Starting phenix.real_space_refine on Fri Feb 6 18:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lay_62932/02_2026/9lay_62932.map" } resolution = 2.62 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= 0.004 sd= 0.095 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 Fe 33 7.16 5 P 12 5.49 5 S 186 5.16 5 C 17334 2.51 5 N 4719 2.21 5 O 4953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27237 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "C" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "D" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "E" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "F" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "H" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "I" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 192 Unusual residues: {'HEM': 2, 'LMT': 1, 'PEV': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 1, 'FES': 1, 'PGV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 165 Unusual residues: {'HEM': 2, 'LMT': 1, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 198 Unusual residues: {'HEM': 2, 'LMT': 1, 'PEV': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 162 42.073 64.313 62.302 1.00 19.17 S ATOM 6166 SG CYS B 159 48.394 65.956 61.546 1.00 18.45 S ATOM 6628 SG CYS B 224 46.582 60.977 65.100 1.00 8.80 S ATOM 6199 SG CYS B 165 45.039 67.171 66.875 1.00 19.85 S ATOM 5481 SG CYS B 66 35.623 61.851 56.647 1.00 44.52 S ATOM 5606 SG CYS B 84 37.280 59.055 55.767 1.00 20.93 S ATOM 5425 SG CYS B 58 39.959 60.993 52.216 1.00 20.81 S ATOM 5463 SG CYS B 63 39.857 64.477 53.011 1.00 24.07 S ATOM 6222 SG CYS B 169 43.675 69.011 74.673 1.00 23.96 S ATOM 6605 SG CYS B 220 45.480 66.093 72.199 1.00 65.61 S ATOM 6563 SG CYS B 214 49.843 68.110 76.251 1.00 18.70 S ATOM 14988 SG CYS E 162 95.653 38.741 62.310 1.00 16.84 S ATOM 15432 SG CYS E 224 96.227 44.346 65.104 1.00 10.79 S ATOM 15003 SG CYS E 165 91.689 39.838 66.880 1.00 19.10 S ATOM 14970 SG CYS E 159 91.087 43.469 61.573 1.00 17.41 S ATOM 14229 SG CYS E 58 99.630 38.541 52.244 1.00 23.73 S ATOM 14267 SG CYS E 63 96.684 36.705 52.967 1.00 21.97 S ATOM 14285 SG CYS E 66 100.509 35.387 57.885 1.00 26.53 S ATOM 14410 SG CYS E 84 102.576 37.174 55.785 1.00 23.58 S ATOM 15026 SG CYS E 169 90.800 37.660 74.702 1.00 24.87 S ATOM 15409 SG CYS E 220 93.305 43.068 72.367 1.00 20.72 S ATOM 15367 SG CYS E 214 88.369 43.535 76.234 1.00 18.46 S ATOM 23774 SG CYS H 159 89.274 91.551 61.550 1.00 14.21 S ATOM 23792 SG CYS H 162 91.046 97.841 62.312 1.00 16.21 S ATOM 23807 SG CYS H 165 92.070 93.894 66.792 1.00 20.28 S ATOM 24236 SG CYS H 224 85.838 95.610 65.101 1.00 10.51 S ATOM 23089 SG CYS H 66 91.474 103.554 57.789 1.00 27.76 S ATOM 23214 SG CYS H 84 88.866 104.648 55.791 1.00 24.54 S ATOM 23033 SG CYS H 58 89.239 101.370 52.232 1.00 24.39 S ATOM 23071 SG CYS H 63 92.323 99.726 52.981 1.00 21.63 S ATOM 24213 SG CYS H 220 88.527 93.664 72.171 1.00 21.21 S ATOM 24171 SG CYS H 214 90.475 89.241 76.056 1.00 17.62 S ATOM 23830 SG CYS H 169 94.341 94.183 74.725 1.00 21.20 S Time building chain proxies: 6.02, per 1000 atoms: 0.22 Number of scatterers: 27237 At special positions: 0 Unit cell: (146.01, 141.36, 133.92, 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) Fe 33 26.01 S 186 16.00 P 12 15.00 O 4953 8.00 N 4719 7.00 C 17334 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 169 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 220 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 214 " pdb=" F3S E 303 " pdb="FE3 F3S E 303 " - pdb=" SG CYS E 220 " pdb="FE1 F3S E 303 " - pdb=" SG CYS E 169 " pdb="FE4 F3S E 303 " - pdb=" SG CYS E 214 " pdb=" F3S H 303 " pdb="FE3 F3S H 303 " - pdb=" SG CYS H 214 " pdb="FE4 F3S H 303 " - pdb=" SG CYS H 169 " pdb="FE1 F3S H 303 " - pdb=" SG CYS H 220 " pdb=" FES B 302 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 66 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 63 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 84 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 58 " pdb=" FES E 302 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 63 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 84 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 66 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 58 " pdb=" FES H 302 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 66 " pdb="FE2 FES H 302 " - pdb=" SG CYS H 63 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 84 " pdb="FE2 FES H 302 " - pdb=" SG CYS H 58 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 224 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 159 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 165 " pdb=" SF4 E 301 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 159 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 162 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 165 " pdb=" SF4 H 301 " pdb="FE4 SF4 H 301 " - pdb=" SG CYS H 224 " pdb="FE1 SF4 H 301 " - pdb=" SG CYS H 159 " pdb="FE2 SF4 H 301 " - pdb=" SG CYS H 162 " pdb="FE3 SF4 H 301 " - pdb=" SG CYS H 165 " Number of angles added : 81 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6138 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 24 sheets defined 51.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.652A pdb=" N ALA A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A 93 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 129 through 150 removed outlier: 3.511A pdb=" N VAL A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.522A pdb=" N PHE A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 386 through 406 removed outlier: 6.832A pdb=" N ASN A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 removed outlier: 3.753A pdb=" N ASN A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.815A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 removed outlier: 3.645A pdb=" N GLN A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 512 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 538 through 559 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.823A pdb=" N GLU A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 117 through 126 removed outlier: 3.945A pdb=" N ASP B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 194 through 209 removed outlier: 3.655A pdb=" N VAL B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.669A pdb=" N VAL B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'C' and resid 3 through 9 removed outlier: 3.679A pdb=" N THR C 8 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.844A pdb=" N ARG C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 98 removed outlier: 4.211A pdb=" N ALA C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 171 through 201 removed outlier: 4.544A pdb=" N TRP C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 235 removed outlier: 4.601A pdb=" N ARG C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 47 through 52 removed outlier: 4.335A pdb=" N ARG D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.693A pdb=" N ALA D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 129 through 150 removed outlier: 3.517A pdb=" N VAL D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 200 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.660A pdb=" N PHE D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 349 through 364 Processing helix chain 'D' and resid 378 through 385 Processing helix chain 'D' and resid 386 through 406 removed outlier: 6.618A pdb=" N ASN D 396 " --> pdb=" O GLU D 392 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 447 removed outlier: 3.916A pdb=" N ASN D 447 " --> pdb=" O GLY D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.030A pdb=" N MET D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 481 removed outlier: 3.602A pdb=" N ALA D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 512 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 538 through 559 Proline residue: D 550 - end of helix Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.780A pdb=" N GLU D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 587 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 48 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.904A pdb=" N ASP E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 174 through 187 Processing helix chain 'E' and resid 188 through 192 removed outlier: 3.624A pdb=" N GLN E 192 " --> pdb=" O PRO E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 209 removed outlier: 3.775A pdb=" N VAL E 200 " --> pdb=" O TYR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 230 through 246 Processing helix chain 'F' and resid 2 through 9 removed outlier: 4.085A pdb=" N LEU F 5 " --> pdb=" O THR F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 37 Processing helix chain 'F' and resid 38 through 41 Processing helix chain 'F' and resid 42 through 55 removed outlier: 3.831A pdb=" N ARG F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 98 removed outlier: 3.728A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 139 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 171 through 201 removed outlier: 4.518A pdb=" N TRP F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 197 " --> pdb=" O VAL F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 235 removed outlier: 4.393A pdb=" N ARG F 209 " --> pdb=" O ARG F 205 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'G' and resid 34 through 43 Processing helix chain 'G' and resid 50 through 53 Processing helix chain 'G' and resid 62 through 76 Processing helix chain 'G' and resid 87 through 96 removed outlier: 3.792A pdb=" N ALA G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER G 93 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 129 through 150 removed outlier: 4.606A pdb=" N VAL G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 200 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.689A pdb=" N PHE G 253 " --> pdb=" O GLY G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 304 through 309 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 349 through 363 Processing helix chain 'G' and resid 378 through 385 Processing helix chain 'G' and resid 386 through 406 removed outlier: 6.690A pdb=" N ASN G 396 " --> pdb=" O GLU G 392 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 397 " --> pdb=" O ARG G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 447 removed outlier: 3.924A pdb=" N ASN G 447 " --> pdb=" O GLY G 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 444 through 447' Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.851A pdb=" N ILE G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 481 removed outlier: 3.637A pdb=" N ALA G 477 " --> pdb=" O PRO G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 512 Processing helix chain 'G' and resid 518 through 533 Processing helix chain 'G' and resid 538 through 559 Proline residue: G 550 - end of helix Processing helix chain 'G' and resid 570 through 596 removed outlier: 3.705A pdb=" N GLU G 584 " --> pdb=" O ALA G 580 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 587 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 48 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 117 through 126 removed outlier: 3.993A pdb=" N ASP H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 158 Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 174 through 187 Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'H' and resid 194 through 209 removed outlier: 3.693A pdb=" N VAL H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 224 Processing helix chain 'H' and resid 230 through 246 Processing helix chain 'I' and resid 2 through 9 removed outlier: 3.822A pdb=" N LEU I 5 " --> pdb=" O THR I 2 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR I 8 " --> pdb=" O LEU I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 37 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.775A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 98 removed outlier: 3.608A pdb=" N LEU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 140 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 171 through 201 removed outlier: 4.538A pdb=" N TRP I 194 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE I 197 " --> pdb=" O VAL I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 235 removed outlier: 4.588A pdb=" N ARG I 209 " --> pdb=" O ARG I 205 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU I 210 " --> pdb=" O THR I 206 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 206 removed outlier: 6.581A pdb=" N VAL A 79 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 206 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYS A 81 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 55 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 243 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 57 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 217 removed outlier: 6.466A pdb=" N ILE A 225 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU A 214 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY A 223 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 216 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 221 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.643A pdb=" N GLN A 284 " --> pdb=" O HIS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517 removed outlier: 6.485A pdb=" N ARG A 516 " --> pdb=" O ASN A 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.375A pdb=" N THR B 4 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL B 99 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 6 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 203 through 206 removed outlier: 6.593A pdb=" N VAL D 79 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE D 206 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS D 81 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 241 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AB2, first strand: chain 'D' and resid 209 through 217 removed outlier: 6.463A pdb=" N ILE D 225 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU D 214 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY D 223 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 216 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA D 221 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AB4, first strand: chain 'D' and resid 283 through 286 removed outlier: 3.527A pdb=" N TYR D 422 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS D 286 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL D 420 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB6, first strand: chain 'D' and resid 516 through 517 removed outlier: 6.731A pdb=" N ARG D 516 " --> pdb=" O ASN D 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 24 removed outlier: 6.537A pdb=" N THR E 4 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL E 99 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS E 6 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 203 through 206 removed outlier: 6.633A pdb=" N VAL G 79 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE G 206 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS G 81 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA G 241 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'G' and resid 209 through 217 removed outlier: 6.508A pdb=" N ILE G 225 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU G 214 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY G 223 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 216 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA G 221 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 426 through 427 Processing sheet with id=AC3, first strand: chain 'G' and resid 283 through 286 removed outlier: 6.639A pdb=" N GLN G 284 " --> pdb=" O HIS G 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 333 through 334 Processing sheet with id=AC5, first strand: chain 'G' and resid 516 through 517 removed outlier: 6.525A pdb=" N ARG G 516 " --> pdb=" O ASN G 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 24 removed outlier: 6.536A pdb=" N THR H 4 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL H 99 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS H 6 " --> pdb=" O VAL H 99 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3756 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: 5.70 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.75: 27564 1.75 - 2.31: 334 2.31 - 2.86: 5 2.86 - 3.42: 0 3.42 - 3.97: 9 Bond restraints: 27912 Sorted by residual: bond pdb=" S4 F3S H 303 " pdb="FE1 F3S H 303 " ideal model delta sigma weight residual 2.233 3.933 -1.700 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.932 -1.699 2.00e-02 2.50e+03 7.21e+03 bond pdb=" S4 F3S E 303 " pdb="FE1 F3S E 303 " ideal model delta sigma weight residual 2.233 3.915 -1.682 2.00e-02 2.50e+03 7.07e+03 bond pdb=" S2 F3S H 303 " pdb="FE3 F3S H 303 " ideal model delta sigma weight residual 2.300 3.971 -1.671 2.00e-02 2.50e+03 6.98e+03 bond pdb=" S1 F3S E 303 " pdb="FE4 F3S E 303 " ideal model delta sigma weight residual 2.258 3.893 -1.635 2.00e-02 2.50e+03 6.68e+03 ... (remaining 27907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 37877 10.07 - 20.14: 1 20.14 - 30.21: 4 30.21 - 40.29: 20 40.29 - 50.36: 6 Bond angle restraints: 37908 Sorted by residual: angle pdb=" S1 F3S H 303 " pdb="FE4 F3S H 303 " pdb=" S3 F3S H 303 " ideal model delta sigma weight residual 114.75 64.39 50.36 3.00e+00 1.11e-01 2.82e+02 angle pdb=" S1 F3S E 303 " pdb="FE4 F3S E 303 " pdb=" S3 F3S E 303 " ideal model delta sigma weight residual 114.75 64.67 50.08 3.00e+00 1.11e-01 2.79e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.73 50.02 3.00e+00 1.11e-01 2.78e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 63.41 49.18 3.00e+00 1.11e-01 2.69e+02 angle pdb=" S3 F3S E 303 " pdb="FE1 F3S E 303 " pdb=" S4 F3S E 303 " ideal model delta sigma weight residual 112.59 63.97 48.62 3.00e+00 1.11e-01 2.63e+02 ... (remaining 37903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 15943 35.18 - 70.37: 557 70.37 - 105.55: 56 105.55 - 140.73: 13 140.73 - 175.92: 6 Dihedral angle restraints: 16575 sinusoidal: 6918 harmonic: 9657 Sorted by residual: dihedral pdb=" C2C HEM F 302 " pdb=" C3C HEM F 302 " pdb=" CAC HEM F 302 " pdb=" CBC HEM F 302 " ideal model delta sinusoidal sigma weight residual 180.00 101.03 78.97 2 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" C2B HEM I 302 " pdb=" C3B HEM I 302 " pdb=" CAB HEM I 302 " pdb=" CBB HEM I 302 " ideal model delta sinusoidal sigma weight residual -0.00 -77.42 77.42 2 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" C2B HEM F 303 " pdb=" C3B HEM F 303 " pdb=" CAB HEM F 303 " pdb=" CBB HEM F 303 " ideal model delta sinusoidal sigma weight residual 0.00 62.63 -62.63 2 1.00e+01 1.00e-02 3.79e+01 ... (remaining 16572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.651: 4035 3.651 - 7.301: 0 7.301 - 10.952: 0 10.952 - 14.603: 0 14.603 - 18.254: 3 Chirality restraints: 4038 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.49 18.25 2.00e-01 2.50e+01 8.33e+03 chirality pdb=" S2 F3S E 303 " pdb="FE1 F3S E 303 " pdb="FE3 F3S E 303 " pdb="FE4 F3S E 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.27 18.04 2.00e-01 2.50e+01 8.13e+03 chirality pdb=" S2 F3S H 303 " pdb="FE1 F3S H 303 " pdb="FE3 F3S H 303 " pdb="FE4 F3S H 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.14 17.91 2.00e-01 2.50e+01 8.02e+03 ... (remaining 4035 not shown) Planarity restraints: 4854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 308 " -0.220 9.50e-02 1.11e+02 9.87e-02 5.97e+00 pdb=" NE ARG A 308 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 308 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 308 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 201 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ASN E 201 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN E 201 " 0.016 2.00e-02 2.50e+03 pdb=" N MET E 202 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 201 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ASN H 201 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN H 201 " 0.016 2.00e-02 2.50e+03 pdb=" N MET H 202 " 0.014 2.00e-02 2.50e+03 ... (remaining 4851 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2398 2.74 - 3.28: 26667 3.28 - 3.82: 50786 3.82 - 4.36: 63563 4.36 - 4.90: 104317 Nonbonded interactions: 247731 Sorted by model distance: nonbonded pdb=" OH TYR I 146 " pdb=" O ASN I 164 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN D 101 " pdb=" OG1 THR D 175 " model vdw 2.204 3.040 nonbonded pdb=" O ALA B 167 " pdb=" OH TYR C 107 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 146 " pdb=" O ASN C 164 " model vdw 2.219 3.040 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.223 2.688 ... (remaining 247726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 652) selection = (chain 'D' and resid 22 through 652) selection = (chain 'G' and resid 22 through 652) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 1 through 303) selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 1 through 239 or resid 302)) selection = (chain 'F' and (resid 1 through 239 or resid 302)) selection = (chain 'I' and (resid 1 through 239 or resid 302)) } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.031 1.700 27951 Z= 1.519 Angle : 1.353 50.621 37989 Z= 0.493 Chirality : 0.495 18.254 4038 Planarity : 0.005 0.099 4854 Dihedral : 18.169 175.917 10437 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.80 % Allowed : 16.28 % Favored : 82.91 % 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: 0.34 (0.14), residues: 3363 helix: 0.75 (0.12), residues: 1566 sheet: 1.14 (0.32), residues: 231 loop : -0.37 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 89 TYR 0.017 0.002 TYR A 422 PHE 0.024 0.002 PHE I 28 TRP 0.015 0.002 TRP B 102 HIS 0.011 0.002 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.03070 (27912) covalent geometry : angle 1.25049 (37908) hydrogen bonds : bond 0.12223 ( 1339) hydrogen bonds : angle 5.94947 ( 3756) metal coordination : bond 0.01229 ( 33) metal coordination : angle 11.23961 ( 81) Misc. bond : bond 0.12022 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 452 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7018 (tmm) cc_final: 0.6399 (ttm) REVERT: A 407 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 484 LYS cc_start: 0.8001 (tttm) cc_final: 0.7555 (mttt) REVERT: A 507 GLN cc_start: 0.7223 (mm110) cc_final: 0.6767 (mp10) REVERT: A 508 ARG cc_start: 0.8382 (ttt180) cc_final: 0.8089 (ttt-90) REVERT: A 527 LYS cc_start: 0.8084 (tptt) cc_final: 0.7728 (tptp) REVERT: B 18 GLU cc_start: 0.8079 (pt0) cc_final: 0.7717 (pt0) REVERT: B 35 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 43 ASP cc_start: 0.7548 (t70) cc_final: 0.7190 (t70) REVERT: B 242 MET cc_start: 0.8750 (tpp) cc_final: 0.8503 (tpt) REVERT: C 9 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7125 (mtp-110) REVERT: C 54 ARG cc_start: 0.8813 (mpt180) cc_final: 0.8544 (mmt180) REVERT: C 111 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7460 (mttm) REVERT: C 209 ARG cc_start: 0.7249 (tpt170) cc_final: 0.6530 (ttp80) REVERT: D 527 LYS cc_start: 0.7998 (tptt) cc_final: 0.7555 (tptp) REVERT: D 620 GLU cc_start: 0.8001 (tt0) cc_final: 0.7774 (tt0) REVERT: D 650 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8412 (mmtp) REVERT: E 11 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8180 (tppt) REVERT: E 50 GLU cc_start: 0.8009 (tt0) cc_final: 0.7736 (tt0) REVERT: F 54 ARG cc_start: 0.8891 (mpt180) cc_final: 0.8688 (mmt180) REVERT: F 91 GLN cc_start: 0.9178 (tt0) cc_final: 0.8913 (tt0) REVERT: F 94 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8302 (mtp180) REVERT: F 144 VAL cc_start: 0.8664 (p) cc_final: 0.8463 (m) REVERT: F 167 TYR cc_start: 0.8079 (m-10) cc_final: 0.7869 (m-80) REVERT: G 527 LYS cc_start: 0.7997 (tptt) cc_final: 0.7472 (tptp) REVERT: G 650 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8339 (mmtp) REVERT: H 18 GLU cc_start: 0.8106 (pt0) cc_final: 0.7687 (pt0) REVERT: H 88 MET cc_start: 0.9129 (mmm) cc_final: 0.8799 (mmm) REVERT: H 242 MET cc_start: 0.8765 (tpp) cc_final: 0.8455 (mmm) REVERT: I 153 HIS cc_start: 0.7252 (p-80) cc_final: 0.6938 (p-80) outliers start: 22 outliers final: 15 residues processed: 471 average time/residue: 0.8392 time to fit residues: 446.7410 Evaluate side-chains 388 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 595 HIS B 12 ASN C 110 HIS C 113 GLN D 47 ASN D 50 ASN D 181 GLN D 309 ASN D 547 GLN D 618 ASN E 213 ASN E 235 GLN F 63 HIS F 138 HIS F 155 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 HIS G 359 GLN I 63 HIS I 113 GLN I 138 HIS I 155 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104139 restraints weight = 27395.567| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.21 r_work: 0.3009 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 27951 Z= 0.182 Angle : 1.431 80.883 37989 Z= 0.417 Chirality : 0.062 2.380 4038 Planarity : 0.004 0.040 4854 Dihedral : 13.123 173.425 4370 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 2.49 % Allowed : 17.34 % Favored : 80.17 % 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: 0.80 (0.14), residues: 3363 helix: 1.23 (0.12), residues: 1599 sheet: 1.01 (0.32), residues: 237 loop : -0.22 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 93 TYR 0.011 0.001 TYR D 134 PHE 0.014 0.001 PHE F 28 TRP 0.009 0.001 TRP G 314 HIS 0.008 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00386 (27912) covalent geometry : angle 1.07595 (37908) hydrogen bonds : bond 0.04930 ( 1339) hydrogen bonds : angle 4.93247 ( 3756) metal coordination : bond 0.00965 ( 33) metal coordination : angle 20.47501 ( 81) Misc. bond : bond 0.09171 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 388 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8894 (mtp) cc_final: 0.8659 (mtp) REVERT: A 362 ASP cc_start: 0.7111 (m-30) cc_final: 0.6834 (m-30) REVERT: A 400 MET cc_start: 0.6763 (tmm) cc_final: 0.6070 (ttm) REVERT: A 407 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 484 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7302 (mttt) REVERT: A 507 GLN cc_start: 0.6911 (mm110) cc_final: 0.6228 (mp10) REVERT: A 508 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7729 (ttt-90) REVERT: A 527 LYS cc_start: 0.7796 (tptt) cc_final: 0.7344 (tptp) REVERT: A 642 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: B 43 ASP cc_start: 0.7340 (t70) cc_final: 0.6980 (t70) REVERT: B 242 MET cc_start: 0.8444 (tpp) cc_final: 0.8221 (tpt) REVERT: C 9 ARG cc_start: 0.7310 (mtt90) cc_final: 0.6605 (mtp-110) REVERT: C 111 LYS cc_start: 0.7458 (mtmm) cc_final: 0.7252 (mttt) REVERT: C 209 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6122 (ttp80) REVERT: D 527 LYS cc_start: 0.7768 (tptt) cc_final: 0.7271 (tptp) REVERT: D 621 GLN cc_start: 0.7860 (mt0) cc_final: 0.7395 (mp10) REVERT: D 650 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8195 (mmtp) REVERT: E 11 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7941 (tppt) REVERT: E 13 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6556 (mtp-110) REVERT: E 219 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8171 (mm-30) REVERT: F 54 ARG cc_start: 0.8469 (mpt180) cc_final: 0.8264 (mmt180) REVERT: F 91 GLN cc_start: 0.8924 (tt0) cc_final: 0.8693 (tt0) REVERT: F 144 VAL cc_start: 0.8558 (p) cc_final: 0.8261 (m) REVERT: F 182 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8380 (tpp) REVERT: G 303 MET cc_start: 0.8020 (mtm) cc_final: 0.7682 (mtp) REVERT: G 332 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6762 (mt-10) REVERT: G 359 GLN cc_start: 0.6572 (tp40) cc_final: 0.6050 (tm-30) REVERT: G 508 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7784 (ttp80) REVERT: G 527 LYS cc_start: 0.7707 (tptt) cc_final: 0.7149 (tptp) REVERT: G 549 ILE cc_start: 0.8148 (mm) cc_final: 0.7905 (mt) REVERT: G 650 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8129 (mmtp) REVERT: H 18 GLU cc_start: 0.8129 (pt0) cc_final: 0.7563 (pt0) REVERT: H 88 MET cc_start: 0.8737 (mmm) cc_final: 0.8416 (mmm) REVERT: H 202 MET cc_start: 0.8852 (mtp) cc_final: 0.8568 (mtp) REVERT: H 242 MET cc_start: 0.8493 (tpp) cc_final: 0.8049 (mmm) REVERT: I 94 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8104 (mtp180) REVERT: I 153 HIS cc_start: 0.7188 (p-80) cc_final: 0.6984 (p-80) REVERT: I 209 ARG cc_start: 0.6974 (tpt170) cc_final: 0.6169 (mtp85) outliers start: 68 outliers final: 28 residues processed: 435 average time/residue: 0.8236 time to fit residues: 405.7858 Evaluate side-chains 393 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 361 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 230 optimal weight: 0.0770 chunk 215 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 12 ASN C 91 GLN C 113 GLN D 547 GLN F 63 HIS F 155 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 HIS I 91 GLN I 113 GLN I 155 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106216 restraints weight = 27558.158| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.19 r_work: 0.3052 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 27951 Z= 0.154 Angle : 1.361 84.191 37989 Z= 0.394 Chirality : 0.053 1.494 4038 Planarity : 0.003 0.043 4854 Dihedral : 11.739 171.248 4361 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.41 % Allowed : 17.82 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.14), residues: 3363 helix: 1.51 (0.13), residues: 1605 sheet: 1.03 (0.32), residues: 237 loop : -0.10 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 93 TYR 0.010 0.001 TYR A 422 PHE 0.010 0.001 PHE D 117 TRP 0.008 0.001 TRP G 314 HIS 0.019 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00324 (27912) covalent geometry : angle 1.02462 (37908) hydrogen bonds : bond 0.04431 ( 1339) hydrogen bonds : angle 4.64710 ( 3756) metal coordination : bond 0.00607 ( 33) metal coordination : angle 19.43632 ( 81) Misc. bond : bond 0.07182 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 382 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8892 (mtp) cc_final: 0.8640 (mtp) REVERT: A 302 LEU cc_start: 0.8419 (tp) cc_final: 0.8205 (tt) REVERT: A 359 GLN cc_start: 0.6354 (tp-100) cc_final: 0.6081 (tm-30) REVERT: A 362 ASP cc_start: 0.7212 (m-30) cc_final: 0.6860 (m-30) REVERT: A 400 MET cc_start: 0.6707 (tmm) cc_final: 0.6024 (ttm) REVERT: A 407 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 484 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7316 (mttt) REVERT: A 507 GLN cc_start: 0.6908 (mm110) cc_final: 0.6227 (mp10) REVERT: A 527 LYS cc_start: 0.7821 (tptt) cc_final: 0.7351 (tptp) REVERT: A 595 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7667 (p-80) REVERT: B 6 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8131 (mtpp) REVERT: B 43 ASP cc_start: 0.7342 (t70) cc_final: 0.6996 (t70) REVERT: B 242 MET cc_start: 0.8393 (tpp) cc_final: 0.8092 (tpt) REVERT: C 9 ARG cc_start: 0.7277 (mtt90) cc_final: 0.6634 (mtp-110) REVERT: C 209 ARG cc_start: 0.7143 (tpt170) cc_final: 0.6200 (ttp80) REVERT: D 414 MET cc_start: 0.7817 (ttm) cc_final: 0.7599 (ptm) REVERT: D 527 LYS cc_start: 0.7773 (tptt) cc_final: 0.7314 (tptp) REVERT: D 547 GLN cc_start: 0.7519 (tp40) cc_final: 0.7227 (tm130) REVERT: D 621 GLN cc_start: 0.7881 (mt0) cc_final: 0.7403 (mp10) REVERT: D 650 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8179 (mmtp) REVERT: E 11 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7954 (tppt) REVERT: E 13 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6615 (mtp-110) REVERT: E 18 GLU cc_start: 0.8073 (pt0) cc_final: 0.7731 (pt0) REVERT: F 91 GLN cc_start: 0.8880 (tt0) cc_final: 0.8680 (tt0) REVERT: F 93 ARG cc_start: 0.8167 (ttt90) cc_final: 0.6775 (mpt-90) REVERT: F 144 VAL cc_start: 0.8503 (p) cc_final: 0.8217 (m) REVERT: F 182 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8438 (tpp) REVERT: G 181 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6969 (mp10) REVERT: G 303 MET cc_start: 0.7936 (mtm) cc_final: 0.7664 (mtp) REVERT: G 365 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7502 (mtp-110) REVERT: G 508 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7829 (ttp80) REVERT: G 515 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7906 (mttp) REVERT: G 527 LYS cc_start: 0.7783 (tptt) cc_final: 0.7178 (tptp) REVERT: G 547 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7369 (tm130) REVERT: G 548 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7020 (mmm160) REVERT: G 549 ILE cc_start: 0.8196 (mm) cc_final: 0.7918 (mt) REVERT: G 621 GLN cc_start: 0.8004 (mt0) cc_final: 0.7389 (mp10) REVERT: G 650 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8138 (mmtp) REVERT: H 6 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: H 13 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6762 (mtp-110) REVERT: H 18 GLU cc_start: 0.8103 (pt0) cc_final: 0.7501 (pt0) REVERT: H 35 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8193 (mt-10) REVERT: H 88 MET cc_start: 0.8703 (mmm) cc_final: 0.8333 (mmm) REVERT: H 202 MET cc_start: 0.8815 (mtp) cc_final: 0.8578 (mtp) REVERT: H 242 MET cc_start: 0.8479 (tpp) cc_final: 0.8039 (mmm) REVERT: I 94 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8061 (mtp180) REVERT: I 209 ARG cc_start: 0.7019 (tpt170) cc_final: 0.6174 (mtp85) REVERT: I 230 PRO cc_start: 0.7670 (Cg_endo) cc_final: 0.7468 (Cg_exo) outliers start: 66 outliers final: 25 residues processed: 420 average time/residue: 0.8135 time to fit residues: 387.2451 Evaluate side-chains 387 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 354 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 548 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 71 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 305 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS B 12 ASN C 113 GLN E 28 ASN F 63 HIS F 155 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 HIS I 113 GLN I 155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103708 restraints weight = 27355.204| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.20 r_work: 0.3017 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 27951 Z= 0.173 Angle : 1.381 86.352 37989 Z= 0.391 Chirality : 0.057 1.511 4038 Planarity : 0.004 0.043 4854 Dihedral : 11.373 176.922 4356 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.82 % Allowed : 17.71 % Favored : 79.47 % 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: 1.10 (0.14), residues: 3363 helix: 1.51 (0.12), residues: 1602 sheet: 1.12 (0.32), residues: 237 loop : -0.09 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.010 0.001 TYR D 422 PHE 0.015 0.001 PHE C 28 TRP 0.010 0.001 TRP B 102 HIS 0.011 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00389 (27912) covalent geometry : angle 0.99432 (37908) hydrogen bonds : bond 0.04623 ( 1339) hydrogen bonds : angle 4.68170 ( 3756) metal coordination : bond 0.00744 ( 33) metal coordination : angle 20.76338 ( 81) Misc. bond : bond 0.09014 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 366 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8898 (mtp) cc_final: 0.8690 (mtp) REVERT: A 286 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6769 (t70) REVERT: A 359 GLN cc_start: 0.6483 (tp-100) cc_final: 0.6250 (tm-30) REVERT: A 362 ASP cc_start: 0.7286 (m-30) cc_final: 0.6935 (m-30) REVERT: A 400 MET cc_start: 0.6697 (tmm) cc_final: 0.6040 (ttm) REVERT: A 407 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 484 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7391 (mttt) REVERT: A 507 GLN cc_start: 0.6916 (mm110) cc_final: 0.6245 (mp10) REVERT: A 527 LYS cc_start: 0.7826 (tptt) cc_final: 0.7365 (tptp) REVERT: A 620 GLU cc_start: 0.8121 (tt0) cc_final: 0.7786 (tt0) REVERT: A 621 GLN cc_start: 0.7960 (mt0) cc_final: 0.7697 (mp10) REVERT: A 642 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: B 18 GLU cc_start: 0.8239 (pt0) cc_final: 0.7713 (pt0) REVERT: B 24 MET cc_start: 0.8282 (mtp) cc_final: 0.8077 (mtp) REVERT: B 242 MET cc_start: 0.8456 (tpp) cc_final: 0.8162 (tpt) REVERT: C 9 ARG cc_start: 0.7370 (mtt90) cc_final: 0.6910 (mtp180) REVERT: C 44 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7311 (tm-30) REVERT: C 105 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5755 (ttp-170) REVERT: C 111 LYS cc_start: 0.7897 (mttt) cc_final: 0.7674 (mttm) REVERT: C 209 ARG cc_start: 0.7162 (tpt170) cc_final: 0.6206 (ttp80) REVERT: D 340 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.5168 (mtm-85) REVERT: D 527 LYS cc_start: 0.7776 (tptt) cc_final: 0.7325 (tptp) REVERT: D 621 GLN cc_start: 0.7918 (mt0) cc_final: 0.7419 (mp10) REVERT: D 650 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8197 (mmtp) REVERT: E 11 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7955 (tppt) REVERT: E 13 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6560 (mtp-110) REVERT: E 18 GLU cc_start: 0.8095 (pt0) cc_final: 0.7744 (pt0) REVERT: F 91 GLN cc_start: 0.8939 (tt0) cc_final: 0.8705 (tt0) REVERT: F 137 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7718 (mp) REVERT: F 144 VAL cc_start: 0.8520 (p) cc_final: 0.8224 (m) REVERT: F 209 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6221 (mtp85) REVERT: G 181 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7091 (mp10) REVERT: G 365 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7512 (mtp-110) REVERT: G 508 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7738 (ttp80) REVERT: G 515 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7917 (mttp) REVERT: G 527 LYS cc_start: 0.7757 (tptt) cc_final: 0.7139 (tptp) REVERT: G 549 ILE cc_start: 0.8201 (mm) cc_final: 0.7931 (mt) REVERT: G 621 GLN cc_start: 0.8027 (mt0) cc_final: 0.7391 (mp10) REVERT: G 650 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8156 (mmtp) REVERT: H 6 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: H 13 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7114 (mtp-110) REVERT: H 18 GLU cc_start: 0.8111 (pt0) cc_final: 0.7502 (pt0) REVERT: H 88 MET cc_start: 0.8731 (mmm) cc_final: 0.8465 (mmm) REVERT: H 92 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7166 (mptt) REVERT: H 242 MET cc_start: 0.8531 (tpp) cc_final: 0.8107 (mmm) REVERT: I 94 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8074 (mtp180) REVERT: I 209 ARG cc_start: 0.7065 (tpt170) cc_final: 0.6203 (mtp85) outliers start: 77 outliers final: 38 residues processed: 414 average time/residue: 0.8278 time to fit residues: 387.0094 Evaluate side-chains 400 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 177 optimal weight: 1.9990 chunk 273 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 286 HIS A 595 HIS B 12 ASN C 109 GLN C 113 GLN F 155 HIS ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN I 113 GLN I 155 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103931 restraints weight = 27271.117| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.18 r_work: 0.3022 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 27951 Z= 0.162 Angle : 1.340 82.339 37989 Z= 0.382 Chirality : 0.058 1.565 4038 Planarity : 0.003 0.043 4854 Dihedral : 11.015 177.610 4356 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.60 % Allowed : 18.19 % Favored : 79.22 % 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: 1.15 (0.14), residues: 3363 helix: 1.54 (0.12), residues: 1602 sheet: 1.12 (0.32), residues: 237 loop : -0.07 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.010 0.001 TYR D 191 PHE 0.013 0.001 PHE C 28 TRP 0.010 0.001 TRP B 102 HIS 0.012 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00358 (27912) covalent geometry : angle 0.97048 (37908) hydrogen bonds : bond 0.04518 ( 1339) hydrogen bonds : angle 4.62984 ( 3756) metal coordination : bond 0.00645 ( 33) metal coordination : angle 20.04599 ( 81) Misc. bond : bond 0.09198 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 364 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7980 (mtm180) REVERT: A 359 GLN cc_start: 0.6523 (tp-100) cc_final: 0.6272 (tm-30) REVERT: A 362 ASP cc_start: 0.7360 (m-30) cc_final: 0.6983 (m-30) REVERT: A 400 MET cc_start: 0.6684 (tmm) cc_final: 0.6042 (ttm) REVERT: A 407 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 484 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7451 (mttt) REVERT: A 507 GLN cc_start: 0.6911 (mm110) cc_final: 0.6256 (mp10) REVERT: A 527 LYS cc_start: 0.7855 (tptt) cc_final: 0.7391 (tptp) REVERT: A 595 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7573 (p-80) REVERT: B 24 MET cc_start: 0.8241 (mtp) cc_final: 0.8023 (mtp) REVERT: B 43 ASP cc_start: 0.7380 (t70) cc_final: 0.7037 (t70) REVERT: B 242 MET cc_start: 0.8468 (tpp) cc_final: 0.8172 (tpt) REVERT: C 9 ARG cc_start: 0.7448 (mtt90) cc_final: 0.6800 (mtp-110) REVERT: C 44 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7363 (tm-30) REVERT: C 105 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.5747 (ttp-170) REVERT: C 111 LYS cc_start: 0.7903 (mttt) cc_final: 0.7669 (mttm) REVERT: C 209 ARG cc_start: 0.7182 (tpt170) cc_final: 0.6305 (mtp85) REVERT: D 340 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.5190 (mtm-85) REVERT: D 524 GLU cc_start: 0.8327 (tt0) cc_final: 0.8108 (tt0) REVERT: D 527 LYS cc_start: 0.7792 (tptt) cc_final: 0.7248 (tptp) REVERT: D 621 GLN cc_start: 0.7943 (mt0) cc_final: 0.7441 (mp10) REVERT: D 650 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8193 (mmtp) REVERT: E 11 LYS cc_start: 0.8379 (ttmt) cc_final: 0.7960 (tppt) REVERT: E 13 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6567 (mtp-110) REVERT: E 18 GLU cc_start: 0.8090 (pt0) cc_final: 0.7754 (pt0) REVERT: F 91 GLN cc_start: 0.8940 (tt0) cc_final: 0.8732 (tt0) REVERT: F 144 VAL cc_start: 0.8511 (p) cc_final: 0.8218 (m) REVERT: F 196 MET cc_start: 0.8895 (ptt) cc_final: 0.8557 (ptt) REVERT: F 209 ARG cc_start: 0.7030 (tpt170) cc_final: 0.6221 (mtp85) REVERT: G 181 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7073 (mp10) REVERT: G 365 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7483 (mtp-110) REVERT: G 508 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7793 (ttp-170) REVERT: G 527 LYS cc_start: 0.7781 (tptt) cc_final: 0.7165 (tptp) REVERT: G 549 ILE cc_start: 0.8204 (mm) cc_final: 0.7941 (mt) REVERT: G 621 GLN cc_start: 0.8018 (mt0) cc_final: 0.7411 (mp10) REVERT: G 650 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8175 (mmtp) REVERT: H 6 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8085 (mtpp) REVERT: H 13 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7117 (mtp-110) REVERT: H 18 GLU cc_start: 0.8133 (pt0) cc_final: 0.7531 (pt0) REVERT: H 88 MET cc_start: 0.8742 (mmm) cc_final: 0.8496 (mmm) REVERT: H 92 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7191 (mptt) REVERT: H 242 MET cc_start: 0.8519 (tpp) cc_final: 0.8097 (mmm) REVERT: I 44 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: I 94 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8083 (mtp180) REVERT: I 209 ARG cc_start: 0.7042 (tpt170) cc_final: 0.6223 (mtp85) outliers start: 71 outliers final: 38 residues processed: 408 average time/residue: 0.8180 time to fit residues: 377.4159 Evaluate side-chains 399 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 44 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 217 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 323 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 286 HIS A 595 HIS B 12 ASN C 113 GLN E 251 ASN F 155 HIS ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN I 155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102234 restraints weight = 27455.581| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.19 r_work: 0.2996 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 27951 Z= 0.191 Angle : 1.339 81.716 37989 Z= 0.390 Chirality : 0.060 1.630 4038 Planarity : 0.004 0.042 4854 Dihedral : 10.935 177.955 4356 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.37 % Allowed : 17.75 % Favored : 78.89 % 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: 1.05 (0.14), residues: 3363 helix: 1.46 (0.12), residues: 1599 sheet: 1.11 (0.32), residues: 237 loop : -0.11 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 93 TYR 0.012 0.001 TYR D 134 PHE 0.016 0.001 PHE I 28 TRP 0.011 0.002 TRP H 102 HIS 0.008 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00433 (27912) covalent geometry : angle 0.98423 (37908) hydrogen bonds : bond 0.04729 ( 1339) hydrogen bonds : angle 4.70711 ( 3756) metal coordination : bond 0.00712 ( 33) metal coordination : angle 19.68785 ( 81) Misc. bond : bond 0.10461 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 349 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7963 (mtm180) REVERT: A 400 MET cc_start: 0.6737 (tmm) cc_final: 0.6073 (ttm) REVERT: A 407 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 414 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7145 (ttp) REVERT: A 484 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7503 (mttt) REVERT: A 507 GLN cc_start: 0.6990 (mm110) cc_final: 0.6354 (mp10) REVERT: A 527 LYS cc_start: 0.7855 (tptt) cc_final: 0.7387 (tptp) REVERT: A 585 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8516 (tp) REVERT: A 595 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7388 (p-80) REVERT: A 642 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 24 MET cc_start: 0.8227 (mtp) cc_final: 0.7961 (mtp) REVERT: B 242 MET cc_start: 0.8513 (tpp) cc_final: 0.8221 (tpt) REVERT: C 9 ARG cc_start: 0.7429 (mtt90) cc_final: 0.6828 (mtp-110) REVERT: C 44 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7382 (tm-30) REVERT: C 105 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5770 (ttp-170) REVERT: C 111 LYS cc_start: 0.7906 (mttt) cc_final: 0.7644 (mttm) REVERT: C 209 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6305 (mtp85) REVERT: D 340 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.5185 (mtm-85) REVERT: D 524 GLU cc_start: 0.8334 (tt0) cc_final: 0.8114 (tt0) REVERT: D 527 LYS cc_start: 0.7796 (tptt) cc_final: 0.7252 (tptp) REVERT: D 621 GLN cc_start: 0.7959 (mt0) cc_final: 0.7467 (mp10) REVERT: D 650 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8207 (mmtp) REVERT: E 11 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7964 (tppt) REVERT: E 13 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6571 (mtp-110) REVERT: F 144 VAL cc_start: 0.8526 (p) cc_final: 0.8238 (m) REVERT: F 209 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6201 (mtp85) REVERT: G 332 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: G 365 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7607 (mtp-110) REVERT: G 508 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7806 (ttp-170) REVERT: G 527 LYS cc_start: 0.7788 (tptt) cc_final: 0.7169 (tptp) REVERT: G 549 ILE cc_start: 0.8226 (mm) cc_final: 0.7981 (mt) REVERT: G 620 GLU cc_start: 0.8167 (tt0) cc_final: 0.7278 (tt0) REVERT: G 621 GLN cc_start: 0.8013 (mt0) cc_final: 0.7432 (mp10) REVERT: G 650 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8182 (mmtp) REVERT: H 6 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: H 13 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7147 (mtp-110) REVERT: H 18 GLU cc_start: 0.8137 (pt0) cc_final: 0.7539 (pt0) REVERT: H 88 MET cc_start: 0.8792 (mmm) cc_final: 0.8456 (mmm) REVERT: H 92 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7176 (mptt) REVERT: H 242 MET cc_start: 0.8539 (tpp) cc_final: 0.8119 (mmm) REVERT: I 44 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: I 94 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8078 (mtp180) REVERT: I 209 ARG cc_start: 0.7048 (tpt170) cc_final: 0.6210 (mtp85) outliers start: 92 outliers final: 46 residues processed: 404 average time/residue: 0.8245 time to fit residues: 375.6749 Evaluate side-chains 401 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 341 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 189 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 286 HIS A 309 ASN A 359 GLN A 595 HIS A 621 GLN B 12 ASN C 113 GLN E 251 ASN F 91 GLN F 155 HIS ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN I 113 GLN I 150 GLN I 155 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100456 restraints weight = 27250.440| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.17 r_work: 0.2972 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 27951 Z= 0.233 Angle : 1.354 80.695 37989 Z= 0.404 Chirality : 0.062 1.650 4038 Planarity : 0.004 0.040 4854 Dihedral : 10.999 171.775 4356 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.37 % Allowed : 17.89 % Favored : 78.74 % 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: 0.90 (0.14), residues: 3363 helix: 1.29 (0.12), residues: 1599 sheet: 1.15 (0.32), residues: 237 loop : -0.17 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 93 TYR 0.013 0.002 TYR D 134 PHE 0.018 0.002 PHE F 28 TRP 0.014 0.002 TRP H 102 HIS 0.005 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00540 (27912) covalent geometry : angle 1.00403 (37908) hydrogen bonds : bond 0.05006 ( 1339) hydrogen bonds : angle 4.82865 ( 3756) metal coordination : bond 0.00930 ( 33) metal coordination : angle 19.70328 ( 81) Misc. bond : bond 0.11615 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 345 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7935 (mtm180) REVERT: A 335 TYR cc_start: 0.7641 (m-80) cc_final: 0.7400 (m-80) REVERT: A 362 ASP cc_start: 0.7259 (m-30) cc_final: 0.6836 (m-30) REVERT: A 400 MET cc_start: 0.6752 (tmm) cc_final: 0.6067 (ttm) REVERT: A 484 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7491 (mttt) REVERT: A 507 GLN cc_start: 0.6973 (mm110) cc_final: 0.6339 (mp10) REVERT: A 527 LYS cc_start: 0.7862 (tptt) cc_final: 0.7382 (tptp) REVERT: A 585 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 621 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: A 642 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: B 18 GLU cc_start: 0.8254 (pt0) cc_final: 0.7746 (pt0) REVERT: B 24 MET cc_start: 0.8260 (mtp) cc_final: 0.7977 (mtp) REVERT: B 242 MET cc_start: 0.8534 (tpp) cc_final: 0.8268 (tpt) REVERT: C 9 ARG cc_start: 0.7438 (mtt90) cc_final: 0.6822 (mtp-110) REVERT: C 44 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7382 (tm-30) REVERT: C 105 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5828 (ttp-170) REVERT: C 209 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6292 (ttp80) REVERT: D 340 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.5105 (mtm-85) REVERT: D 524 GLU cc_start: 0.8409 (tt0) cc_final: 0.8156 (tt0) REVERT: D 527 LYS cc_start: 0.7798 (tptt) cc_final: 0.7245 (tptp) REVERT: D 621 GLN cc_start: 0.7965 (mt0) cc_final: 0.7469 (mp10) REVERT: D 650 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8204 (mmtp) REVERT: E 11 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7983 (tppt) REVERT: E 13 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6625 (mtp-110) REVERT: E 18 GLU cc_start: 0.8111 (pt0) cc_final: 0.7769 (pt0) REVERT: F 54 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.5757 (mmt180) REVERT: F 144 VAL cc_start: 0.8535 (p) cc_final: 0.8242 (m) REVERT: F 209 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6285 (mtp85) REVERT: G 332 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: G 508 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7763 (ttp80) REVERT: G 527 LYS cc_start: 0.7785 (tptt) cc_final: 0.7173 (tptp) REVERT: G 620 GLU cc_start: 0.8173 (tt0) cc_final: 0.7302 (tt0) REVERT: G 621 GLN cc_start: 0.8013 (mt0) cc_final: 0.7453 (mp10) REVERT: G 650 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8206 (mmtp) REVERT: H 6 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (mtpp) REVERT: H 13 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7193 (mtp-110) REVERT: H 88 MET cc_start: 0.8790 (mmm) cc_final: 0.8449 (mmm) REVERT: H 92 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7145 (mptt) REVERT: H 242 MET cc_start: 0.8580 (tpp) cc_final: 0.8171 (mmm) REVERT: I 44 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: I 94 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8085 (mtp180) REVERT: I 209 ARG cc_start: 0.7025 (tpt170) cc_final: 0.6212 (mtp85) outliers start: 92 outliers final: 56 residues processed: 404 average time/residue: 0.7766 time to fit residues: 354.9403 Evaluate side-chains 412 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 342 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 621 GLN Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 286 HIS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 274 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 286 HIS A 359 GLN A 595 HIS B 12 ASN C 113 GLN D 547 GLN D 618 ASN E 251 ASN F 155 HIS G 359 GLN ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 213 ASN I 113 GLN I 155 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103142 restraints weight = 27432.676| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.20 r_work: 0.2996 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 27951 Z= 0.161 Angle : 1.314 81.056 37989 Z= 0.384 Chirality : 0.059 1.599 4038 Planarity : 0.003 0.041 4854 Dihedral : 10.702 175.504 4356 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 18.70 % Favored : 78.74 % 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: 1.04 (0.14), residues: 3363 helix: 1.44 (0.12), residues: 1602 sheet: 1.11 (0.33), residues: 237 loop : -0.11 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 93 TYR 0.011 0.001 TYR D 134 PHE 0.020 0.001 PHE A 622 TRP 0.010 0.001 TRP H 102 HIS 0.006 0.001 HIS A 595 Details of bonding type rmsd covalent geometry : bond 0.00355 (27912) covalent geometry : angle 0.97373 (37908) hydrogen bonds : bond 0.04579 ( 1339) hydrogen bonds : angle 4.68976 ( 3756) metal coordination : bond 0.00699 ( 33) metal coordination : angle 19.14565 ( 81) Misc. bond : bond 0.11079 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 351 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7959 (mtm180) REVERT: A 335 TYR cc_start: 0.7695 (m-80) cc_final: 0.7425 (m-80) REVERT: A 359 GLN cc_start: 0.6591 (tp40) cc_final: 0.6259 (tm-30) REVERT: A 362 ASP cc_start: 0.7263 (m-30) cc_final: 0.6840 (m-30) REVERT: A 400 MET cc_start: 0.6704 (tmm) cc_final: 0.6030 (ttm) REVERT: A 484 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7480 (mttt) REVERT: A 507 GLN cc_start: 0.6942 (mm110) cc_final: 0.6295 (mp10) REVERT: A 527 LYS cc_start: 0.7860 (tptt) cc_final: 0.7390 (tptp) REVERT: A 595 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7388 (p-80) REVERT: A 642 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: B 24 MET cc_start: 0.8163 (mtp) cc_final: 0.7935 (mtp) REVERT: B 242 MET cc_start: 0.8510 (tpp) cc_final: 0.8214 (tpt) REVERT: C 9 ARG cc_start: 0.7430 (mtt90) cc_final: 0.6800 (mtp-110) REVERT: C 44 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7371 (tm-30) REVERT: C 105 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5626 (ttp-170) REVERT: C 111 LYS cc_start: 0.7869 (mttt) cc_final: 0.7581 (mttm) REVERT: C 209 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6309 (mtp85) REVERT: D 340 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.5179 (mtm-85) REVERT: D 524 GLU cc_start: 0.8386 (tt0) cc_final: 0.8152 (tt0) REVERT: D 527 LYS cc_start: 0.7760 (tptt) cc_final: 0.7312 (tptp) REVERT: D 621 GLN cc_start: 0.7944 (mt0) cc_final: 0.7422 (mp10) REVERT: D 650 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8186 (mmtp) REVERT: E 11 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7943 (tppt) REVERT: E 13 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6569 (mtp-110) REVERT: E 18 GLU cc_start: 0.8077 (pt0) cc_final: 0.7730 (pt0) REVERT: F 1 MET cc_start: 0.2975 (mmm) cc_final: 0.2307 (mpt) REVERT: F 54 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.5627 (mmt180) REVERT: F 144 VAL cc_start: 0.8493 (p) cc_final: 0.8203 (m) REVERT: F 209 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6214 (mtp85) REVERT: G 332 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: G 508 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7802 (ttp-170) REVERT: G 527 LYS cc_start: 0.7756 (tptt) cc_final: 0.7095 (tptm) REVERT: G 621 GLN cc_start: 0.7975 (mt0) cc_final: 0.7409 (mp10) REVERT: G 650 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8157 (mmtp) REVERT: H 13 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7051 (mtp-110) REVERT: H 18 GLU cc_start: 0.8135 (pt0) cc_final: 0.7492 (pt0) REVERT: H 88 MET cc_start: 0.8747 (mmm) cc_final: 0.8430 (mmm) REVERT: H 92 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7117 (mptt) REVERT: H 242 MET cc_start: 0.8528 (tpp) cc_final: 0.8102 (mmm) REVERT: I 44 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: I 94 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8046 (mtp180) REVERT: I 105 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6809 (ttp-110) REVERT: I 209 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6177 (mtp85) outliers start: 70 outliers final: 44 residues processed: 395 average time/residue: 0.7949 time to fit residues: 354.4313 Evaluate side-chains 401 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 286 HIS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 106 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 12 ASN C 113 GLN D 547 GLN E 28 ASN F 155 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN I 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100959 restraints weight = 27490.405| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.16 r_work: 0.2989 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 27951 Z= 0.215 Angle : 1.336 80.615 37989 Z= 0.398 Chirality : 0.061 1.630 4038 Planarity : 0.004 0.041 4854 Dihedral : 10.729 170.188 4356 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.82 % Allowed : 18.51 % Favored : 78.67 % 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: 0.92 (0.14), residues: 3363 helix: 1.33 (0.12), residues: 1599 sheet: 1.14 (0.33), residues: 237 loop : -0.18 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 93 TYR 0.012 0.002 TYR D 134 PHE 0.017 0.002 PHE I 28 TRP 0.015 0.002 TRP H 102 HIS 0.005 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00495 (27912) covalent geometry : angle 0.99527 (37908) hydrogen bonds : bond 0.04859 ( 1339) hydrogen bonds : angle 4.77799 ( 3756) metal coordination : bond 0.00828 ( 33) metal coordination : angle 19.32925 ( 81) Misc. bond : bond 0.11457 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 347 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8004 (mtm180) REVERT: A 286 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6696 (t70) REVERT: A 335 TYR cc_start: 0.7619 (m-80) cc_final: 0.7372 (m-80) REVERT: A 362 ASP cc_start: 0.7306 (m-30) cc_final: 0.6850 (m-30) REVERT: A 400 MET cc_start: 0.6740 (tmm) cc_final: 0.6078 (ttm) REVERT: A 407 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 414 MET cc_start: 0.7581 (ptm) cc_final: 0.7231 (ttp) REVERT: A 484 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7530 (mttt) REVERT: A 507 GLN cc_start: 0.6981 (mm110) cc_final: 0.6347 (mp10) REVERT: A 527 LYS cc_start: 0.7873 (tptt) cc_final: 0.7404 (tptp) REVERT: A 621 GLN cc_start: 0.8241 (mp10) cc_final: 0.7889 (mp10) REVERT: B 24 MET cc_start: 0.8247 (mtp) cc_final: 0.7952 (mtp) REVERT: B 242 MET cc_start: 0.8541 (tpp) cc_final: 0.8275 (tpt) REVERT: C 9 ARG cc_start: 0.7465 (mtt90) cc_final: 0.6893 (mmm160) REVERT: C 44 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7411 (tm-30) REVERT: C 105 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5844 (ttp-170) REVERT: C 111 LYS cc_start: 0.7859 (mttt) cc_final: 0.7548 (mttm) REVERT: C 179 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 209 ARG cc_start: 0.7176 (tpt170) cc_final: 0.6282 (ttp80) REVERT: D 524 GLU cc_start: 0.8403 (tt0) cc_final: 0.8152 (tt0) REVERT: D 527 LYS cc_start: 0.7804 (tptt) cc_final: 0.7257 (tptp) REVERT: D 621 GLN cc_start: 0.7967 (mt0) cc_final: 0.7459 (mp10) REVERT: D 650 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8207 (mmtp) REVERT: E 11 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7978 (tppt) REVERT: E 13 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6668 (mtp-110) REVERT: E 18 GLU cc_start: 0.8097 (pt0) cc_final: 0.7753 (pt0) REVERT: F 54 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.5738 (mmt180) REVERT: F 144 VAL cc_start: 0.8530 (p) cc_final: 0.8246 (m) REVERT: F 206 THR cc_start: 0.7290 (p) cc_final: 0.6893 (t) REVERT: F 209 ARG cc_start: 0.7068 (tpt170) cc_final: 0.6290 (mtp85) REVERT: G 332 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: G 508 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7807 (ttp-170) REVERT: G 527 LYS cc_start: 0.7798 (tptt) cc_final: 0.7165 (tptm) REVERT: G 620 GLU cc_start: 0.8188 (tt0) cc_final: 0.7279 (tt0) REVERT: G 621 GLN cc_start: 0.7992 (mt0) cc_final: 0.7459 (mp10) REVERT: G 650 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8211 (mmtp) REVERT: H 13 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7177 (mtp-110) REVERT: H 18 GLU cc_start: 0.8163 (pt0) cc_final: 0.7529 (pt0) REVERT: H 88 MET cc_start: 0.8804 (mmm) cc_final: 0.8377 (mmm) REVERT: H 92 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7164 (mptt) REVERT: H 242 MET cc_start: 0.8553 (tpp) cc_final: 0.8141 (mmm) REVERT: I 44 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: I 94 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8082 (mtp180) REVERT: I 209 ARG cc_start: 0.7025 (tpt170) cc_final: 0.6216 (mtp85) outliers start: 77 outliers final: 46 residues processed: 397 average time/residue: 0.7313 time to fit residues: 327.0705 Evaluate side-chains 399 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 342 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 286 HIS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 241 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 147 optimal weight: 0.0040 chunk 144 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 287 optimal weight: 0.4980 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN B 12 ASN C 113 GLN D 547 GLN E 251 ASN F 155 HIS ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN I 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.104366 restraints weight = 27476.415| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.13 r_work: 0.3024 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 27951 Z= 0.154 Angle : 1.303 81.166 37989 Z= 0.380 Chirality : 0.059 1.581 4038 Planarity : 0.003 0.043 4854 Dihedral : 10.450 174.401 4356 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 19.39 % Favored : 78.45 % 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: 1.10 (0.14), residues: 3363 helix: 1.50 (0.12), residues: 1602 sheet: 1.11 (0.32), residues: 237 loop : -0.09 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 93 TYR 0.011 0.001 TYR D 191 PHE 0.011 0.001 PHE C 28 TRP 0.013 0.001 TRP E 102 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00336 (27912) covalent geometry : angle 0.96912 (37908) hydrogen bonds : bond 0.04468 ( 1339) hydrogen bonds : angle 4.63624 ( 3756) metal coordination : bond 0.00634 ( 33) metal coordination : angle 18.88900 ( 81) Misc. bond : bond 0.10372 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7839 (mtm180) REVERT: A 286 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6695 (t70) REVERT: A 304 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 335 TYR cc_start: 0.7701 (m-80) cc_final: 0.7366 (m-80) REVERT: A 359 GLN cc_start: 0.6740 (tp-100) cc_final: 0.6455 (tm-30) REVERT: A 362 ASP cc_start: 0.7404 (m-30) cc_final: 0.6975 (m-30) REVERT: A 385 LEU cc_start: 0.6388 (mt) cc_final: 0.6142 (tp) REVERT: A 400 MET cc_start: 0.6764 (tmm) cc_final: 0.6087 (ttm) REVERT: A 407 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 484 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7592 (mttt) REVERT: A 507 GLN cc_start: 0.7031 (mm110) cc_final: 0.6418 (mp10) REVERT: A 527 LYS cc_start: 0.7935 (tptt) cc_final: 0.7483 (tptp) REVERT: A 642 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 24 MET cc_start: 0.8201 (mtp) cc_final: 0.7973 (mtp) REVERT: B 242 MET cc_start: 0.8548 (tpp) cc_final: 0.8264 (tpt) REVERT: C 9 ARG cc_start: 0.7504 (mtt90) cc_final: 0.6939 (mmm160) REVERT: C 44 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7446 (tm-30) REVERT: C 105 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.5762 (ttp-170) REVERT: C 111 LYS cc_start: 0.7852 (mttt) cc_final: 0.7580 (mttm) REVERT: C 179 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 209 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6377 (mtp85) REVERT: D 350 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7246 (tmm160) REVERT: D 524 GLU cc_start: 0.8393 (tt0) cc_final: 0.8186 (tt0) REVERT: D 527 LYS cc_start: 0.7839 (tptt) cc_final: 0.7308 (tptp) REVERT: D 621 GLN cc_start: 0.7990 (mt0) cc_final: 0.7498 (mp10) REVERT: D 650 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8245 (mmtp) REVERT: E 11 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8009 (tppt) REVERT: E 13 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6594 (mtp-110) REVERT: E 18 GLU cc_start: 0.8098 (pt0) cc_final: 0.7770 (pt0) REVERT: E 20 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7794 (mttp) REVERT: F 1 MET cc_start: 0.3008 (mmm) cc_final: 0.2576 (mpt) REVERT: F 144 VAL cc_start: 0.8512 (p) cc_final: 0.8246 (m) REVERT: F 196 MET cc_start: 0.8893 (ptt) cc_final: 0.8556 (ptt) REVERT: F 206 THR cc_start: 0.7304 (p) cc_final: 0.6966 (t) REVERT: F 209 ARG cc_start: 0.7061 (tpt170) cc_final: 0.6324 (mtp85) REVERT: G 332 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: G 508 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7852 (ttp-170) REVERT: G 527 LYS cc_start: 0.7856 (tptt) cc_final: 0.7264 (tptp) REVERT: G 621 GLN cc_start: 0.7989 (mt0) cc_final: 0.7494 (mp10) REVERT: G 650 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8209 (mmtp) REVERT: H 13 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7088 (mtp-110) REVERT: H 18 GLU cc_start: 0.8166 (pt0) cc_final: 0.7563 (pt0) REVERT: H 35 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8260 (mt-10) REVERT: H 88 MET cc_start: 0.8790 (mmm) cc_final: 0.8582 (mmm) REVERT: H 92 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7195 (mptt) REVERT: H 242 MET cc_start: 0.8556 (tpp) cc_final: 0.8135 (mmm) REVERT: I 44 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: I 94 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8100 (mtp180) REVERT: I 209 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6287 (mtp85) outliers start: 59 outliers final: 40 residues processed: 382 average time/residue: 0.8158 time to fit residues: 350.6891 Evaluate side-chains 390 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 507 GLN Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain I residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 317 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 621 GLN B 12 ASN C 113 GLN E 251 ASN F 155 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103515 restraints weight = 27313.443| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.19 r_work: 0.3015 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 27951 Z= 0.233 Angle : 1.381 80.929 37989 Z= 0.459 Chirality : 0.062 1.592 4038 Planarity : 0.005 0.190 4854 Dihedral : 10.474 174.451 4356 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 2.09 % Allowed : 19.69 % Favored : 78.23 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.09 (0.14), residues: 3363 helix: 1.48 (0.12), residues: 1608 sheet: 1.12 (0.32), residues: 237 loop : -0.09 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 93 TYR 0.010 0.001 TYR D 191 PHE 0.011 0.001 PHE C 28 TRP 0.011 0.002 TRP E 102 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00491 (27912) covalent geometry : angle 1.07201 (37908) hydrogen bonds : bond 0.04516 ( 1339) hydrogen bonds : angle 4.63759 ( 3756) metal coordination : bond 0.00624 ( 33) metal coordination : angle 18.88791 ( 81) Misc. bond : bond 0.10198 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9931.31 seconds wall clock time: 170 minutes 5.72 seconds (10205.72 seconds total)