Starting phenix.real_space_refine on Tue Nov 19 18:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_35092_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_35092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_35092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_35092_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/11_2024/8i02_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.99, per 1000 atoms: 0.60 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: 4.81 Conformation dependent library (CDL) restraints added in 2.3 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: 2.03 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: 6.54 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 22 1.17 - 1.33: 5661 1.33 - 1.49: 6677 1.49 - 1.66: 7868 1.66 - 1.82: 139 Bond restraints: 20367 Sorted by residual: bond pdb=" C CYS A 337 " pdb=" O CYS A 337 " ideal model delta sigma weight residual 1.235 1.010 0.226 1.26e-02 6.30e+03 3.21e+02 bond pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 1.469 1.696 -0.228 1.28e-02 6.10e+03 3.17e+02 bond pdb=" C PHE A 359 " pdb=" O PHE A 359 " ideal model delta sigma weight residual 1.236 1.086 0.150 1.15e-02 7.56e+03 1.70e+02 bond pdb=" C SER A 370 " pdb=" O SER A 370 " ideal model delta sigma weight residual 1.234 1.076 0.158 1.28e-02 6.10e+03 1.52e+02 bond pdb=" C SER A 352 " pdb=" O SER A 352 " ideal model delta sigma weight residual 1.236 1.093 0.143 1.19e-02 7.06e+03 1.44e+02 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 27244 3.56 - 7.11: 312 7.11 - 10.67: 42 10.67 - 14.22: 11 14.22 - 17.78: 4 Bond angle restraints: 27613 Sorted by residual: angle pdb=" C HIS A 371 " pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 119.84 137.62 -17.78 1.25e+00 6.40e-01 2.02e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" C GLU A 378 " ideal model delta sigma weight residual 112.72 127.03 -14.31 1.14e+00 7.69e-01 1.58e+02 angle pdb=" O VAL A 369 " pdb=" C VAL A 369 " pdb=" N SER A 370 " ideal model delta sigma weight residual 122.69 110.83 11.86 1.14e+00 7.69e-01 1.08e+02 angle pdb=" C ASN A 365 " pdb=" CA ASN A 365 " pdb=" CB ASN A 365 " ideal model delta sigma weight residual 110.26 95.25 15.01 1.50e+00 4.44e-01 1.00e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" CB GLU A 378 " ideal model delta sigma weight residual 110.70 97.65 13.05 1.49e+00 4.50e-01 7.67e+01 ... (remaining 27608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10511 17.95 - 35.90: 1230 35.90 - 53.85: 338 53.85 - 71.80: 90 71.80 - 89.74: 35 Dihedral angle restraints: 12204 sinusoidal: 4947 harmonic: 7257 Sorted by residual: dihedral pdb=" CA ASN G 438 " pdb=" C ASN G 438 " pdb=" N PRO G 439 " pdb=" CA PRO G 439 " ideal model delta harmonic sigma weight residual 180.00 99.24 80.76 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N PRO F 146 " pdb=" CA PRO F 146 " ideal model delta harmonic sigma weight residual 180.00 121.06 58.94 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual 180.00 122.23 57.77 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2962 0.181 - 0.361: 19 0.361 - 0.542: 4 0.542 - 0.723: 1 0.723 - 0.904: 2 Chirality restraints: 2988 Sorted by residual: chirality pdb=" CA SER A 376 " pdb=" N SER A 376 " pdb=" C SER A 376 " pdb=" CB SER A 376 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLU A 377 " pdb=" N GLU A 377 " pdb=" C GLU A 377 " pdb=" CB GLU A 377 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2985 not shown) Planarity restraints: 3562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 336 " 0.036 2.00e-02 2.50e+03 7.52e-02 5.66e+01 pdb=" C GLU A 336 " -0.130 2.00e-02 2.50e+03 pdb=" O GLU A 336 " 0.050 2.00e-02 2.50e+03 pdb=" N CYS A 337 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 373 " -0.030 2.00e-02 2.50e+03 6.08e-02 3.69e+01 pdb=" C THR A 373 " 0.105 2.00e-02 2.50e+03 pdb=" O THR A 373 " -0.040 2.00e-02 2.50e+03 pdb=" N TRP A 374 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 247 " 0.024 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C GLN C 247 " -0.087 2.00e-02 2.50e+03 pdb=" O GLN C 247 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP C 248 " 0.030 2.00e-02 2.50e+03 ... (remaining 3559 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 45 2.27 - 2.99: 10466 2.99 - 3.70: 33105 3.70 - 4.42: 54880 4.42 - 5.14: 94177 Nonbonded interactions: 192673 Sorted by model distance: nonbonded pdb=" OG SER A 354 " pdb=" OD2 ASP B 67 " model vdw 1.549 3.040 nonbonded pdb=" OD2 ASP B 173 " pdb="ZN ZN B 501 " model vdw 1.810 2.230 nonbonded pdb=" NH1 ARG A 80 " pdb=" O ASN A 234 " model vdw 2.053 3.120 nonbonded pdb=" OG SER A 306 " pdb=" NH1 ARG A 310 " model vdw 2.058 3.120 nonbonded pdb=" OH TYR A1018 " pdb=" OD1 ASP A1020 " model vdw 2.075 3.040 ... (remaining 192668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 170 through 178 or resid 180 through 329)) selection = (chain 'E' and (resid 170 through 290 or resid 294 through 329)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 47.420 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: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.790 ------------------------------------------------------------------------------- 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 : 0.010 0.228 20367 Z= 0.627 Angle : 1.030 17.781 27613 Z= 0.604 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 *********************** 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 : 2.246 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: 1.1522 time to fit residues: 793.8339 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 : 2.427 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 0.042 20367 Z= 0.231 Angle : 0.725 9.543 27613 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 *********************** 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 : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7744 (t) REVERT: F 220 GLU cc_start: 0.5533 (pm20) cc_final: 0.5326 (pm20) REVERT: F 360 LYS cc_start: 0.7410 (ttpp) cc_final: 0.6942 (mtmt) REVERT: F 361 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7645 (mttm) REVERT: F 368 LYS cc_start: 0.7459 (ptpp) cc_final: 0.6980 (tptt) REVERT: F 373 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6576 (p) REVERT: A 79 GLU cc_start: 0.7946 (pt0) cc_final: 0.7527 (mt-10) REVERT: A 182 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: A 226 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 351 ILE cc_start: 0.7520 (mm) cc_final: 0.7125 (tt) REVERT: A 374 TRP cc_start: 0.3845 (OUTLIER) cc_final: 0.3295 (t60) REVERT: A 386 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6397 (mtpp) REVERT: A 439 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5524 (tp30) REVERT: A 527 LYS cc_start: 0.6856 (tptt) cc_final: 0.5957 (mppt) REVERT: A 619 ARG cc_start: 0.5611 (ptp-110) cc_final: 0.5205 (mtm-85) REVERT: A 795 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7673 (mtp85) REVERT: A 871 THR cc_start: 0.7306 (t) cc_final: 0.7104 (m) REVERT: A 989 ARG cc_start: 0.7894 (mmt90) cc_final: 0.7670 (mtm180) REVERT: B 57 THR cc_start: 0.8276 (p) cc_final: 0.7812 (m) REVERT: C 75 MET cc_start: 0.7339 (pp-130) cc_final: 0.6938 (ptp) REVERT: C 175 LYS cc_start: 0.6790 (pptt) cc_final: 0.6497 (tppt) REVERT: C 197 LYS cc_start: 0.6650 (tmtt) cc_final: 0.6438 (ttpt) REVERT: C 214 LEU cc_start: 0.6981 (mt) cc_final: 0.6757 (mt) REVERT: C 306 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7361 (pp) REVERT: D 241 LYS cc_start: 0.6694 (mtmm) cc_final: 0.6341 (mtmt) REVERT: D 319 TYR cc_start: 0.6800 (m-10) cc_final: 0.6591 (m-10) REVERT: E 169 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6943 (mttp) REVERT: G 344 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.4582 (t80) REVERT: G 550 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7136 (p90) REVERT: G 565 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6034 (m-30) outliers start: 141 outliers final: 52 residues processed: 426 average time/residue: 1.2040 time to fit residues: 587.8590 Evaluate side-chains 320 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 2.376 ------------------------------------------------------------------------------- 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 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 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 122 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 183 optimal weight: 0.0000 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 221 optimal weight: 0.0770 chunk 238 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 overall best weight: 0.9946 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20367 Z= 0.254 Angle : 0.705 9.773 27613 Z= 0.368 Chirality : 0.045 0.225 2988 Planarity : 0.006 0.072 3562 Dihedral : 8.339 70.325 2737 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.19 % Favored : 90.52 % Rotamer: Outliers : 6.07 % Allowed : 25.46 % Favored : 68.48 % 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: -0.36 (0.16), residues: 984 sheet: -1.98 (0.36), residues: 209 loop : -2.84 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 792 HIS 0.007 0.001 HIS C 152 PHE 0.020 0.002 PHE A 381 TYR 0.033 0.002 TYR D 272 ARG 0.008 0.001 ARG B 75 *********************** 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 412 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 279 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7600 (ttpp) cc_final: 0.7063 (mtmt) REVERT: F 361 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7383 (ttmm) REVERT: F 368 LYS cc_start: 0.7483 (ptpp) cc_final: 0.7149 (tptt) REVERT: F 373 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6761 (p) REVERT: A 182 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: A 342 ARG cc_start: 0.6388 (mtt180) cc_final: 0.5785 (mtt90) REVERT: A 423 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6718 (ptt-90) REVERT: A 439 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5467 (tp30) REVERT: A 527 LYS cc_start: 0.6785 (tptt) cc_final: 0.5949 (mppt) REVERT: A 859 HIS cc_start: 0.6919 (t-90) cc_final: 0.6602 (m90) REVERT: A 970 ILE cc_start: 0.8149 (pt) cc_final: 0.7855 (pt) REVERT: B 45 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6019 (p90) REVERT: B 57 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7840 (m) REVERT: B 74 TRP cc_start: 0.8218 (t60) cc_final: 0.7958 (t-100) REVERT: B 88 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: C 164 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6166 (mt-10) REVERT: C 306 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7741 (pp) REVERT: C 407 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8228 (tt) REVERT: D 214 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7470 (p) REVERT: D 241 LYS cc_start: 0.6767 (mtmm) cc_final: 0.6404 (mtmt) REVERT: D 272 TYR cc_start: 0.7347 (m-80) cc_final: 0.7141 (m-10) REVERT: E 169 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6931 (mttm) REVERT: E 224 ASP cc_start: 0.6829 (m-30) cc_final: 0.6581 (m-30) REVERT: E 241 LYS cc_start: 0.6299 (ptpt) cc_final: 0.5785 (ttpt) REVERT: E 246 MET cc_start: 0.6615 (mtm) cc_final: 0.4863 (pp-130) REVERT: G 449 ARG cc_start: 0.7313 (mtp-110) cc_final: 0.6953 (ttm110) REVERT: G 550 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7005 (p90) REVERT: G 565 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6188 (m-30) outliers start: 133 outliers final: 60 residues processed: 380 average time/residue: 0.8620 time to fit residues: 373.2737 Evaluate side-chains 321 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 206 ILE Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 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 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 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 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 C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP 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 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 218 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 210 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN A 159 ASN A 757 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 85 GLN B 87 HIS B 125 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS D 303 ASN E 201 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20367 Z= 0.243 Angle : 0.687 9.269 27613 Z= 0.357 Chirality : 0.045 0.242 2988 Planarity : 0.006 0.072 3562 Dihedral : 7.996 67.916 2727 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.78 % Favored : 91.06 % Rotamer: Outliers : 5.93 % Allowed : 25.78 % Favored : 68.29 % 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: -2.16 (0.16), residues: 2415 helix: -0.07 (0.16), residues: 993 sheet: -1.79 (0.35), residues: 213 loop : -2.64 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 792 HIS 0.005 0.001 HIS B 207 PHE 0.021 0.002 PHE A1031 TYR 0.037 0.002 TYR C 70 ARG 0.010 0.000 ARG F 366 *********************** 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 412 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 282 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 361 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7783 (ttmm) REVERT: A 44 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: A 182 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: A 342 ARG cc_start: 0.6409 (mtt180) cc_final: 0.5728 (mtt90) REVERT: A 423 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6679 (ptt-90) REVERT: A 439 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5539 (tp30) REVERT: A 527 LYS cc_start: 0.6721 (tptt) cc_final: 0.5895 (mppt) REVERT: A 859 HIS cc_start: 0.6867 (t-90) cc_final: 0.6608 (m90) REVERT: A 896 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: A 970 ILE cc_start: 0.7982 (pt) cc_final: 0.7727 (pt) REVERT: B 45 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6057 (p90) REVERT: B 88 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: C 68 HIS cc_start: 0.5852 (m-70) cc_final: 0.5450 (t-90) REVERT: C 86 TYR cc_start: 0.7211 (m-80) cc_final: 0.6947 (m-10) REVERT: C 93 ILE cc_start: 0.7313 (mm) cc_final: 0.7069 (mp) REVERT: C 306 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7650 (pt) REVERT: C 407 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8264 (tt) REVERT: D 241 LYS cc_start: 0.7023 (mtmm) cc_final: 0.6514 (mtmt) REVERT: E 169 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6904 (mttm) REVERT: E 216 ILE cc_start: 0.7456 (pp) cc_final: 0.6834 (mm) REVERT: E 241 LYS cc_start: 0.6542 (ptpt) cc_final: 0.5911 (ttpt) REVERT: E 246 MET cc_start: 0.6503 (mtm) cc_final: 0.4979 (pp-130) REVERT: G 294 ILE cc_start: 0.2511 (OUTLIER) cc_final: 0.2212 (mp) REVERT: G 341 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.3494 (mt) REVERT: G 397 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8488 (tp) REVERT: G 400 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7614 (ptmt) REVERT: G 449 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.7029 (ttm110) REVERT: G 550 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6936 (p90) REVERT: G 565 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6210 (m-30) outliers start: 130 outliers final: 67 residues processed: 385 average time/residue: 1.2930 time to fit residues: 566.5600 Evaluate side-chains 338 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 256 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 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 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 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 573 CYS 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 742 GLU 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 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 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 155 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 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 215 LYS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 210 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 593 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 85 GLN B 87 HIS 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 352 GLN G 357 HIS ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20367 Z= 0.199 Angle : 0.651 8.547 27613 Z= 0.338 Chirality : 0.043 0.232 2988 Planarity : 0.005 0.069 3562 Dihedral : 7.700 64.985 2725 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.49 % Favored : 91.39 % Rotamer: Outliers : 4.88 % Allowed : 27.19 % Favored : 67.93 % 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: -1.86 (0.16), residues: 2415 helix: 0.21 (0.16), residues: 991 sheet: -1.65 (0.35), residues: 217 loop : -2.48 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 792 HIS 0.007 0.001 HIS G 357 PHE 0.019 0.001 PHE A1031 TYR 0.029 0.002 TYR D 272 ARG 0.011 0.000 ARG F 366 *********************** 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 372 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 265 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7669 (tmmt) cc_final: 0.6850 (mtmt) REVERT: F 361 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7711 (ttmm) REVERT: A 44 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: A 181 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.8044 (m) REVERT: A 182 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6296 (tm-30) REVERT: A 342 ARG cc_start: 0.6400 (mtt180) cc_final: 0.5694 (mtt90) REVERT: A 423 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6428 (ptt-90) REVERT: A 527 LYS cc_start: 0.6710 (tptt) cc_final: 0.6054 (mppt) REVERT: A 552 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7893 (ptp90) REVERT: A 554 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6831 (ptt90) REVERT: A 859 HIS cc_start: 0.6770 (t-90) cc_final: 0.6507 (m90) REVERT: A 896 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: B 45 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5997 (p90) REVERT: B 51 ILE cc_start: 0.8540 (mt) cc_final: 0.8320 (mt) REVERT: B 63 ARG cc_start: 0.6780 (ttm170) cc_final: 0.6513 (mtp85) REVERT: C 68 HIS cc_start: 0.5805 (m-70) cc_final: 0.5568 (t-90) REVERT: C 86 TYR cc_start: 0.7098 (m-80) cc_final: 0.6871 (m-10) REVERT: C 306 ILE cc_start: 0.8036 (pt) cc_final: 0.7659 (pt) REVERT: C 407 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8234 (tt) REVERT: E 246 MET cc_start: 0.6432 (mtm) cc_final: 0.4896 (pp-130) REVERT: G 352 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: G 397 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8462 (tp) REVERT: G 400 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7617 (ptmt) REVERT: G 449 ARG cc_start: 0.7438 (mtp-110) cc_final: 0.7051 (ttm110) REVERT: G 458 ASP cc_start: 0.6784 (m-30) cc_final: 0.6581 (m-30) REVERT: G 550 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6997 (p90) REVERT: G 565 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6196 (m-30) outliers start: 107 outliers final: 53 residues processed: 345 average time/residue: 1.2882 time to fit residues: 504.3236 Evaluate side-chains 304 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 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 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 606 GLU 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 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 888 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 132 VAL 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 203 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 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 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 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 79 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN A 159 ASN A 226 GLN A 593 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 85 GLN B 87 HIS B 88 GLN B 125 ASN B 369 ASN C 183 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN D 170 HIS E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20367 Z= 0.361 Angle : 0.759 11.272 27613 Z= 0.391 Chirality : 0.048 0.296 2988 Planarity : 0.006 0.070 3562 Dihedral : 7.788 70.686 2716 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.19 % Favored : 90.64 % Rotamer: Outliers : 5.16 % Allowed : 27.42 % Favored : 67.43 % 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: -2.00 (0.16), residues: 2415 helix: -0.03 (0.16), residues: 1000 sheet: -1.63 (0.34), residues: 220 loop : -2.48 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 792 HIS 0.007 0.001 HIS B 207 PHE 0.032 0.002 PHE A 381 TYR 0.026 0.002 TYR A 574 ARG 0.012 0.001 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 264 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7722 (tmmt) cc_final: 0.6874 (mtmt) REVERT: F 361 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7728 (ttmm) REVERT: A 181 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8118 (m) REVERT: A 182 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: A 342 ARG cc_start: 0.6392 (mtt180) cc_final: 0.5753 (mtt90) REVERT: A 527 LYS cc_start: 0.6808 (tptt) cc_final: 0.6087 (mppt) REVERT: A 859 HIS cc_start: 0.6963 (t-90) cc_final: 0.6691 (m90) REVERT: B 45 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5998 (p90) REVERT: B 57 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 63 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6769 (mtp85) REVERT: B 92 ASN cc_start: 0.8303 (t0) cc_final: 0.8024 (t0) REVERT: C 86 TYR cc_start: 0.7148 (m-80) cc_final: 0.6940 (m-10) REVERT: C 306 ILE cc_start: 0.8107 (pt) cc_final: 0.7750 (pt) REVERT: C 388 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7442 (ppp) REVERT: E 169 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6989 (mttm) REVERT: E 216 ILE cc_start: 0.7565 (pp) cc_final: 0.7193 (mm) REVERT: E 221 ASN cc_start: 0.8484 (p0) cc_final: 0.8162 (p0) REVERT: E 246 MET cc_start: 0.6681 (mtm) cc_final: 0.5015 (pp-130) REVERT: G 397 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8520 (tp) REVERT: G 400 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7694 (ptmt) REVERT: G 449 ARG cc_start: 0.7526 (mtp-110) cc_final: 0.7109 (ttm110) REVERT: G 550 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.6780 (p90) REVERT: G 565 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6384 (m-30) outliers start: 113 outliers final: 65 residues processed: 345 average time/residue: 1.2599 time to fit residues: 496.3401 Evaluate side-chains 319 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 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 363 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 322 ASP 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 64 ILE Chi-restraints excluded: chain C residue 132 VAL 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 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 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 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 226 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 234 optimal weight: 0.0020 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN A 159 ASN A 461 HIS A 593 HIS A 998 GLN B 24 GLN B 37 ASN B 85 GLN B 87 HIS C 94 GLN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20367 Z= 0.185 Angle : 0.641 9.015 27613 Z= 0.331 Chirality : 0.043 0.261 2988 Planarity : 0.005 0.073 3562 Dihedral : 7.270 62.415 2716 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.03 % Favored : 91.84 % Rotamer: Outliers : 3.97 % Allowed : 28.70 % Favored : 67.34 % 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: -1.64 (0.17), residues: 2415 helix: 0.34 (0.16), residues: 997 sheet: -1.35 (0.35), residues: 214 loop : -2.37 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 390 HIS 0.021 0.001 HIS A 461 PHE 0.020 0.001 PHE A1031 TYR 0.022 0.001 TYR A 891 ARG 0.011 0.000 ARG F 366 *********************** 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 355 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 268 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6644 (t) REVERT: F 361 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7712 (ttmm) REVERT: A 182 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6336 (tm-30) REVERT: A 342 ARG cc_start: 0.6324 (mtt180) cc_final: 0.5766 (mtt90) REVERT: A 350 ASN cc_start: 0.6850 (p0) cc_final: 0.6617 (p0) REVERT: A 423 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6597 (ptt-90) REVERT: A 552 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7156 (ptp90) REVERT: A 554 ARG cc_start: 0.7126 (ptm-80) cc_final: 0.6833 (ptt90) REVERT: A 574 TYR cc_start: 0.6763 (t80) cc_final: 0.6553 (t80) REVERT: A 801 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: A 859 HIS cc_start: 0.6789 (t-90) cc_final: 0.6514 (m90) REVERT: B 45 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5856 (p90) REVERT: B 51 ILE cc_start: 0.8537 (mt) cc_final: 0.8259 (mt) REVERT: B 63 ARG cc_start: 0.6799 (ttm170) cc_final: 0.6505 (mtp180) REVERT: C 306 ILE cc_start: 0.8020 (pt) cc_final: 0.7622 (pt) REVERT: C 340 ILE cc_start: 0.7915 (mm) cc_final: 0.7667 (mm) REVERT: C 388 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7461 (ppp) REVERT: C 407 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8252 (tt) REVERT: E 216 ILE cc_start: 0.7487 (pp) cc_final: 0.7171 (mm) REVERT: E 246 MET cc_start: 0.6337 (mtm) cc_final: 0.4848 (pp-130) REVERT: G 397 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 400 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7657 (ptmt) REVERT: G 449 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7068 (ttm110) REVERT: G 550 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7023 (p90) REVERT: G 565 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6286 (m-30) outliers start: 87 outliers final: 45 residues processed: 327 average time/residue: 1.2986 time to fit residues: 483.2002 Evaluate side-chains 297 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 2.585 ------------------------------------------------------------------------------- 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 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 182 GLU 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 461 HIS 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 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 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 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 132 VAL 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 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL 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 446 SER Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 85 GLN B 87 HIS B 92 ASN C 94 GLN 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** G 352 GLN G 438 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20367 Z= 0.228 Angle : 0.673 9.268 27613 Z= 0.347 Chirality : 0.044 0.322 2988 Planarity : 0.006 0.069 3562 Dihedral : 7.094 67.200 2712 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.24 % Favored : 91.64 % Rotamer: Outliers : 4.47 % Allowed : 28.65 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % Rama-Z (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: -1.58 (0.17), residues: 2415 helix: 0.37 (0.16), residues: 994 sheet: -1.31 (0.36), residues: 207 loop : -2.30 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 412 HIS 0.028 0.001 HIS A 461 PHE 0.025 0.002 PHE B 249 TYR 0.027 0.002 TYR C 86 ARG 0.012 0.001 ARG F 366 *********************** 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 348 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 250 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6366 (t) REVERT: F 208 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.6949 (mtt90) REVERT: F 361 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7703 (ttmm) REVERT: A 44 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 182 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 342 ARG cc_start: 0.6215 (mtt180) cc_final: 0.5657 (mtt90) REVERT: A 423 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6579 (ptt-90) REVERT: A 443 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6405 (mt) REVERT: A 554 ARG cc_start: 0.7207 (ptm-80) cc_final: 0.6907 (ptt90) REVERT: A 859 HIS cc_start: 0.6954 (t-90) cc_final: 0.6695 (m90) REVERT: A 982 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7106 (tpp-160) REVERT: B 45 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5922 (p90) REVERT: B 51 ILE cc_start: 0.8568 (mt) cc_final: 0.8348 (mt) REVERT: B 57 THR cc_start: 0.8228 (p) cc_final: 0.7748 (m) REVERT: B 63 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6581 (mtp85) REVERT: B 75 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.6923 (ptt180) REVERT: C 77 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6434 (pp) REVERT: C 164 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5398 (mp0) REVERT: C 306 ILE cc_start: 0.8017 (pt) cc_final: 0.7618 (pt) REVERT: C 388 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7503 (ppp) REVERT: D 261 GLN cc_start: 0.7115 (mm110) cc_final: 0.6803 (mm110) REVERT: E 169 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7110 (mttm) REVERT: E 216 ILE cc_start: 0.7473 (pp) cc_final: 0.7146 (mm) REVERT: E 221 ASN cc_start: 0.8242 (p0) cc_final: 0.8023 (p0) REVERT: E 246 MET cc_start: 0.6600 (mtm) cc_final: 0.4955 (pp-130) REVERT: E 270 ASP cc_start: 0.3268 (OUTLIER) cc_final: 0.2792 (p0) REVERT: G 397 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8520 (tp) REVERT: G 400 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7698 (ptmt) REVERT: G 449 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.7081 (ttm110) REVERT: G 550 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6865 (p90) REVERT: G 565 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6302 (m-30) outliers start: 98 outliers final: 55 residues processed: 325 average time/residue: 1.3583 time to fit residues: 506.6456 Evaluate side-chains 316 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 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 302 LEU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 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 887 ASP Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR 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 77 LEU Chi-restraints excluded: chain C residue 124 ASN 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 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 85 GLN B 87 HIS B 92 ASN C 94 GLN C 183 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN G 352 GLN G 438 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20367 Z= 0.212 Angle : 0.668 12.010 27613 Z= 0.344 Chirality : 0.044 0.376 2988 Planarity : 0.005 0.069 3562 Dihedral : 6.947 68.458 2711 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 3.97 % Allowed : 29.11 % Favored : 66.93 % 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: -1.47 (0.17), residues: 2415 helix: 0.45 (0.16), residues: 993 sheet: -1.21 (0.36), residues: 207 loop : -2.23 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 412 HIS 0.004 0.001 HIS A 461 PHE 0.028 0.001 PHE B 249 TYR 0.023 0.002 TYR A 574 ARG 0.011 0.000 ARG F 366 *********************** 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 340 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6549 (OUTLIER) cc_final: 0.6291 (t) REVERT: F 208 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.6909 (mtt90) REVERT: F 361 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7709 (ttmm) REVERT: A 44 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: A 182 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6081 (tm-30) REVERT: A 342 ARG cc_start: 0.6212 (mtt180) cc_final: 0.5671 (mtt90) REVERT: A 423 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6607 (ptt-90) REVERT: A 443 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6436 (mt) REVERT: A 552 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7857 (ptp90) REVERT: A 554 ARG cc_start: 0.7174 (ptm-80) cc_final: 0.6841 (ptt90) REVERT: A 789 GLN cc_start: 0.6164 (OUTLIER) cc_final: 0.5646 (mp-120) REVERT: A 859 HIS cc_start: 0.6955 (t-90) cc_final: 0.6697 (m90) REVERT: A 982 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7023 (tpp-160) REVERT: B 45 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5909 (p90) REVERT: B 51 ILE cc_start: 0.8555 (mt) cc_final: 0.8338 (mt) REVERT: B 57 THR cc_start: 0.8224 (p) cc_final: 0.7739 (m) REVERT: B 63 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6506 (mtp85) REVERT: B 75 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6899 (ptt180) REVERT: C 77 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6535 (pp) REVERT: C 164 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: C 388 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7507 (ppp) REVERT: D 261 GLN cc_start: 0.7257 (mm110) cc_final: 0.6934 (mm110) REVERT: E 169 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6971 (mttm) REVERT: E 246 MET cc_start: 0.6404 (mtm) cc_final: 0.4902 (pp-130) REVERT: E 270 ASP cc_start: 0.3322 (OUTLIER) cc_final: 0.2777 (p0) REVERT: G 348 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5797 (m-70) REVERT: G 397 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8518 (tp) REVERT: G 400 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7679 (ptmt) REVERT: G 449 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7079 (ttm110) REVERT: G 531 ARG cc_start: 0.7181 (tpt170) cc_final: 0.6627 (mpt-90) REVERT: G 550 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6934 (p90) REVERT: G 565 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6305 (m-30) outliers start: 87 outliers final: 48 residues processed: 315 average time/residue: 1.3227 time to fit residues: 473.3785 Evaluate side-chains 306 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 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 302 LEU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 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 77 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 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain 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 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 242 optimal weight: 0.0670 chunk 222 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 chunk 153 optimal weight: 10.0000 overall best weight: 0.4330 ------------------------------------------------------------------------------- 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 363 ASN A 159 ASN A 461 HIS A 593 HIS A 998 GLN B 85 GLN B 87 HIS B 92 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 183 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 438 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20367 Z= 0.181 Angle : 0.648 10.530 27613 Z= 0.334 Chirality : 0.043 0.390 2988 Planarity : 0.005 0.069 3562 Dihedral : 6.690 67.932 2708 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 3.28 % Allowed : 29.97 % Favored : 66.74 % 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: -1.26 (0.17), residues: 2415 helix: 0.66 (0.17), residues: 993 sheet: -1.07 (0.37), residues: 206 loop : -2.15 (0.17), residues: 1216 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 0.033 0.001 PHE A 889 TYR 0.037 0.001 TYR C 86 ARG 0.013 0.000 ARG F 366 ********************** 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 335 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 149 THR cc_start: 0.6346 (OUTLIER) cc_final: 0.6141 (t) REVERT: F 361 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7689 (ttmm) REVERT: A 44 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: A 182 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6125 (tm-30) REVERT: A 342 ARG cc_start: 0.6175 (mtt180) cc_final: 0.5653 (mtt90) REVERT: A 423 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6583 (ptt-90) REVERT: A 552 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7330 (ptp90) REVERT: A 554 ARG cc_start: 0.7049 (ptm-80) cc_final: 0.6719 (ptt90) REVERT: A 859 HIS cc_start: 0.6844 (t-90) cc_final: 0.6594 (m90) REVERT: B 45 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5914 (p90) REVERT: B 51 ILE cc_start: 0.8489 (mt) cc_final: 0.8267 (mt) REVERT: B 57 THR cc_start: 0.8164 (p) cc_final: 0.7687 (m) REVERT: B 63 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6474 (mtp85) REVERT: B 211 THR cc_start: 0.8832 (t) cc_final: 0.8583 (m) REVERT: C 164 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5587 (mp0) REVERT: D 203 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8588 (p) REVERT: E 169 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7019 (mttm) REVERT: E 216 ILE cc_start: 0.7370 (pp) cc_final: 0.7078 (mp) REVERT: E 239 PHE cc_start: 0.7343 (t80) cc_final: 0.7117 (t80) REVERT: E 246 MET cc_start: 0.6386 (mtm) cc_final: 0.4995 (pp-130) REVERT: G 348 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5832 (m-70) REVERT: G 352 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: G 400 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7675 (ptmt) REVERT: G 449 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7089 (ttm110) REVERT: G 531 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6593 (mtt90) REVERT: G 550 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7091 (p90) REVERT: G 565 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6264 (m-30) outliers start: 72 outliers final: 41 residues processed: 312 average time/residue: 1.2932 time to fit residues: 458.8694 Evaluate side-chains 298 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 182 GLU 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 461 HIS 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 795 ARG Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 260 THR 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 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 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 LEU 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 348 HIS Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 379 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN A 998 GLN B 92 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 94 GLN ** C 260 HIS ** 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 = 0.4258 r_free = 0.4258 target = 0.198471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148115 restraints weight = 21143.935| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.65 r_work: 0.3506 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20367 Z= 0.226 Angle : 0.676 10.996 27613 Z= 0.348 Chirality : 0.044 0.346 2988 Planarity : 0.006 0.079 3562 Dihedral : 6.711 70.507 2703 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 3.33 % Allowed : 30.11 % Favored : 66.56 % 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: -1.23 (0.17), residues: 2415 helix: 0.65 (0.17), residues: 991 sheet: -1.04 (0.36), residues: 207 loop : -2.11 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 412 HIS 0.012 0.001 HIS A 461 PHE 0.038 0.002 PHE A 889 TYR 0.032 0.002 TYR G 344 ARG 0.013 0.001 ARG F 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8176.42 seconds wall clock time: 207 minutes 8.18 seconds (12428.18 seconds total)