Starting phenix.real_space_refine on Thu Mar 5 16:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pme_13530/03_2026/7pme_13530.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 12 5.49 5 Mg 7 5.21 5 S 148 5.16 5 C 14851 2.51 5 N 3963 2.21 5 O 4389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.42, per 1000 atoms: 0.23 Number of scatterers: 23370 At special positions: 0 Unit cell: (169.4, 209, 182.6, 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) S 148 16.00 P 12 15.00 Mg 7 11.99 O 4389 8.00 N 3963 7.00 C 14851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 996.3 milliseconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5464 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 35 sheets defined 54.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.502A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.827A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.146A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.122A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.618A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.887A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.676A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.756A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.767A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.591A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.086A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.635A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.515A pdb=" N THR A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.266A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.501A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.118A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.610A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.660A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.743A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.729A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.331A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.614A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.769A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.299A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.421A pdb=" N TYR D 119 " --> pdb=" O LEU D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.555A pdb=" N GLU D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 191 through 207 removed outlier: 3.774A pdb=" N LYS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 259 through 269 removed outlier: 4.161A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 271 No H-bonds generated for 'chain 'D' and resid 270 through 271' Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.065A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.667A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.887A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.646A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 367 through 375 Processing helix chain 'D' and resid 392 through 424 Processing helix chain 'D' and resid 448 through 480 Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.740A pdb=" N LEU D 486 " --> pdb=" O PRO D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.754A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.580A pdb=" N LEU D 580 " --> pdb=" O GLN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 4.116A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 635 through 653 Processing helix chain 'D' and resid 674 through 685 removed outlier: 3.655A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 723 through 736 removed outlier: 3.789A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 734 " --> pdb=" O ASN D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 754 through 792 Processing helix chain 'E' and resid 5 through 19 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.155A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 79 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.513A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.647A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.637A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.703A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.313A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.604A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.770A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.344A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.163A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.599A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.644A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 183 through 194 removed outlier: 3.697A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 232 Processing helix chain 'G' and resid 252 through 260 Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 286 through 295 removed outlier: 3.760A pdb=" N ARG G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.330A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.581A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.787A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.259A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.326A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.797A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.240A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.624A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.975A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.096A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.331A pdb=" N LEU D 107 " --> pdb=" O ARG D 660 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE D 662 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA D 109 " --> pdb=" O ILE D 662 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 659 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE D 160 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N CYS D 661 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER D 162 " --> pdb=" O CYS D 661 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN D 157 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU D 436 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 159 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 438 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 161 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 5.708A pdb=" N ALA D 209 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 216 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.235A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 377 through 382 Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC4, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC5, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AC6, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.615A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.991A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.600A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.004A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 1177 hydrogen bonds defined for protein. 3270 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: 4.24 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3908 1.32 - 1.44: 6294 1.44 - 1.57: 13398 1.57 - 1.69: 20 1.69 - 1.81: 243 Bond restraints: 23863 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" O3A ANP D1901 " pdb=" PB ANP D1901 " ideal model delta sigma weight residual 1.700 1.561 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 23858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 32063 3.77 - 7.53: 165 7.53 - 11.30: 24 11.30 - 15.06: 2 15.06 - 18.83: 2 Bond angle restraints: 32256 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.12 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB ANP D1901 " pdb=" N3B ANP D1901 " pdb=" PG ANP D1901 " ideal model delta sigma weight residual 126.95 108.67 18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.27 10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.63 10.07 1.80e+00 3.09e-01 3.13e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.16 9.54 1.80e+00 3.09e-01 2.81e+01 ... (remaining 32251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.36: 13789 25.36 - 50.73: 484 50.73 - 76.09: 116 76.09 - 101.46: 43 101.46 - 126.82: 9 Dihedral angle restraints: 14441 sinusoidal: 5959 harmonic: 8482 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.18 126.82 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.24 126.76 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.27 126.74 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 14438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2819 0.056 - 0.112: 601 0.112 - 0.168: 101 0.168 - 0.223: 7 0.223 - 0.279: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C3' ANP D1901 " pdb=" C2' ANP D1901 " pdb=" C4' ANP D1901 " pdb=" O3' ANP D1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3527 not shown) Planarity restraints: 4117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 231 " -0.262 9.50e-02 1.11e+02 1.21e-01 1.97e+01 pdb=" NE ARG D 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 231 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG D 231 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 231 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR C 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 89 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C THR F 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR F 89 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE F 90 " -0.026 2.00e-02 2.50e+03 ... (remaining 4114 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 8 2.08 - 2.78: 5041 2.78 - 3.49: 31786 3.49 - 4.19: 55047 4.19 - 4.90: 99088 Nonbonded interactions: 190970 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" CG2 DTH I 4 " model vdw 1.375 3.460 nonbonded pdb=" CG2 DTH H 4 " pdb=" OE2 GLU G 205 " model vdw 1.375 3.460 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.732 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.733 3.620 ... (remaining 190965 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.580 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 23869 Z= 0.239 Angle : 0.830 18.831 32274 Z= 0.468 Chirality : 0.048 0.279 3530 Planarity : 0.007 0.121 4111 Dihedral : 15.513 126.822 8959 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.08 % Allowed : 0.04 % Favored : 99.88 % Cbeta Deviations : 0.11 % 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: -1.26 (0.14), residues: 2837 helix: -1.75 (0.11), residues: 1340 sheet: 0.29 (0.25), residues: 384 loop : 0.32 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.011 ARG D 231 TYR 0.029 0.005 TYR G 306 PHE 0.050 0.002 PHE A 564 TRP 0.032 0.004 TRP F 340 HIS 0.005 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00490 (23863) covalent geometry : angle 0.82647 (32256) hydrogen bonds : bond 0.15768 ( 1171) hydrogen bonds : angle 6.88255 ( 3270) link_TRANS : bond 0.01200 ( 6) link_TRANS : angle 3.50167 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.686 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: A 323 MET cc_start: 0.8216 (mmm) cc_final: 0.8014 (mmm) REVERT: B 27 ILE cc_start: 0.5414 (pt) cc_final: 0.4910 (pt) REVERT: D 150 MET cc_start: 0.8567 (ttp) cc_final: 0.8349 (ttm) REVERT: D 783 MET cc_start: 0.7751 (mmm) cc_final: 0.7404 (mmp) REVERT: E 12 PHE cc_start: 0.6453 (m-10) cc_final: 0.5819 (m-80) REVERT: E 29 TYR cc_start: 0.6369 (m-80) cc_final: 0.6096 (m-80) REVERT: E 89 TYR cc_start: 0.6834 (m-80) cc_final: 0.6556 (m-80) REVERT: F 305 MET cc_start: 0.8619 (mmm) cc_final: 0.8245 (mmt) REVERT: G 180 LEU cc_start: 0.8586 (tp) cc_final: 0.7579 (tm) outliers start: 2 outliers final: 3 residues processed: 235 average time/residue: 0.8797 time to fit residues: 229.0819 Evaluate side-chains 131 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 493 GLN A 775 GLN B 75 GLN C 162 ASN C 280 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN D 398 ASN D 493 GLN D 775 GLN E 75 GLN F 162 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.059647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040094 restraints weight = 105807.749| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.64 r_work: 0.2784 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23869 Z= 0.136 Angle : 0.639 8.311 32274 Z= 0.331 Chirality : 0.043 0.197 3530 Planarity : 0.004 0.046 4111 Dihedral : 10.787 129.395 3295 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 1.17 % Allowed : 4.38 % Favored : 94.45 % 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: 0.88 (0.15), residues: 2837 helix: 0.61 (0.13), residues: 1386 sheet: 0.69 (0.27), residues: 378 loop : 0.80 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 343 TYR 0.016 0.001 TYR F 294 PHE 0.025 0.001 PHE E 16 TRP 0.021 0.002 TRP A 484 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00291 (23863) covalent geometry : angle 0.63934 (32256) hydrogen bonds : bond 0.04046 ( 1171) hydrogen bonds : angle 5.07866 ( 3270) link_TRANS : bond 0.00110 ( 6) link_TRANS : angle 0.77933 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8141 (mtt) cc_final: 0.7824 (mmt) REVERT: A 135 MET cc_start: 0.8630 (mtp) cc_final: 0.8374 (mtp) REVERT: A 305 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8512 (tpp) REVERT: A 323 MET cc_start: 0.8806 (mmm) cc_final: 0.8442 (mmm) REVERT: A 478 MET cc_start: 0.8644 (tmm) cc_final: 0.8440 (tmm) REVERT: C 305 MET cc_start: 0.9528 (mmm) cc_final: 0.9318 (mmt) REVERT: D 305 MET cc_start: 0.8934 (tpp) cc_final: 0.8664 (tpp) REVERT: D 648 MET cc_start: 0.9395 (mmm) cc_final: 0.9181 (mmm) REVERT: D 783 MET cc_start: 0.8130 (mmm) cc_final: 0.7755 (mmt) REVERT: E 89 TYR cc_start: 0.6911 (m-80) cc_final: 0.6556 (m-80) REVERT: F 167 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8719 (mt-10) REVERT: F 205 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8244 (mt-10) REVERT: F 299 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: G 180 LEU cc_start: 0.8616 (tp) cc_final: 0.8232 (tm) REVERT: G 313 MET cc_start: 0.9619 (OUTLIER) cc_final: 0.9361 (tpp) outliers start: 29 outliers final: 10 residues processed: 145 average time/residue: 0.7317 time to fit residues: 119.7792 Evaluate side-chains 135 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 313 MET Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 257 optimal weight: 0.8980 chunk 271 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.058500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038795 restraints weight = 106483.800| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.66 r_work: 0.2740 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23869 Z= 0.175 Angle : 0.590 7.760 32274 Z= 0.300 Chirality : 0.042 0.207 3530 Planarity : 0.004 0.047 4111 Dihedral : 9.658 129.470 3294 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.13 % Allowed : 5.55 % Favored : 93.32 % 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: 1.46 (0.16), residues: 2837 helix: 1.36 (0.14), residues: 1377 sheet: 0.83 (0.27), residues: 387 loop : 0.71 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 343 TYR 0.012 0.001 TYR A 259 PHE 0.027 0.001 PHE E 12 TRP 0.021 0.002 TRP G 79 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00398 (23863) covalent geometry : angle 0.59012 (32256) hydrogen bonds : bond 0.03913 ( 1171) hydrogen bonds : angle 4.80278 ( 3270) link_TRANS : bond 0.00141 ( 6) link_TRANS : angle 0.59626 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8002 (mmt) REVERT: A 305 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8577 (tpp) REVERT: A 467 MET cc_start: 0.9277 (ttp) cc_final: 0.8926 (tmm) REVERT: A 478 MET cc_start: 0.8724 (tmm) cc_final: 0.8413 (tmm) REVERT: D 305 MET cc_start: 0.9018 (tpp) cc_final: 0.8701 (tpp) REVERT: D 648 MET cc_start: 0.9436 (mmm) cc_final: 0.9148 (mmm) REVERT: D 783 MET cc_start: 0.8137 (mmm) cc_final: 0.7723 (mmp) REVERT: D 790 MET cc_start: 0.4317 (ppp) cc_final: 0.3937 (pp-130) REVERT: E 89 TYR cc_start: 0.6978 (m-80) cc_final: 0.6534 (m-80) REVERT: F 167 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8942 (mp0) REVERT: F 299 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9063 (mtm) REVERT: G 137 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8903 (mm-40) REVERT: G 205 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8483 (mt-10) outliers start: 28 outliers final: 11 residues processed: 134 average time/residue: 0.6994 time to fit residues: 107.4113 Evaluate side-chains 128 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 115 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 66 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.059544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039949 restraints weight = 105745.207| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.65 r_work: 0.2782 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23869 Z= 0.100 Angle : 0.537 7.411 32274 Z= 0.270 Chirality : 0.040 0.190 3530 Planarity : 0.003 0.039 4111 Dihedral : 9.060 132.812 3292 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.80 % Allowed : 6.92 % Favored : 92.28 % 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: 1.73 (0.16), residues: 2837 helix: 1.69 (0.14), residues: 1383 sheet: 0.85 (0.28), residues: 366 loop : 0.73 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 542 TYR 0.009 0.001 TYR A 456 PHE 0.047 0.001 PHE E 12 TRP 0.015 0.001 TRP A 781 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00215 (23863) covalent geometry : angle 0.53688 (32256) hydrogen bonds : bond 0.03271 ( 1171) hydrogen bonds : angle 4.62111 ( 3270) link_TRANS : bond 0.00132 ( 6) link_TRANS : angle 0.67790 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8387 (mtt) cc_final: 0.7992 (mmt) REVERT: A 305 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8586 (tpp) REVERT: A 323 MET cc_start: 0.8778 (mmm) cc_final: 0.8429 (mmm) REVERT: A 467 MET cc_start: 0.9269 (ttp) cc_final: 0.8994 (tmm) REVERT: B 105 MET cc_start: 0.8136 (mpm) cc_final: 0.7883 (mpp) REVERT: C 137 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (mp10) REVERT: D 305 MET cc_start: 0.8987 (tpp) cc_final: 0.8636 (tpp) REVERT: D 648 MET cc_start: 0.9438 (mmm) cc_final: 0.9082 (mmm) REVERT: D 783 MET cc_start: 0.8100 (mmm) cc_final: 0.7672 (mmp) REVERT: D 790 MET cc_start: 0.4203 (ppp) cc_final: 0.3894 (pp-130) REVERT: F 167 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8673 (mt-10) REVERT: F 299 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9167 (mtm) REVERT: G 205 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8481 (mt-10) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 0.7340 time to fit residues: 108.9397 Evaluate side-chains 126 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 484 TRP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.059248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.039599 restraints weight = 105217.401| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.63 r_work: 0.2772 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23869 Z= 0.113 Angle : 0.536 10.163 32274 Z= 0.266 Chirality : 0.040 0.190 3530 Planarity : 0.003 0.040 4111 Dihedral : 8.792 129.126 3292 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.76 % Allowed : 8.00 % Favored : 91.23 % 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: 1.90 (0.16), residues: 2837 helix: 1.91 (0.14), residues: 1376 sheet: 0.78 (0.28), residues: 369 loop : 0.75 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 542 TYR 0.010 0.001 TYR A 456 PHE 0.046 0.001 PHE E 12 TRP 0.016 0.001 TRP A 781 HIS 0.007 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00258 (23863) covalent geometry : angle 0.53569 (32256) hydrogen bonds : bond 0.03219 ( 1171) hydrogen bonds : angle 4.54247 ( 3270) link_TRANS : bond 0.00128 ( 6) link_TRANS : angle 0.65600 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8290 (mtt) cc_final: 0.7923 (mmt) REVERT: A 135 MET cc_start: 0.8674 (mtt) cc_final: 0.8472 (mpp) REVERT: A 305 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8596 (tpp) REVERT: A 467 MET cc_start: 0.9271 (ttp) cc_final: 0.8960 (tmm) REVERT: A 478 MET cc_start: 0.8756 (tmm) cc_final: 0.8393 (tmm) REVERT: C 137 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: D 305 MET cc_start: 0.8993 (tpp) cc_final: 0.8634 (tpp) REVERT: D 648 MET cc_start: 0.9441 (mmm) cc_final: 0.9138 (mmm) REVERT: D 783 MET cc_start: 0.8081 (mmm) cc_final: 0.7668 (mmp) REVERT: F 137 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: F 167 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8958 (mp0) REVERT: F 176 MET cc_start: 0.9017 (mmt) cc_final: 0.8678 (mmt) REVERT: F 299 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9153 (mtm) REVERT: F 313 MET cc_start: 0.9446 (mmm) cc_final: 0.9224 (tpp) REVERT: G 205 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8485 (mt-10) outliers start: 19 outliers final: 9 residues processed: 125 average time/residue: 0.7455 time to fit residues: 105.8041 Evaluate side-chains 122 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 90 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038430 restraints weight = 105991.699| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.64 r_work: 0.2728 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23869 Z= 0.188 Angle : 0.574 10.326 32274 Z= 0.285 Chirality : 0.042 0.193 3530 Planarity : 0.003 0.040 4111 Dihedral : 8.712 127.763 3292 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.05 % Allowed : 8.29 % Favored : 90.67 % 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: 1.91 (0.16), residues: 2837 helix: 1.96 (0.14), residues: 1377 sheet: 0.83 (0.28), residues: 368 loop : 0.68 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 542 TYR 0.013 0.001 TYR A 259 PHE 0.013 0.001 PHE F 223 TRP 0.019 0.001 TRP A 781 HIS 0.012 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00431 (23863) covalent geometry : angle 0.57365 (32256) hydrogen bonds : bond 0.03582 ( 1171) hydrogen bonds : angle 4.59361 ( 3270) link_TRANS : bond 0.00155 ( 6) link_TRANS : angle 0.59010 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8227 (mtt) cc_final: 0.7950 (mmt) REVERT: A 305 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8609 (tpp) REVERT: A 323 MET cc_start: 0.8803 (mmm) cc_final: 0.8485 (mmm) REVERT: A 467 MET cc_start: 0.9278 (ttp) cc_final: 0.8957 (tmm) REVERT: A 478 MET cc_start: 0.8836 (tmm) cc_final: 0.8541 (tmm) REVERT: B 105 MET cc_start: 0.8213 (mpm) cc_final: 0.7929 (mpp) REVERT: C 137 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8677 (mp10) REVERT: C 167 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: D 305 MET cc_start: 0.9026 (tpp) cc_final: 0.8682 (tpp) REVERT: D 648 MET cc_start: 0.9435 (mmm) cc_final: 0.9172 (mmm) REVERT: D 783 MET cc_start: 0.8036 (mmm) cc_final: 0.7632 (mmp) REVERT: E 12 PHE cc_start: 0.6105 (m-80) cc_final: 0.5901 (m-80) REVERT: F 137 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: F 167 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8953 (mp0) REVERT: F 176 MET cc_start: 0.9030 (mmt) cc_final: 0.8707 (mmt) REVERT: F 286 ASP cc_start: 0.8733 (t0) cc_final: 0.8516 (t0) REVERT: F 299 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9197 (mtm) outliers start: 26 outliers final: 11 residues processed: 135 average time/residue: 0.7379 time to fit residues: 113.5418 Evaluate side-chains 131 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 176 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 255 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 208 optimal weight: 30.0000 chunk 229 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.058359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038611 restraints weight = 105934.623| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.65 r_work: 0.2733 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23869 Z= 0.156 Angle : 0.561 10.483 32274 Z= 0.278 Chirality : 0.041 0.211 3530 Planarity : 0.003 0.040 4111 Dihedral : 8.609 128.580 3292 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.13 % Allowed : 8.77 % Favored : 90.10 % 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: 1.89 (0.16), residues: 2837 helix: 1.99 (0.14), residues: 1377 sheet: 0.69 (0.28), residues: 371 loop : 0.64 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.010 0.001 TYR A 259 PHE 0.042 0.001 PHE B 12 TRP 0.019 0.001 TRP A 781 HIS 0.013 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00358 (23863) covalent geometry : angle 0.56145 (32256) hydrogen bonds : bond 0.03434 ( 1171) hydrogen bonds : angle 4.57024 ( 3270) link_TRANS : bond 0.00137 ( 6) link_TRANS : angle 0.63886 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8200 (mtt) cc_final: 0.7939 (mmt) REVERT: A 135 MET cc_start: 0.8500 (mpp) cc_final: 0.8246 (mpp) REVERT: A 305 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8619 (tpp) REVERT: A 323 MET cc_start: 0.8835 (mmm) cc_final: 0.8532 (mmm) REVERT: A 467 MET cc_start: 0.9289 (ttp) cc_final: 0.8973 (tmm) REVERT: A 478 MET cc_start: 0.8841 (tmm) cc_final: 0.8566 (tmm) REVERT: C 137 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: C 167 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: D 305 MET cc_start: 0.9013 (tpp) cc_final: 0.8669 (tpp) REVERT: D 648 MET cc_start: 0.9412 (mmm) cc_final: 0.9134 (mmm) REVERT: D 783 MET cc_start: 0.8092 (mmm) cc_final: 0.7704 (mmp) REVERT: D 788 MET cc_start: 0.7399 (tpt) cc_final: 0.7127 (mmt) REVERT: F 137 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: F 167 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8970 (mp0) REVERT: F 286 ASP cc_start: 0.8696 (t0) cc_final: 0.8489 (t0) REVERT: F 299 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.9198 (mtm) REVERT: G 160 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8670 (t) REVERT: G 283 MET cc_start: 0.9098 (mmt) cc_final: 0.8872 (mmm) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.7239 time to fit residues: 109.0368 Evaluate side-chains 132 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 280 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 245 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 243 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.058171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038412 restraints weight = 105735.066| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.64 r_work: 0.2725 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23869 Z= 0.172 Angle : 0.583 10.946 32274 Z= 0.287 Chirality : 0.042 0.211 3530 Planarity : 0.003 0.041 4111 Dihedral : 8.555 127.746 3292 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 9.29 % Favored : 89.70 % 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: 1.88 (0.16), residues: 2837 helix: 2.04 (0.14), residues: 1367 sheet: 0.70 (0.28), residues: 368 loop : 0.56 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.011 0.001 TYR A 259 PHE 0.056 0.001 PHE B 12 TRP 0.019 0.001 TRP A 781 HIS 0.014 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00396 (23863) covalent geometry : angle 0.58281 (32256) hydrogen bonds : bond 0.03483 ( 1171) hydrogen bonds : angle 4.58039 ( 3270) link_TRANS : bond 0.00156 ( 6) link_TRANS : angle 0.62078 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8202 (mtt) cc_final: 0.7936 (mmt) REVERT: A 135 MET cc_start: 0.8565 (mpp) cc_final: 0.8275 (mpp) REVERT: A 305 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: A 467 MET cc_start: 0.9301 (ttp) cc_final: 0.8965 (tmm) REVERT: A 478 MET cc_start: 0.8849 (tmm) cc_final: 0.8607 (tmm) REVERT: C 132 MET cc_start: 0.9246 (ppp) cc_final: 0.8962 (ptp) REVERT: C 137 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: C 167 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: D 305 MET cc_start: 0.9028 (tpp) cc_final: 0.8677 (tpp) REVERT: D 648 MET cc_start: 0.9417 (mmm) cc_final: 0.9144 (mmm) REVERT: D 783 MET cc_start: 0.8095 (mmm) cc_final: 0.7733 (mmp) REVERT: F 137 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: F 286 ASP cc_start: 0.8665 (t0) cc_final: 0.8438 (t0) REVERT: F 299 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9196 (mtm) REVERT: F 313 MET cc_start: 0.9419 (mmm) cc_final: 0.9216 (mmm) REVERT: G 160 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8691 (t) REVERT: G 283 MET cc_start: 0.9074 (mmt) cc_final: 0.8857 (mmm) outliers start: 25 outliers final: 13 residues processed: 129 average time/residue: 0.6789 time to fit residues: 100.3839 Evaluate side-chains 131 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 280 optimal weight: 0.0070 chunk 114 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 269 optimal weight: 0.0470 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.059271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039563 restraints weight = 105833.308| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.67 r_work: 0.2771 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23869 Z= 0.097 Angle : 0.570 15.233 32274 Z= 0.276 Chirality : 0.040 0.208 3530 Planarity : 0.003 0.044 4111 Dihedral : 8.317 127.384 3292 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.72 % Allowed : 9.65 % Favored : 89.62 % 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: 1.97 (0.16), residues: 2837 helix: 2.11 (0.15), residues: 1370 sheet: 0.84 (0.27), residues: 388 loop : 0.56 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG B 110 TYR 0.029 0.001 TYR F 166 PHE 0.056 0.001 PHE B 12 TRP 0.020 0.001 TRP A 781 HIS 0.014 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00213 (23863) covalent geometry : angle 0.57030 (32256) hydrogen bonds : bond 0.03067 ( 1171) hydrogen bonds : angle 4.47312 ( 3270) link_TRANS : bond 0.00152 ( 6) link_TRANS : angle 0.72201 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8297 (mtt) cc_final: 0.8020 (mmp) REVERT: A 135 MET cc_start: 0.8503 (mpp) cc_final: 0.8172 (mpp) REVERT: A 305 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8614 (tpp) REVERT: A 323 MET cc_start: 0.8849 (mmm) cc_final: 0.8542 (mmm) REVERT: A 467 MET cc_start: 0.9282 (ttp) cc_final: 0.9024 (tmm) REVERT: A 790 MET cc_start: -0.1280 (ttm) cc_final: -0.1903 (ppp) REVERT: B 105 MET cc_start: 0.8229 (mpm) cc_final: 0.7939 (mpp) REVERT: C 132 MET cc_start: 0.9250 (ppp) cc_final: 0.8934 (ptp) REVERT: C 137 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: C 167 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: C 313 MET cc_start: 0.9344 (mmm) cc_final: 0.8781 (tpt) REVERT: D 305 MET cc_start: 0.8980 (tpp) cc_final: 0.8711 (tpp) REVERT: D 783 MET cc_start: 0.8019 (mmm) cc_final: 0.7603 (mmp) REVERT: D 788 MET cc_start: 0.7825 (tpt) cc_final: 0.7488 (ptp) REVERT: F 137 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: F 299 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9169 (mtm) REVERT: F 313 MET cc_start: 0.9372 (mmm) cc_final: 0.9137 (mmm) REVERT: G 160 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8550 (t) REVERT: G 283 MET cc_start: 0.9019 (mmt) cc_final: 0.8811 (mmm) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 0.6924 time to fit residues: 102.1818 Evaluate side-chains 127 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 282 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038083 restraints weight = 106692.434| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.66 r_work: 0.2716 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23869 Z= 0.219 Angle : 0.629 14.729 32274 Z= 0.307 Chirality : 0.043 0.212 3530 Planarity : 0.004 0.041 4111 Dihedral : 8.367 127.891 3292 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.60 % Allowed : 10.06 % Favored : 89.34 % 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: 1.93 (0.16), residues: 2837 helix: 2.05 (0.15), residues: 1370 sheet: 0.84 (0.27), residues: 390 loop : 0.55 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 110 TYR 0.025 0.001 TYR F 166 PHE 0.056 0.001 PHE B 12 TRP 0.021 0.002 TRP A 781 HIS 0.019 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00502 (23863) covalent geometry : angle 0.62926 (32256) hydrogen bonds : bond 0.03618 ( 1171) hydrogen bonds : angle 4.56059 ( 3270) link_TRANS : bond 0.00192 ( 6) link_TRANS : angle 0.60248 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8311 (mtt) cc_final: 0.8082 (mmt) REVERT: A 135 MET cc_start: 0.8625 (mpp) cc_final: 0.8345 (mpp) REVERT: A 305 MET cc_start: 0.9186 (tpp) cc_final: 0.8610 (tpp) REVERT: A 323 MET cc_start: 0.8907 (mmm) cc_final: 0.8603 (mmm) REVERT: A 467 MET cc_start: 0.9289 (ttp) cc_final: 0.8950 (tmm) REVERT: A 790 MET cc_start: -0.1288 (ttm) cc_final: -0.1930 (ppp) REVERT: C 132 MET cc_start: 0.9240 (ppp) cc_final: 0.8995 (ptp) REVERT: C 137 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: C 167 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: D 305 MET cc_start: 0.9045 (tpp) cc_final: 0.8748 (tpp) REVERT: D 648 MET cc_start: 0.9369 (mmm) cc_final: 0.9102 (mmm) REVERT: D 783 MET cc_start: 0.8106 (mmm) cc_final: 0.7705 (mmp) REVERT: D 788 MET cc_start: 0.7587 (tpt) cc_final: 0.7209 (mtt) REVERT: F 137 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: F 286 ASP cc_start: 0.8604 (t0) cc_final: 0.8375 (t0) REVERT: F 299 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.9216 (mtm) REVERT: G 283 MET cc_start: 0.9017 (mmt) cc_final: 0.8810 (mmm) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.6745 time to fit residues: 94.1041 Evaluate side-chains 125 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 137 GLN Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 266 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.059046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039338 restraints weight = 105613.605| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.66 r_work: 0.2763 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23869 Z= 0.106 Angle : 0.576 13.810 32274 Z= 0.279 Chirality : 0.041 0.209 3530 Planarity : 0.003 0.046 4111 Dihedral : 8.178 131.131 3292 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.64 % Allowed : 9.90 % Favored : 89.46 % 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: 2.01 (0.16), residues: 2837 helix: 2.16 (0.15), residues: 1364 sheet: 0.83 (0.27), residues: 388 loop : 0.57 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 110 TYR 0.020 0.001 TYR F 166 PHE 0.055 0.001 PHE B 12 TRP 0.021 0.001 TRP A 781 HIS 0.019 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00240 (23863) covalent geometry : angle 0.57556 (32256) hydrogen bonds : bond 0.03121 ( 1171) hydrogen bonds : angle 4.44516 ( 3270) link_TRANS : bond 0.00144 ( 6) link_TRANS : angle 0.70591 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8947.94 seconds wall clock time: 152 minutes 53.40 seconds (9173.40 seconds total)