Starting phenix.real_space_refine on Sat Jul 4 13:08:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.map" model { file = "/net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p30_17381/07_2026/8p30_17381.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 Zn 2 6.06 5 S 124 5.16 5 Cl 2 4.86 5 C 13670 2.51 5 N 3366 2.21 5 O 3910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21074 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5913 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 35, 'TRANS': 712} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 12, 'PHE:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4404 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 552} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 4, 'NDG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Restraints were copied for chains: B, D, G, H Time building chain proxies: 7.74, per 1000 atoms: 0.37 Number of scatterers: 21074 At special positions: 0 Unit cell: (148.334, 100.967, 175.757, 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 2 29.99 Cl 2 17.00 S 124 16.00 O 3910 8.00 N 3366 7.00 C 13670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 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=2, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 7 " " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " MAN E 4 " - " MAN E 6 " " BMA G 3 " - " MAN G 4 " " MAN G 4 " - " MAN G 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 546 " " NAG B 903 " - " ASN B 103 " " NAG B 904 " - " ASN B 322 " " NAG B 905 " - " ASN B 432 " " NAG B 906 " - " ASN B 546 " " NAG C 701 " - " ASN C 131 " " NAG C 702 " - " ASN C 357 " " NAG D 701 " - " ASN D 131 " " NAG D 702 " - " ASN D 357 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN B 690 " " NAG H 1 " - " ASN B 90 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 827.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 374 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 378 " 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4964 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 12 sheets defined 72.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.651A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.514A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.715A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.970A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.529A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.203A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 306 through 318 removed outlier: 3.825A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.283A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.787A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.836A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.807A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.740A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.674A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.517A pdb=" N ILE A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 768 Processing helix chain 'B' and resid 22 through 53 removed outlier: 3.650A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.512A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.714A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 250 removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.528A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.202A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 306 through 318 removed outlier: 3.824A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.282A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.787A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 431 through 465 removed outlier: 3.836A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.808A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 522 " --> pdb=" O ARG B 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.741A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.674A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.517A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 768 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.580A pdb=" N VAL C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.845A pdb=" N TYR C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Proline residue: C 46 - end of helix removed outlier: 3.721A pdb=" N VAL C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.579A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.943A pdb=" N SER C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 85 through 115 removed outlier: 3.602A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 167 through 188 removed outlier: 3.517A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.649A pdb=" N TYR C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 219 through 229 removed outlier: 3.900A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.740A pdb=" N TRP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.661A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.550A pdb=" N HIS C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.744A pdb=" N TYR C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.584A pdb=" N TRP C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 429 through 445 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.814A pdb=" N MET C 450 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.839A pdb=" N TRP C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 485 through 498 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 552 through 582 removed outlier: 3.640A pdb=" N LEU C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Proline residue: C 571 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.581A pdb=" N VAL D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.845A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Proline residue: D 46 - end of helix removed outlier: 3.720A pdb=" N VAL D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 70 removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.943A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 3.601A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 167 through 188 removed outlier: 3.517A pdb=" N GLY D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.647A pdb=" N TYR D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 219 through 229 removed outlier: 3.901A pdb=" N GLY D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.740A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.660A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 322 removed outlier: 3.550A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.745A pdb=" N TYR D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 Processing helix chain 'D' and resid 372 through 384 Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.584A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Proline residue: D 417 - end of helix Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 429 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.812A pdb=" N MET D 450 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.840A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 482 Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 511 through 532 Processing helix chain 'D' and resid 552 through 582 removed outlier: 3.640A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Proline residue: D 571 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 removed outlier: 6.781A pdb=" N ASP A 693 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.031A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 670 through 673 removed outlier: 6.781A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AB2, first strand: chain 'C' and resid 535 through 540 Processing sheet with id=AB3, first strand: chain 'D' and resid 535 through 540 1295 hydrogen bonds defined for protein. 3783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4750 1.33 - 1.45: 5022 1.45 - 1.57: 11660 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21636 Sorted by residual: bond pdb=" C YCP D 703 " pdb=" OXT YCP D 703 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C YCP C 703 " pdb=" OXT YCP C 703 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sigma weight residual 1.392 1.430 -0.038 2.00e-02 2.50e+03 3.53e+00 ... (remaining 21631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28924 1.74 - 3.47: 470 3.47 - 5.21: 84 5.21 - 6.95: 28 6.95 - 8.68: 6 Bond angle restraints: 29512 Sorted by residual: angle pdb=" CA PRO C 353 " pdb=" N PRO C 353 " pdb=" CD PRO C 353 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" CA PRO D 353 " pdb=" N PRO D 353 " pdb=" CD PRO D 353 " ideal model delta sigma weight residual 112.00 104.11 7.89 1.40e+00 5.10e-01 3.17e+01 angle pdb=" CA YCP D 703 " pdb=" C YCP D 703 " pdb=" OXT YCP D 703 " ideal model delta sigma weight residual 120.80 112.55 8.25 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA YCP C 703 " pdb=" C YCP C 703 " pdb=" OXT YCP C 703 " ideal model delta sigma weight residual 120.80 112.59 8.21 1.70e+00 3.46e-01 2.33e+01 angle pdb=" CA GLY B 352 " pdb=" C GLY B 352 " pdb=" O GLY B 352 " ideal model delta sigma weight residual 122.37 120.24 2.13 7.30e-01 1.88e+00 8.49e+00 ... (remaining 29507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 12353 23.80 - 47.60: 509 47.60 - 71.39: 80 71.39 - 95.19: 32 95.19 - 118.99: 16 Dihedral angle restraints: 12990 sinusoidal: 5254 harmonic: 7736 Sorted by residual: dihedral pdb=" CA ASN B 718 " pdb=" C ASN B 718 " pdb=" N ASP B 719 " pdb=" CA ASP B 719 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN A 718 " pdb=" C ASN A 718 " pdb=" N ASP A 719 " pdb=" CA ASP A 719 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C2 MAN E 4 " pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " pdb=" C5 MAN E 4 " ideal model delta sinusoidal sigma weight residual -57.62 61.37 -118.99 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 12987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2830 0.055 - 0.111: 487 0.111 - 0.166: 47 0.166 - 0.222: 2 0.222 - 0.277: 8 Chirality restraints: 3374 Sorted by residual: chirality pdb=" C4 NDG B 902 " pdb=" C3 NDG B 902 " pdb=" C5 NDG B 902 " pdb=" O4 NDG B 902 " both_signs ideal model delta sigma weight residual False -2.30 -2.58 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NDG A 902 " pdb=" C3 NDG A 902 " pdb=" C5 NDG A 902 " pdb=" O4 NDG A 902 " both_signs ideal model delta sigma weight residual False -2.30 -2.57 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3371 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 352 " -0.091 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO C 353 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 353 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 353 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 352 " 0.091 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO D 353 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO D 353 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 353 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 396 " -0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE C 396 " 0.085 2.00e-02 2.50e+03 pdb=" O PHE C 396 " -0.031 2.00e-02 2.50e+03 pdb=" N PHE C 397 " -0.029 2.00e-02 2.50e+03 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 158 2.60 - 3.18: 18635 3.18 - 3.75: 33729 3.75 - 4.33: 45305 4.33 - 4.90: 75541 Nonbonded interactions: 173368 Sorted by model distance: nonbonded pdb=" SG CYS C 126 " pdb=" SG CYS C 139 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS D 126 " pdb=" SG CYS D 139 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 309 " pdb=" SG CYS C 358 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 309 " pdb=" SG CYS D 358 " model vdw 2.032 3.760 nonbonded pdb=" OE2 GLU B 402 " pdb="ZN ZN B 901 " model vdw 2.050 2.230 ... (remaining 173363 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.250 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.004 0.067 21678 Z= 0.170 Angle : 0.603 8.682 29614 Z= 0.302 Chirality : 0.043 0.277 3374 Planarity : 0.005 0.133 3684 Dihedral : 14.221 118.989 8008 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.23 % Allowed : 9.19 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2634 helix: 1.71 (0.13), residues: 1684 sheet: 0.55 (0.69), residues: 54 loop : -0.71 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.010 0.001 TYR C 348 PHE 0.011 0.001 PHE C 460 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (21636) covalent geometry : angle 0.58752 / 0.30 (29512) SS BOND : bond 0.00085 / 0.04 ( 6) SS BOND : angle 0.63967 / 0.34 ( 12) hydrogen bonds : bond 0.13839 / 9.29 ( 1287) hydrogen bonds : angle 5.58948 / 3.98 ( 3783) metal coordination : bond 0.00150 / 0.07 ( 4) Misc. bond : bond 0.00108 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00407 / 0.19 ( 4) link_ALPHA1-3 : angle 3.12896 / 1.68 ( 12) link_ALPHA1-6 : bond 0.00501 / 0.23 ( 4) link_ALPHA1-6 : angle 1.77722 / 1.01 ( 12) link_BETA1-4 : bond 0.01050 / 0.48 ( 6) link_BETA1-4 : angle 3.63799 / 2.74 ( 18) link_NAG-ASN : bond 0.00264 / 0.18 ( 16) link_NAG-ASN : angle 1.98713 / 1.38 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 445 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 VAL cc_start: 0.8119 (p) cc_final: 0.7905 (p) REVERT: A 151 ILE cc_start: 0.8719 (mt) cc_final: 0.8506 (mm) REVERT: A 360 MET cc_start: 0.7841 (ttt) cc_final: 0.7610 (ttt) REVERT: B 107 VAL cc_start: 0.8066 (p) cc_final: 0.7851 (p) REVERT: B 360 MET cc_start: 0.7874 (ttt) cc_final: 0.7625 (ttt) REVERT: B 376 MET cc_start: 0.8885 (ttm) cc_final: 0.8595 (ttt) REVERT: B 401 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (t70) REVERT: C 52 ILE cc_start: 0.8479 (mt) cc_final: 0.7868 (mm) REVERT: C 69 MET cc_start: 0.8596 (mmp) cc_final: 0.8108 (mmp) REVERT: C 198 PHE cc_start: 0.8254 (t80) cc_final: 0.7968 (t80) REVERT: C 202 LEU cc_start: 0.8576 (tp) cc_final: 0.8239 (tp) REVERT: C 241 TRP cc_start: 0.7707 (m100) cc_final: 0.7249 (m-10) REVERT: C 391 TRP cc_start: 0.8031 (m100) cc_final: 0.7551 (m100) REVERT: C 414 ILE cc_start: 0.8130 (mt) cc_final: 0.7478 (mt) REVERT: C 476 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7677 (mt-10) REVERT: C 508 MET cc_start: 0.8415 (mmm) cc_final: 0.8053 (mtt) REVERT: D 52 ILE cc_start: 0.8522 (mt) cc_final: 0.7926 (mm) REVERT: D 69 MET cc_start: 0.8672 (mmp) cc_final: 0.8175 (mmp) REVERT: D 202 LEU cc_start: 0.8556 (tp) cc_final: 0.8103 (tp) REVERT: D 241 TRP cc_start: 0.7728 (m100) cc_final: 0.7283 (m-10) REVERT: D 391 TRP cc_start: 0.8063 (m100) cc_final: 0.7635 (m100) REVERT: D 437 VAL cc_start: 0.9129 (t) cc_final: 0.8900 (p) REVERT: D 508 MET cc_start: 0.8391 (mmm) cc_final: 0.8054 (mtt) outliers start: 5 outliers final: 0 residues processed: 448 average time/residue: 0.1334 time to fit residues: 94.1302 Evaluate side-chains 241 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 401 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 96 GLN A 380 GLN A 718 ASN B 24 GLN B 96 GLN B 718 ASN C 67 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 410 ASN C 545 GLN D 67 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 410 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.087406 restraints weight = 41962.021| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.90 r_work: 0.2989 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21678 Z= 0.193 Angle : 0.634 13.324 29614 Z= 0.310 Chirality : 0.044 0.277 3374 Planarity : 0.004 0.075 3684 Dihedral : 10.320 109.372 3508 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.47 % Allowed : 11.75 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.17), residues: 2634 helix: 1.77 (0.13), residues: 1702 sheet: 0.24 (0.53), residues: 82 loop : -0.47 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 192 TYR 0.014 0.002 TYR B 516 PHE 0.024 0.002 PHE B 40 TRP 0.018 0.002 TRP B 48 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (21636) covalent geometry : angle 0.62207 / 0.31 (29512) SS BOND : bond 0.00172 / 0.08 ( 6) SS BOND : angle 0.42524 / 0.22 ( 12) hydrogen bonds : bond 0.04704 / 3.16 ( 1287) hydrogen bonds : angle 4.23481 / 3.03 ( 3783) metal coordination : bond 0.00212 / 0.10 ( 4) Misc. bond : bond 0.00100 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00663 / 0.30 ( 4) link_ALPHA1-3 : angle 2.79681 / 1.50 ( 12) link_ALPHA1-6 : bond 0.00245 / 0.11 ( 4) link_ALPHA1-6 : angle 2.31382 / 1.29 ( 12) link_BETA1-4 : bond 0.01070 / 0.46 ( 6) link_BETA1-4 : angle 3.00389 / 2.27 ( 18) link_NAG-ASN : bond 0.00289 / 0.20 ( 16) link_NAG-ASN : angle 1.90424 / 1.29 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TRP cc_start: 0.7924 (m100) cc_final: 0.7535 (m100) REVERT: A 462 MET cc_start: 0.8433 (mtt) cc_final: 0.7795 (mtm) REVERT: B 48 TRP cc_start: 0.8911 (t-100) cc_final: 0.8656 (t60) REVERT: B 323 MET cc_start: 0.8254 (mmm) cc_final: 0.8038 (mmm) REVERT: B 376 MET cc_start: 0.9214 (ttm) cc_final: 0.8895 (ttt) REVERT: B 401 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8296 (t70) REVERT: B 462 MET cc_start: 0.8414 (mtt) cc_final: 0.7769 (mtm) REVERT: C 50 MET cc_start: 0.8849 (tpp) cc_final: 0.8382 (mpp) REVERT: C 68 ARG cc_start: 0.8606 (tpt90) cc_final: 0.8055 (mmm160) REVERT: C 385 MET cc_start: 0.7840 (mmt) cc_final: 0.7446 (mmt) REVERT: C 397 PHE cc_start: 0.7949 (t80) cc_final: 0.7669 (t80) REVERT: C 489 PHE cc_start: 0.9110 (t80) cc_final: 0.8774 (t80) REVERT: C 512 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8133 (m) REVERT: D 50 MET cc_start: 0.8819 (tpp) cc_final: 0.8337 (mpp) REVERT: D 68 ARG cc_start: 0.8600 (tpt90) cc_final: 0.8075 (tpt90) REVERT: D 69 MET cc_start: 0.8417 (mmp) cc_final: 0.8177 (mmp) REVERT: D 325 ASP cc_start: 0.6868 (t0) cc_final: 0.6605 (t0) REVERT: D 414 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7649 (mt) REVERT: D 437 VAL cc_start: 0.9123 (t) cc_final: 0.8892 (p) REVERT: D 512 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8117 (m) REVERT: D 545 GLN cc_start: 0.7588 (mt0) cc_final: 0.7275 (mt0) outliers start: 53 outliers final: 22 residues processed: 288 average time/residue: 0.1306 time to fit residues: 59.1652 Evaluate side-chains 235 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 206 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 241 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 545 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084780 restraints weight = 41500.786| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.97 r_work: 0.2971 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21678 Z= 0.172 Angle : 0.606 12.499 29614 Z= 0.294 Chirality : 0.043 0.283 3374 Planarity : 0.004 0.061 3684 Dihedral : 9.413 105.687 3508 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.43 % Allowed : 12.45 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2634 helix: 1.81 (0.13), residues: 1706 sheet: 0.10 (0.50), residues: 86 loop : -0.51 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 70 TYR 0.013 0.001 TYR C 60 PHE 0.024 0.002 PHE B 40 TRP 0.015 0.001 TRP C 509 HIS 0.009 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (21636) covalent geometry : angle 0.59400 / 0.29 (29512) SS BOND : bond 0.00236 / 0.12 ( 6) SS BOND : angle 0.34173 / 0.20 ( 12) hydrogen bonds : bond 0.04281 / 2.86 ( 1287) hydrogen bonds : angle 4.02247 / 2.89 ( 3783) metal coordination : bond 0.00192 / 0.09 ( 4) Misc. bond : bond 0.00097 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00740 / 0.36 ( 4) link_ALPHA1-3 : angle 2.76721 / 1.47 ( 12) link_ALPHA1-6 : bond 0.00397 / 0.18 ( 4) link_ALPHA1-6 : angle 2.28712 / 1.32 ( 12) link_BETA1-4 : bond 0.00913 / 0.42 ( 6) link_BETA1-4 : angle 2.92348 / 2.22 ( 18) link_NAG-ASN : bond 0.00222 / 0.15 ( 16) link_NAG-ASN : angle 1.84557 / 1.22 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TRP cc_start: 0.8864 (t-100) cc_final: 0.8423 (t-100) REVERT: B 302 TRP cc_start: 0.7647 (m100) cc_final: 0.7309 (m100) REVERT: B 323 MET cc_start: 0.8413 (mmm) cc_final: 0.8092 (mmm) REVERT: B 376 MET cc_start: 0.9303 (ttm) cc_final: 0.8940 (ttt) REVERT: B 401 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8205 (t70) REVERT: C 33 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7757 (p90) REVERT: C 397 PHE cc_start: 0.8020 (t80) cc_final: 0.7661 (t80) REVERT: C 407 MET cc_start: 0.8426 (tpt) cc_final: 0.7981 (tpt) REVERT: C 509 TRP cc_start: 0.7427 (m-10) cc_final: 0.6899 (m-90) REVERT: C 516 LEU cc_start: 0.9097 (mp) cc_final: 0.8894 (mp) REVERT: D 33 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7741 (p90) REVERT: D 68 ARG cc_start: 0.8305 (tpt90) cc_final: 0.7940 (tpt90) REVERT: D 96 PHE cc_start: 0.9011 (t80) cc_final: 0.8794 (t80) REVERT: D 407 MET cc_start: 0.8480 (tpt) cc_final: 0.8073 (tpt) REVERT: D 414 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7811 (mt) REVERT: D 509 TRP cc_start: 0.7886 (m-10) cc_final: 0.7270 (m-90) REVERT: D 516 LEU cc_start: 0.9084 (mp) cc_final: 0.8881 (mp) outliers start: 52 outliers final: 27 residues processed: 268 average time/residue: 0.1222 time to fit residues: 53.2034 Evaluate side-chains 235 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 501 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 137 optimal weight: 0.0570 chunk 258 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084778 restraints weight = 41745.878| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.83 r_work: 0.3007 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21678 Z= 0.142 Angle : 0.570 12.072 29614 Z= 0.274 Chirality : 0.042 0.272 3374 Planarity : 0.004 0.055 3684 Dihedral : 8.563 102.306 3508 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.15 % Allowed : 13.57 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.16), residues: 2634 helix: 1.94 (0.13), residues: 1700 sheet: 0.15 (0.49), residues: 86 loop : -0.51 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.011 0.001 TYR D 101 PHE 0.026 0.001 PHE B 40 TRP 0.015 0.001 TRP A 48 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21636) covalent geometry : angle 0.55838 / 0.27 (29512) SS BOND : bond 0.00172 / 0.09 ( 6) SS BOND : angle 0.41511 / 0.24 ( 12) hydrogen bonds : bond 0.03976 / 2.66 ( 1287) hydrogen bonds : angle 3.90798 / 2.81 ( 3783) metal coordination : bond 0.00160 / 0.07 ( 4) Misc. bond : bond 0.00091 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00723 / 0.34 ( 4) link_ALPHA1-3 : angle 2.58196 / 1.36 ( 12) link_ALPHA1-6 : bond 0.00549 / 0.25 ( 4) link_ALPHA1-6 : angle 2.09752 / 1.23 ( 12) link_BETA1-4 : bond 0.01000 / 0.45 ( 6) link_BETA1-4 : angle 2.80045 / 2.13 ( 18) link_NAG-ASN : bond 0.00219 / 0.15 ( 16) link_NAG-ASN : angle 1.77913 / 1.16 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8954 (mt) cc_final: 0.8749 (mt) REVERT: B 48 TRP cc_start: 0.8922 (t-100) cc_final: 0.8440 (t-100) REVERT: B 100 LEU cc_start: 0.8987 (mt) cc_final: 0.8779 (mt) REVERT: B 401 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8089 (t70) REVERT: C 33 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7661 (p90) REVERT: C 50 MET cc_start: 0.8950 (tpp) cc_final: 0.8331 (mpp) REVERT: C 68 ARG cc_start: 0.8431 (tpt90) cc_final: 0.8127 (tpt90) REVERT: C 198 PHE cc_start: 0.8422 (t80) cc_final: 0.8198 (t80) REVERT: C 397 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7702 (t80) REVERT: C 407 MET cc_start: 0.8525 (tpt) cc_final: 0.8097 (tpt) REVERT: C 414 ILE cc_start: 0.7807 (mt) cc_final: 0.7579 (mt) REVERT: C 509 TRP cc_start: 0.7751 (m-10) cc_final: 0.7244 (m-90) REVERT: C 516 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8858 (mp) REVERT: D 33 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7651 (p90) REVERT: D 68 ARG cc_start: 0.8441 (tpt90) cc_final: 0.8051 (tpt90) REVERT: D 198 PHE cc_start: 0.8425 (t80) cc_final: 0.8216 (t80) REVERT: D 407 MET cc_start: 0.8550 (tpt) cc_final: 0.8118 (tpt) REVERT: D 414 ILE cc_start: 0.8091 (mt) cc_final: 0.7864 (mt) REVERT: D 476 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7546 (mt-10) REVERT: D 509 TRP cc_start: 0.7991 (m-10) cc_final: 0.7457 (m-90) outliers start: 46 outliers final: 30 residues processed: 262 average time/residue: 0.1244 time to fit residues: 52.6350 Evaluate side-chains 241 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 30 optimal weight: 0.0270 chunk 182 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 139 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086696 restraints weight = 41323.647| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.66 r_work: 0.3061 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21678 Z= 0.105 Angle : 0.549 11.903 29614 Z= 0.260 Chirality : 0.041 0.258 3374 Planarity : 0.004 0.051 3684 Dihedral : 7.916 99.061 3508 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.54 % Allowed : 14.13 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.17), residues: 2634 helix: 2.03 (0.13), residues: 1720 sheet: 0.10 (0.50), residues: 86 loop : -0.38 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 78 TYR 0.013 0.001 TYR D 101 PHE 0.026 0.001 PHE C 96 TRP 0.024 0.001 TRP A 302 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (21636) covalent geometry : angle 0.53786 / 0.26 (29512) SS BOND : bond 0.00229 / 0.14 ( 6) SS BOND : angle 0.69660 / 0.39 ( 12) hydrogen bonds : bond 0.03626 / 2.43 ( 1287) hydrogen bonds : angle 3.78012 / 2.73 ( 3783) metal coordination : bond 0.00287 / 0.15 ( 4) Misc. bond : bond 0.00049 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00889 / 0.41 ( 4) link_ALPHA1-3 : angle 2.35810 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00868 / 0.40 ( 4) link_ALPHA1-6 : angle 1.86434 / 1.11 ( 12) link_BETA1-4 : bond 0.01042 / 0.49 ( 6) link_BETA1-4 : angle 2.78365 / 2.11 ( 18) link_NAG-ASN : bond 0.00279 / 0.19 ( 16) link_NAG-ASN : angle 1.69160 / 1.10 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.7949 (mmm) cc_final: 0.7663 (mmm) REVERT: B 48 TRP cc_start: 0.8880 (t-100) cc_final: 0.8335 (t-100) REVERT: B 108 LEU cc_start: 0.7608 (tp) cc_final: 0.7307 (tp) REVERT: C 33 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8045 (p90) REVERT: C 50 MET cc_start: 0.8972 (tpp) cc_final: 0.8442 (mpp) REVERT: C 68 ARG cc_start: 0.8451 (tpt90) cc_final: 0.8116 (tpt90) REVERT: C 198 PHE cc_start: 0.8390 (t80) cc_final: 0.8169 (t80) REVERT: C 391 TRP cc_start: 0.8636 (m100) cc_final: 0.8226 (m100) REVERT: C 397 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7712 (t80) REVERT: C 407 MET cc_start: 0.8582 (tpt) cc_final: 0.8157 (tpt) REVERT: C 414 ILE cc_start: 0.7836 (mt) cc_final: 0.7601 (mt) REVERT: C 509 TRP cc_start: 0.7978 (m-10) cc_final: 0.7485 (m-90) REVERT: D 33 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8048 (p90) REVERT: D 50 MET cc_start: 0.9016 (tpp) cc_final: 0.8431 (mpp) REVERT: D 68 ARG cc_start: 0.8453 (tpt90) cc_final: 0.8039 (tpt90) REVERT: D 84 LEU cc_start: 0.7924 (mm) cc_final: 0.7716 (mp) REVERT: D 262 PHE cc_start: 0.7125 (m-10) cc_final: 0.6821 (m-80) REVERT: D 391 TRP cc_start: 0.8606 (m100) cc_final: 0.8195 (m100) REVERT: D 407 MET cc_start: 0.8618 (tpt) cc_final: 0.8196 (tpt) REVERT: D 414 ILE cc_start: 0.8121 (mt) cc_final: 0.7893 (mt) REVERT: D 476 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 509 TRP cc_start: 0.8111 (m-10) cc_final: 0.7821 (m-90) outliers start: 33 outliers final: 19 residues processed: 252 average time/residue: 0.1220 time to fit residues: 49.9930 Evaluate side-chains 228 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 206 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN A 277 ASN A 718 ASN B 250 ASN B 277 ASN B 380 GLN B 599 ASN B 718 ASN C 27 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN D 27 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081063 restraints weight = 41548.515| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.49 r_work: 0.2964 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21678 Z= 0.266 Angle : 0.660 11.779 29614 Z= 0.322 Chirality : 0.045 0.269 3374 Planarity : 0.005 0.061 3684 Dihedral : 8.254 97.549 3506 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 13.67 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2634 helix: 1.80 (0.12), residues: 1710 sheet: -0.02 (0.47), residues: 86 loop : -0.41 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 70 TYR 0.019 0.002 TYR C 524 PHE 0.024 0.002 PHE D 96 TRP 0.027 0.002 TRP A 302 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (21636) covalent geometry : angle 0.64952 / 0.32 (29512) SS BOND : bond 0.00226 / 0.13 ( 6) SS BOND : angle 0.53581 / 0.31 ( 12) hydrogen bonds : bond 0.04356 / 2.92 ( 1287) hydrogen bonds : angle 4.00453 / 2.88 ( 3783) metal coordination : bond 0.00562 / 0.27 ( 4) Misc. bond : bond 0.00129 / 0.06 ( 2) link_ALPHA1-3 : bond 0.00412 / 0.20 ( 4) link_ALPHA1-3 : angle 2.51725 / 1.34 ( 12) link_ALPHA1-6 : bond 0.00260 / 0.12 ( 4) link_ALPHA1-6 : angle 2.58718 / 1.51 ( 12) link_BETA1-4 : bond 0.00945 / 0.43 ( 6) link_BETA1-4 : angle 2.77001 / 2.09 ( 18) link_NAG-ASN : bond 0.00161 / 0.11 ( 16) link_NAG-ASN : angle 1.72874 / 1.13 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8248 (tmm) cc_final: 0.8026 (tmm) REVERT: A 323 MET cc_start: 0.7988 (mmm) cc_final: 0.7752 (mmm) REVERT: A 392 LEU cc_start: 0.9275 (mt) cc_final: 0.8804 (mt) REVERT: A 408 MET cc_start: 0.9299 (mmm) cc_final: 0.9086 (mmm) REVERT: B 48 TRP cc_start: 0.8897 (t-100) cc_final: 0.8322 (t-100) REVERT: B 108 LEU cc_start: 0.7505 (tp) cc_final: 0.7189 (tp) REVERT: B 190 MET cc_start: 0.8254 (tmm) cc_final: 0.8018 (tmm) REVERT: B 408 MET cc_start: 0.9299 (mmm) cc_final: 0.9092 (mmm) REVERT: C 33 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7946 (p90) REVERT: C 50 MET cc_start: 0.9031 (tpp) cc_final: 0.8758 (mmp) REVERT: C 68 ARG cc_start: 0.8432 (tpt90) cc_final: 0.8016 (tpt90) REVERT: C 198 PHE cc_start: 0.8353 (t80) cc_final: 0.8138 (t80) REVERT: C 344 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7946 (p90) REVERT: C 391 TRP cc_start: 0.8691 (m100) cc_final: 0.8381 (m100) REVERT: C 397 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7667 (t80) REVERT: C 414 ILE cc_start: 0.7871 (mt) cc_final: 0.7653 (mt) REVERT: C 509 TRP cc_start: 0.8083 (m-10) cc_final: 0.7480 (m-90) REVERT: D 33 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7942 (p90) REVERT: D 50 MET cc_start: 0.9063 (tpp) cc_final: 0.8702 (mmp) REVERT: D 68 ARG cc_start: 0.8557 (tpt90) cc_final: 0.8130 (tpt90) REVERT: D 344 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7950 (p90) REVERT: D 391 TRP cc_start: 0.8665 (m100) cc_final: 0.8298 (m100) REVERT: D 414 ILE cc_start: 0.8130 (mt) cc_final: 0.7909 (mt) REVERT: D 509 TRP cc_start: 0.8128 (m-10) cc_final: 0.7665 (m-90) outliers start: 49 outliers final: 36 residues processed: 248 average time/residue: 0.1210 time to fit residues: 49.0615 Evaluate side-chains 242 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 559 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 191 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 599 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082876 restraints weight = 41382.957| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.67 r_work: 0.3002 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21678 Z= 0.153 Angle : 0.594 11.989 29614 Z= 0.283 Chirality : 0.043 0.261 3374 Planarity : 0.004 0.049 3684 Dihedral : 7.899 93.145 3506 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.54 % Allowed : 15.49 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.16), residues: 2634 helix: 1.88 (0.12), residues: 1708 sheet: -0.04 (0.47), residues: 86 loop : -0.30 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 70 TYR 0.021 0.001 TYR B 183 PHE 0.020 0.001 PHE D 96 TRP 0.029 0.001 TRP D 77 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (21636) covalent geometry : angle 0.58374 / 0.28 (29512) SS BOND : bond 0.00210 / 0.11 ( 6) SS BOND : angle 0.44919 / 0.26 ( 12) hydrogen bonds : bond 0.03988 / 2.67 ( 1287) hydrogen bonds : angle 3.89278 / 2.80 ( 3783) metal coordination : bond 0.00184 / 0.09 ( 4) Misc. bond : bond 0.00094 / 0.05 ( 2) link_ALPHA1-3 : bond 0.00696 / 0.32 ( 4) link_ALPHA1-3 : angle 2.35461 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00741 / 0.34 ( 4) link_ALPHA1-6 : angle 2.23987 / 1.34 ( 12) link_BETA1-4 : bond 0.00995 / 0.44 ( 6) link_BETA1-4 : angle 2.75509 / 2.08 ( 18) link_NAG-ASN : bond 0.00202 / 0.14 ( 16) link_NAG-ASN : angle 1.70757 / 1.10 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8920 (t80) REVERT: A 306 ARG cc_start: 0.8786 (ptt-90) cc_final: 0.8501 (ptt-90) REVERT: A 323 MET cc_start: 0.7973 (mmm) cc_final: 0.7759 (mmm) REVERT: A 509 ASP cc_start: 0.8446 (t0) cc_final: 0.8172 (t0) REVERT: B 48 TRP cc_start: 0.8890 (t-100) cc_final: 0.8276 (t-100) REVERT: B 108 LEU cc_start: 0.7667 (tp) cc_final: 0.7337 (tp) REVERT: B 190 MET cc_start: 0.8189 (tmm) cc_final: 0.7964 (tmm) REVERT: B 408 MET cc_start: 0.9256 (mmm) cc_final: 0.9052 (mmm) REVERT: C 33 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8179 (p90) REVERT: C 50 MET cc_start: 0.9059 (tpp) cc_final: 0.8827 (mmp) REVERT: C 68 ARG cc_start: 0.8405 (tpt90) cc_final: 0.8002 (tpt90) REVERT: C 198 PHE cc_start: 0.8354 (t80) cc_final: 0.8141 (t80) REVERT: C 344 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7739 (p90) REVERT: C 391 TRP cc_start: 0.8624 (m100) cc_final: 0.8295 (m100) REVERT: C 397 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7804 (t80) REVERT: C 407 MET cc_start: 0.8768 (tpt) cc_final: 0.8312 (tpt) REVERT: C 414 ILE cc_start: 0.7887 (mt) cc_final: 0.7665 (mt) REVERT: C 509 TRP cc_start: 0.8089 (m-10) cc_final: 0.7578 (m-90) REVERT: C 524 TYR cc_start: 0.8454 (t80) cc_final: 0.8157 (t80) REVERT: D 33 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8058 (p90) REVERT: D 50 MET cc_start: 0.9033 (tpp) cc_final: 0.8762 (mmp) REVERT: D 68 ARG cc_start: 0.8471 (tpt90) cc_final: 0.8088 (tpt90) REVERT: D 344 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7747 (p90) REVERT: D 385 MET cc_start: 0.7588 (mmp) cc_final: 0.7374 (mmp) REVERT: D 391 TRP cc_start: 0.8557 (m100) cc_final: 0.8324 (m100) REVERT: D 414 ILE cc_start: 0.8136 (mt) cc_final: 0.7911 (mt) REVERT: D 509 TRP cc_start: 0.8174 (m-10) cc_final: 0.7954 (m-90) outliers start: 33 outliers final: 22 residues processed: 235 average time/residue: 0.1244 time to fit residues: 47.4150 Evaluate side-chains 230 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 358 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 187 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 599 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.131671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084077 restraints weight = 41033.450| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.10 r_work: 0.2917 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21678 Z= 0.216 Angle : 0.635 12.136 29614 Z= 0.305 Chirality : 0.044 0.263 3374 Planarity : 0.004 0.048 3684 Dihedral : 7.917 88.117 3506 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.91 % Allowed : 14.74 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2634 helix: 1.79 (0.12), residues: 1712 sheet: -0.02 (0.47), residues: 86 loop : -0.32 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 78 TYR 0.023 0.002 TYR B 183 PHE 0.030 0.002 PHE C 96 TRP 0.019 0.002 TRP A 48 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (21636) covalent geometry : angle 0.62457 / 0.30 (29512) SS BOND : bond 0.00194 / 0.10 ( 6) SS BOND : angle 0.51546 / 0.30 ( 12) hydrogen bonds : bond 0.04167 / 2.78 ( 1287) hydrogen bonds : angle 3.97649 / 2.86 ( 3783) metal coordination : bond 0.00431 / 0.21 ( 4) Misc. bond : bond 0.00111 / 0.06 ( 2) link_ALPHA1-3 : bond 0.00537 / 0.25 ( 4) link_ALPHA1-3 : angle 2.36120 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00596 / 0.27 ( 4) link_ALPHA1-6 : angle 2.49017 / 1.48 ( 12) link_BETA1-4 : bond 0.01028 / 0.47 ( 6) link_BETA1-4 : angle 2.76983 / 2.10 ( 18) link_NAG-ASN : bond 0.00166 / 0.12 ( 16) link_NAG-ASN : angle 1.70767 / 1.11 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8035 (tp) cc_final: 0.7592 (tp) REVERT: A 392 LEU cc_start: 0.9275 (mt) cc_final: 0.8812 (mt) REVERT: A 640 MET cc_start: 0.8868 (mmm) cc_final: 0.8648 (mmm) REVERT: B 48 TRP cc_start: 0.8902 (t-100) cc_final: 0.8578 (t60) REVERT: B 108 LEU cc_start: 0.7595 (tp) cc_final: 0.7278 (tp) REVERT: B 183 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8672 (t80) REVERT: B 360 MET cc_start: 0.7972 (ppp) cc_final: 0.7765 (ppp) REVERT: B 408 MET cc_start: 0.9206 (mmm) cc_final: 0.9001 (mmm) REVERT: B 509 ASP cc_start: 0.8134 (t0) cc_final: 0.7866 (t0) REVERT: B 640 MET cc_start: 0.8867 (mmm) cc_final: 0.8651 (mmm) REVERT: C 33 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8161 (p90) REVERT: C 50 MET cc_start: 0.9056 (tpp) cc_final: 0.8791 (mmp) REVERT: C 68 ARG cc_start: 0.8395 (tpt90) cc_final: 0.8016 (tpt90) REVERT: C 198 PHE cc_start: 0.8385 (t80) cc_final: 0.8179 (t80) REVERT: C 344 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7747 (p90) REVERT: C 391 TRP cc_start: 0.8493 (m100) cc_final: 0.8174 (m100) REVERT: C 397 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7724 (t80) REVERT: C 414 ILE cc_start: 0.7856 (mt) cc_final: 0.7636 (mt) REVERT: C 509 TRP cc_start: 0.8066 (m-10) cc_final: 0.7664 (m-90) REVERT: D 33 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8046 (p90) REVERT: D 50 MET cc_start: 0.9031 (tpp) cc_final: 0.8740 (mmp) REVERT: D 344 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7733 (p90) REVERT: D 385 MET cc_start: 0.7604 (mmt) cc_final: 0.7372 (mmp) REVERT: D 391 TRP cc_start: 0.8518 (m100) cc_final: 0.8290 (m100) REVERT: D 414 ILE cc_start: 0.8117 (mt) cc_final: 0.7897 (mt) REVERT: D 509 TRP cc_start: 0.8120 (m-10) cc_final: 0.7870 (m-90) outliers start: 41 outliers final: 28 residues processed: 235 average time/residue: 0.1164 time to fit residues: 44.8471 Evaluate side-chains 234 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 559 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 6 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 201 optimal weight: 0.4980 chunk 166 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 224 optimal weight: 0.4980 chunk 176 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 ASN B 599 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084991 restraints weight = 41221.303| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.50 r_work: 0.3031 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21678 Z= 0.110 Angle : 0.581 11.920 29614 Z= 0.272 Chirality : 0.041 0.248 3374 Planarity : 0.004 0.049 3684 Dihedral : 7.209 77.346 3506 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.12 % Allowed : 15.39 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2634 helix: 1.97 (0.13), residues: 1708 sheet: -0.29 (0.50), residues: 70 loop : -0.20 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 78 TYR 0.032 0.001 TYR A 183 PHE 0.031 0.001 PHE C 96 TRP 0.026 0.001 TRP A 48 HIS 0.004 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21636) covalent geometry : angle 0.57115 / 0.27 (29512) SS BOND : bond 0.00182 / 0.08 ( 6) SS BOND : angle 0.35869 / 0.21 ( 12) hydrogen bonds : bond 0.03706 / 2.48 ( 1287) hydrogen bonds : angle 3.78900 / 2.72 ( 3783) metal coordination : bond 0.00206 / 0.10 ( 4) Misc. bond : bond 0.00040 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00907 / 0.42 ( 4) link_ALPHA1-3 : angle 2.08693 / 1.09 ( 12) link_ALPHA1-6 : bond 0.01219 / 0.56 ( 4) link_ALPHA1-6 : angle 2.13892 / 1.28 ( 12) link_BETA1-4 : bond 0.01063 / 0.49 ( 6) link_BETA1-4 : angle 2.76891 / 2.09 ( 18) link_NAG-ASN : bond 0.00285 / 0.20 ( 16) link_NAG-ASN : angle 1.66550 / 1.07 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8067 (tp) cc_final: 0.7678 (tp) REVERT: A 183 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8840 (t80) REVERT: A 392 LEU cc_start: 0.9246 (mt) cc_final: 0.8800 (mt) REVERT: B 48 TRP cc_start: 0.8816 (t-100) cc_final: 0.8327 (t-100) REVERT: B 108 LEU cc_start: 0.7661 (tp) cc_final: 0.7362 (tp) REVERT: B 183 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8686 (t80) REVERT: B 509 ASP cc_start: 0.8037 (t0) cc_final: 0.7773 (t0) REVERT: C 33 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8173 (p90) REVERT: C 50 MET cc_start: 0.9046 (tpp) cc_final: 0.8832 (mmp) REVERT: C 68 ARG cc_start: 0.8360 (tpt90) cc_final: 0.8026 (tpt90) REVERT: C 215 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8265 (mm) REVERT: C 344 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7603 (p90) REVERT: C 391 TRP cc_start: 0.8480 (m100) cc_final: 0.8144 (m100) REVERT: C 397 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7706 (t80) REVERT: C 414 ILE cc_start: 0.7848 (mt) cc_final: 0.7625 (mt) REVERT: C 509 TRP cc_start: 0.8134 (m-10) cc_final: 0.7894 (m-10) REVERT: D 33 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8270 (p90) REVERT: D 50 MET cc_start: 0.9015 (tpp) cc_final: 0.8766 (mmp) REVERT: D 344 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7604 (p90) REVERT: D 391 TRP cc_start: 0.8587 (m100) cc_final: 0.8334 (m100) REVERT: D 414 ILE cc_start: 0.8134 (mt) cc_final: 0.7924 (mt) outliers start: 24 outliers final: 14 residues processed: 233 average time/residue: 0.1131 time to fit residues: 43.1917 Evaluate side-chains 227 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 222 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN A 718 ASN B 599 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.133033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.084072 restraints weight = 41276.068| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.00 r_work: 0.2963 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21678 Z= 0.134 Angle : 0.599 12.242 29614 Z= 0.280 Chirality : 0.042 0.246 3374 Planarity : 0.004 0.048 3684 Dihedral : 6.838 77.827 3506 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.17 % Allowed : 15.53 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 2634 helix: 1.97 (0.13), residues: 1708 sheet: -0.30 (0.50), residues: 70 loop : -0.16 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 78 TYR 0.028 0.001 TYR A 183 PHE 0.035 0.001 PHE C 96 TRP 0.033 0.001 TRP D 509 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21636) covalent geometry : angle 0.59003 / 0.28 (29512) SS BOND : bond 0.00173 / 0.09 ( 6) SS BOND : angle 0.45835 / 0.27 ( 12) hydrogen bonds : bond 0.03765 / 2.51 ( 1287) hydrogen bonds : angle 3.84163 / 2.77 ( 3783) metal coordination : bond 0.00181 / 0.09 ( 4) Misc. bond : bond 0.00067 / 0.03 ( 2) link_ALPHA1-3 : bond 0.00744 / 0.34 ( 4) link_ALPHA1-3 : angle 1.98300 / 1.05 ( 12) link_ALPHA1-6 : bond 0.01373 / 0.63 ( 4) link_ALPHA1-6 : angle 1.90256 / 1.09 ( 12) link_BETA1-4 : bond 0.01059 / 0.48 ( 6) link_BETA1-4 : angle 2.75362 / 2.07 ( 18) link_NAG-ASN : bond 0.00200 / 0.14 ( 16) link_NAG-ASN : angle 1.64987 / 1.07 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8143 (tp) cc_final: 0.7745 (tp) REVERT: A 183 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8743 (t80) REVERT: A 392 LEU cc_start: 0.9253 (mt) cc_final: 0.8823 (mt) REVERT: B 48 TRP cc_start: 0.8844 (t-100) cc_final: 0.8570 (t60) REVERT: B 108 LEU cc_start: 0.7754 (tp) cc_final: 0.7468 (tp) REVERT: B 183 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8567 (t80) REVERT: B 360 MET cc_start: 0.8017 (ppp) cc_final: 0.7762 (ppp) REVERT: B 509 ASP cc_start: 0.8009 (t0) cc_final: 0.7706 (t0) REVERT: C 33 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8051 (p90) REVERT: C 50 MET cc_start: 0.9025 (tpp) cc_final: 0.8793 (mmp) REVERT: C 68 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8079 (tpt90) REVERT: C 262 PHE cc_start: 0.7432 (m-80) cc_final: 0.7215 (m-80) REVERT: C 344 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7592 (p90) REVERT: C 391 TRP cc_start: 0.8382 (m100) cc_final: 0.8050 (m100) REVERT: C 397 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7631 (t80) REVERT: C 414 ILE cc_start: 0.7909 (mt) cc_final: 0.7702 (mt) REVERT: C 509 TRP cc_start: 0.8080 (m-10) cc_final: 0.7859 (m-10) REVERT: D 33 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8052 (p90) REVERT: D 50 MET cc_start: 0.9002 (tpp) cc_final: 0.8729 (mmp) REVERT: D 344 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7589 (p90) REVERT: D 391 TRP cc_start: 0.8423 (m100) cc_final: 0.8107 (m100) REVERT: D 414 ILE cc_start: 0.8124 (mt) cc_final: 0.7922 (mt) outliers start: 25 outliers final: 15 residues processed: 235 average time/residue: 0.1209 time to fit residues: 46.3022 Evaluate side-chains 226 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 397 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 473 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 129 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 240 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN A 718 ASN B 599 ASN B 718 ASN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.134309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085876 restraints weight = 41183.216| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.54 r_work: 0.3038 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21678 Z= 0.109 Angle : 0.586 11.874 29614 Z= 0.273 Chirality : 0.041 0.238 3374 Planarity : 0.004 0.048 3684 Dihedral : 6.301 77.266 3506 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.26 % Allowed : 15.67 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2634 helix: 1.97 (0.13), residues: 1712 sheet: -0.34 (0.50), residues: 70 loop : -0.08 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 78 TYR 0.029 0.001 TYR A 183 PHE 0.035 0.001 PHE C 96 TRP 0.042 0.001 TRP D 509 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21636) covalent geometry : angle 0.57711 / 0.27 (29512) SS BOND : bond 0.00158 / 0.07 ( 6) SS BOND : angle 0.35082 / 0.21 ( 12) hydrogen bonds : bond 0.03566 / 2.38 ( 1287) hydrogen bonds : angle 3.79757 / 2.74 ( 3783) metal coordination : bond 0.00168 / 0.08 ( 4) Misc. bond : bond 0.00038 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00796 / 0.37 ( 4) link_ALPHA1-3 : angle 1.93434 / 1.04 ( 12) link_ALPHA1-6 : bond 0.01666 / 0.76 ( 4) link_ALPHA1-6 : angle 1.73723 / 0.86 ( 12) link_BETA1-4 : bond 0.01120 / 0.52 ( 6) link_BETA1-4 : angle 2.81204 / 2.10 ( 18) link_NAG-ASN : bond 0.00245 / 0.17 ( 16) link_NAG-ASN : angle 1.62140 / 1.05 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5209.88 seconds wall clock time: 89 minutes 47.04 seconds (5387.04 seconds total)