74 TRP cc_start: 0.8376 (t60) cc_final: 0.8044 (t-100) REVERT: B 92 ASN cc_start: 0.7999 (t0) cc_final: 0.7778 (t0) REVERT: C 68 HIS cc_start: 0.6299 (m-70) cc_final: 0.5589 (t-90) REVERT: C 75 MET cc_start: 0.7567 (pp-130) cc_final: 0.6919 (ptp) REVERT: C 94 GLN cc_start: 0.7173 (tp-100) cc_final: 0.6428 (mm-40) REVERT: C 164 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: C 175 LYS cc_start: 0.7095 (pptt) cc_final: 0.6215 (mppt) REVERT: C 197 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6493 (ttpt) REVERT: C 331 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8164 (pt) REVERT: C 407 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7976 (tt) REVERT: D 241 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6546 (tmtt) REVERT: D 304 TYR cc_start: 0.7311 (m-10) cc_final: 0.7055 (m-10) REVERT: E 221 ASN cc_start: 0.8199 (p0) cc_final: 0.7908 (p0) REVERT: E 246 MET cc_start: 0.7305 (mtm) cc_final: 0.5000 (pp-130) REVERT: G 339 MET cc_start: 0.3146 (OUTLIER) cc_final: 0.2682 (mpm) REVERT: G 371 MET cc_start: 0.7104 (ptm) cc_final: 0.6882 (ptm) REVERT: G 400 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7368 (ptmt) REVERT: G 449 ARG cc_start: 0.7605 (mtp-110) cc_final: 0.6932 (ttm110) REVERT: G 535 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6796 (mt-10) REVERT: G 550 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7244 (p90) REVERT: G 565 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6260 (m-30) outliers start: 76 outliers final: 39 residues processed: 330 average time/residue: 1.3462 time to fit residues: 515.3014 Evaluate side-chains 304 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 ARG 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 78 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 467 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 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 970 ILE 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 79 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 164 GLU 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 331 ILE 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 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 339 MET 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 438 ASN Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 203 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 113 optimal weight: 0.0040 chunk 234 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 912 ASN A 998 GLN B 24 GLN B 85 GLN C 63 GLN C 183 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.200637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149199 restraints weight = 21313.301| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.83 r_work: 0.3550 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20383 Z= 0.124 Angle : 0.638 9.727 27616 Z= 0.327 Chirality : 0.043 0.358 2988 Planarity : 0.005 0.078 3562 Dihedral : 6.616 62.828 2707 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.99 % Favored : 91.88 % Rotamer: Outliers : 3.38 % Allowed : 29.43 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2415 helix: 0.81 (0.17), residues: 996 sheet: -1.07 (0.37), residues: 207 loop : -2.14 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.033 0.001 HIS A 461 PHE 0.030 0.001 PHE A 889 TYR 0.027 0.001 TYR C 178 ARG 0.013 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 711) hydrogen bonds : angle 4.31402 ( 2013) metal coordination : bond 0.00349 ( 16) metal coordination : angle 0.76833 ( 3) covalent geometry : bond 0.00295 (20367) covalent geometry : angle 0.63848 (27613) *********************** 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 336 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.5891 (OUTLIER) cc_final: 0.5660 (t) REVERT: F 207 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8132 (t) REVERT: F 208 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: F 215 LYS cc_start: 0.5364 (mmmm) cc_final: 0.5031 (mmmm) REVERT: F 220 GLU cc_start: 0.5407 (pm20) cc_final: 0.4648 (pm20) REVERT: F 361 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7639 (ttmm) REVERT: F 367 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7730 (tppt) REVERT: F 368 LYS cc_start: 0.7703 (ptpp) cc_final: 0.7096 (pptt) REVERT: A 44 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: A 182 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: A 342 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6556 (mtt90) REVERT: A 552 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7650 (ptp90) REVERT: A 554 ARG cc_start: 0.7167 (ptm-80) cc_final: 0.6772 (ptt90) REVERT: A 801 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7194 (t0) REVERT: A 859 HIS cc_start: 0.7349 (t-90) cc_final: 0.6898 (m90) REVERT: A 989 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7493 (mtm180) REVERT: A 1004 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6256 (m-30) REVERT: B 45 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6264 (p90) REVERT: B 57 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7728 (m) REVERT: B 63 ARG cc_start: 0.7228 (ttm170) cc_final: 0.6675 (mtp85) REVERT: B 74 TRP cc_start: 0.8356 (t60) cc_final: 0.8045 (t-100) REVERT: B 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7912 (t0) REVERT: C 68 HIS cc_start: 0.6281 (m-70) cc_final: 0.5663 (t-90) REVERT: C 75 MET cc_start: 0.7706 (pp-130) cc_final: 0.6953 (ptp) REVERT: C 164 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: C 175 LYS cc_start: 0.6978 (pptt) cc_final: 0.6165 (mppt) REVERT: C 197 LYS cc_start: 0.7079 (tmtt) cc_final: 0.6491 (ttpt) REVERT: C 331 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8174 (pt) REVERT: C 388 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7777 (ppp) REVERT: C 407 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7980 (tt) REVERT: D 241 LYS cc_start: 0.7397 (mtmm) cc_final: 0.6831 (tmtt) REVERT: D 246 MET cc_start: 0.7670 (pmm) cc_final: 0.7092 (pmt) REVERT: D 304 TYR cc_start: 0.7312 (m-10) cc_final: 0.7068 (m-10) REVERT: E 169 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7208 (mptp) REVERT: E 246 MET cc_start: 0.7266 (mtm) cc_final: 0.5044 (pp-130) REVERT: E 270 ASP cc_start: 0.3546 (OUTLIER) cc_final: 0.2643 (p0) REVERT: E 286 GLU cc_start: 0.7331 (tp30) cc_final: 0.6997 (tp30) REVERT: G 339 MET cc_start: 0.3280 (OUTLIER) cc_final: 0.2757 (mpm) REVERT: G 371 MET cc_start: 0.7124 (ptm) cc_final: 0.6856 (ptm) REVERT: G 400 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7388 (ptmt) REVERT: G 438 ASN cc_start: 0.7180 (t0) cc_final: 0.6592 (t0) REVERT: G 449 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.6965 (ttm110) REVERT: G 535 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6954 (mt-10) REVERT: G 550 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7152 (p90) REVERT: G 565 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6308 (m-30) outliers start: 74 outliers final: 38 residues processed: 314 average time/residue: 1.4519 time to fit residues: 517.1224 Evaluate side-chains 308 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 ARG 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 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR 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 772 GLN Chi-restraints excluded: chain A residue 801 ASP 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 970 ILE 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 211 THR Chi-restraints excluded: chain B residue 260 THR 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 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 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 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 170 HIS 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 G residue 339 MET 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 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 177 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 C 183 HIS C 205 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.200362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148571 restraints weight = 21284.617| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.89 r_work: 0.3556 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20383 Z= 0.127 Angle : 0.641 9.397 27616 Z= 0.330 Chirality : 0.043 0.383 2988 Planarity : 0.005 0.079 3562 Dihedral : 6.604 63.845 2706 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 3.15 % Allowed : 29.88 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2415 helix: 0.84 (0.17), residues: 1003 sheet: -1.02 (0.37), residues: 205 loop : -2.11 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 412 HIS 0.006 0.001 HIS C 319 PHE 0.034 0.001 PHE A 889 TYR 0.026 0.001 TYR C 70 ARG 0.012 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 711) hydrogen bonds : angle 4.35188 ( 2013) metal coordination : bond 0.00443 ( 16) metal coordination : angle 0.88635 ( 3) covalent geometry : bond 0.00302 (20367) covalent geometry : angle 0.64132 (27613) ********************** 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 327 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 208 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (ttm110) REVERT: F 215 LYS cc_start: 0.5437 (mmmm) cc_final: 0.5163 (mmmm) REVERT: F 220 GLU cc_start: 0.5202 (pm20) cc_final: 0.4614 (pm20) REVERT: F 361 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7707 (ttmm) REVERT: F 367 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7716 (tppt) REVERT: F 368 LYS cc_start: 0.7610 (ptpp) cc_final: 0.7096 (tmtp) REVERT: A 182 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: A 342 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6549 (mtt90) REVERT: A 552 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7679 (ptp90) REVERT: A 554 ARG cc_start: 0.7174 (ptm-80) cc_final: 0.6789 (ptt90) REVERT: A 801 ASP cc_start: 0.7483 (m-30) cc_final: 0.7229 (t0) REVERT: A 859 HIS cc_start: 0.7430 (t-90) cc_final: 0.6990 (m90) REVERT: A 989 ARG cc_start: 0.7789 (mmt90) cc_final: 0.7586 (mtm180) REVERT: A 1004 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6274 (m-30) REVERT: B 45 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6318 (p90) REVERT: B 57 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7735 (m) REVERT: B 63 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6706 (mtp85) REVERT: B 74 TRP cc_start: 0.8328 (t60) cc_final: 0.8073 (t-100) REVERT: B 92 ASN cc_start: 0.8188 (t0) cc_final: 0.7949 (t0) REVERT: C 68 HIS cc_start: 0.6329 (m-70) cc_final: 0.5693 (t-90) REVERT: C 75 MET cc_start: 0.7684 (pp-130) cc_final: 0.6962 (ptp) REVERT: C 164 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: C 197 LYS cc_start: 0.7091 (tmtt) cc_final: 0.6495 (tppt) REVERT: C 331 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8179 (pt) REVERT: C 388 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7801 (ppp) REVERT: D 241 LYS cc_start: 0.7371 (mtmm) cc_final: 0.6771 (tmtt) REVERT: D 246 MET cc_start: 0.7685 (pmm) cc_final: 0.7118 (pmt) REVERT: D 270 ASP cc_start: 0.7495 (m-30) cc_final: 0.7225 (m-30) REVERT: D 304 TYR cc_start: 0.7310 (m-10) cc_final: 0.7067 (m-10) REVERT: E 169 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7245 (mptp) REVERT: E 246 MET cc_start: 0.7277 (mtm) cc_final: 0.4965 (pp-130) REVERT: E 270 ASP cc_start: 0.3621 (OUTLIER) cc_final: 0.2596 (p0) REVERT: G 339 MET cc_start: 0.3197 (OUTLIER) cc_final: 0.2751 (mpm) REVERT: G 352 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: G 371 MET cc_start: 0.7123 (ptm) cc_final: 0.6890 (ptm) REVERT: G 400 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7349 (ptmt) REVERT: G 438 ASN cc_start: 0.7517 (t0) cc_final: 0.7065 (t0) REVERT: G 449 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.6983 (ttm110) REVERT: G 535 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6993 (mt-10) REVERT: G 550 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7056 (p90) REVERT: G 565 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6329 (m-30) outliers start: 69 outliers final: 39 residues processed: 307 average time/residue: 1.7184 time to fit residues: 604.6298 Evaluate side-chains 305 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 ARG 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 78 ILE 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 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 772 GLN 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 900 ASN 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 211 THR Chi-restraints excluded: chain B residue 260 THR 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 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 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 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 170 HIS 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 G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 217 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 912 ASN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.200384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148903 restraints weight = 21395.772| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.80 r_work: 0.3549 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20383 Z= 0.125 Angle : 0.643 10.746 27616 Z= 0.330 Chirality : 0.043 0.350 2988 Planarity : 0.005 0.079 3562 Dihedral : 6.526 63.814 2703 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.99 % Favored : 91.88 % Rotamer: Outliers : 3.15 % Allowed : 29.97 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2415 helix: 0.88 (0.17), residues: 990 sheet: -1.02 (0.37), residues: 205 loop : -2.05 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 412 HIS 0.019 0.001 HIS A 461 PHE 0.038 0.001 PHE A 889 TYR 0.025 0.001 TYR C 70 ARG 0.013 0.000 ARG F 366 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 711) hydrogen bonds : angle 4.35675 ( 2013) metal coordination : bond 0.00417 ( 16) metal coordination : angle 0.89355 ( 3) covalent geometry : bond 0.00298 (20367) covalent geometry : angle 0.64261 (27613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21984.66 seconds wall clock time: 391 minutes 32.97 seconds (23492.97 seconds total)