Starting phenix.real_space_refine on Fri Feb 6 19:18:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lb0_62934/02_2026/9lb0_62934.map" } resolution = 2.74 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= 0.001 sd= 0.012 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 6 5.49 5 S 186 5.16 5 C 17318 2.51 5 N 4716 2.21 5 O 4899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s 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: 27158 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 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: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 176 Unusual residues: {'HEM': 2, 'LMT': 1, 'MQ7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'MQ7:plan-2': 2, 'MQ7:plan-3': 2, 'MQ7:plan-4': 2, 'MQ7:plan-7': 1, 'MQ7:plan-8': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 177 Unusual residues: {'HEM': 2, 'LMT': 1, 'MQ7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'MQ7:plan-2': 2, 'MQ7:plan-3': 2, 'MQ7:plan-4': 2, 'MQ7:plan-7': 1, 'MQ7:plan-8': 1} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 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: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 177 Unusual residues: {'HEM': 2, 'LMT': 1, 'MQ7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'MQ7:plan-2': 2, 'MQ7:plan-3': 2, 'MQ7:plan-4': 2, 'MQ7:plan-7': 1, 'MQ7:plan-8': 1} Unresolved non-hydrogen planarities: 40 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 162 95.715 45.171 70.971 1.00 78.61 S ATOM 6166 SG CYS B 159 93.016 51.004 71.679 1.00 89.36 S ATOM 6628 SG CYS B 224 90.388 46.531 67.983 1.00107.00 S ATOM 6199 SG CYS B 165 96.275 49.239 66.356 1.00 99.47 S ATOM 5481 SG CYS B 66 98.465 38.505 77.003 1.00125.14 S ATOM 5606 SG CYS B 84 95.016 38.190 77.545 1.00102.16 S ATOM 5425 SG CYS B 58 94.726 41.246 81.388 1.00110.41 S ATOM 5463 SG CYS B 63 97.397 43.459 80.281 1.00 98.86 S ATOM 6222 SG CYS B 169 98.516 49.320 58.224 1.00 98.80 S ATOM 6605 SG CYS B 220 92.858 48.805 60.552 1.00 91.60 S ATOM 6563 SG CYS B 214 93.919 53.527 56.758 1.00109.52 S ATOM 14988 SG CYS E 162 40.821 70.331 70.977 1.00 75.39 S ATOM 15432 SG CYS E 224 44.654 74.271 68.071 1.00105.76 S ATOM 15003 SG CYS E 165 44.048 67.798 66.363 1.00 95.59 S ATOM 14970 SG CYS E 159 47.212 69.741 71.705 1.00 86.05 S ATOM 14229 SG CYS E 58 37.873 73.076 81.316 1.00 99.67 S ATOM 14267 SG CYS E 63 38.434 69.687 80.269 1.00101.66 S ATOM 14285 SG CYS E 66 35.126 71.619 75.557 1.00103.22 S ATOM 14410 SG CYS E 84 35.036 74.559 77.611 1.00 99.65 S ATOM 15026 SG CYS E 169 43.036 65.875 58.112 1.00 97.25 S ATOM 15409 SG CYS E 220 45.320 70.935 60.875 1.00 92.99 S ATOM 15367 SG CYS E 214 48.829 67.681 56.878 1.00106.02 S ATOM 23774 SG CYS H 159 86.363 100.013 71.677 1.00 87.84 S ATOM 23792 SG CYS H 162 90.051 105.300 70.970 1.00 78.19 S ATOM 23807 SG CYS H 165 86.247 103.724 66.359 1.00 99.40 S ATOM 24236 SG CYS H 224 91.559 99.987 68.043 1.00109.88 S ATOM 23089 SG CYS H 66 94.004 109.591 75.688 1.00 97.46 S ATOM 23214 SG CYS H 84 96.602 108.122 77.609 1.00 99.16 S ATOM 23033 SG CYS H 58 93.863 106.433 81.356 1.00106.90 S ATOM 23071 SG CYS H 63 90.628 107.643 80.314 1.00101.72 S ATOM 24213 SG CYS H 220 88.442 100.879 60.703 1.00102.91 S ATOM 24171 SG CYS H 214 83.826 99.610 56.711 1.00105.99 S Time building chain proxies: 6.46, per 1000 atoms: 0.24 Number of scatterers: 27158 At special positions: 0 Unit cell: (140.8, 145.92, 134.4, 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 6 15.00 O 4899 8.00 N 4716 7.00 C 17318 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: 2.58 Conformation dependent library (CDL) restraints added in 902.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 220 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 214 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 169 " 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="FE1 F3S H 303 " - pdb=" SG CYS H 220 " pdb="FE4 F3S H 303 " - pdb=" SG CYS H 169 " pdb=" FES B 302 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 63 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 66 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 58 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 84 " pdb=" FES E 302 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 63 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 66 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 58 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 84 " pdb=" FES H 302 " pdb="FE2 FES H 302 " - pdb=" SG CYS H 63 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 66 " 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="FE1 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 224 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 159 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 165 " pdb=" SF4 E 301 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 162 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 159 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 224 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 165 " pdb=" SF4 H 301 " pdb="FE2 SF4 H 301 " - pdb=" SG CYS H 162 " pdb="FE1 SF4 H 301 " - pdb=" SG CYS H 159 " pdb="FE4 SF4 H 301 " - pdb=" SG CYS H 224 " 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: 125 helices and 21 sheets defined 50.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 49 through 53 removed outlier: 4.014A pdb=" N ARG A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 129 through 150 removed outlier: 3.616A pdb=" N VAL A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.996A 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: 3.873A 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 324 through 328 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 363 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 386 through 405 removed outlier: 6.896A pdb=" N ASN A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 471 through 483 removed outlier: 3.514A pdb=" N VAL A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 removed outlier: 4.519A pdb=" N ARG A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 removed outlier: 3.515A pdb=" N PHE A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) 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: 3.697A pdb=" N GLU A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.857A 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: 4.079A pdb=" N ASP B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.437A pdb=" N ILE B 143 " --> pdb=" O ALA B 140 " (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 193 Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.873A pdb=" N VAL B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.786A pdb=" N VAL B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 removed outlier: 3.559A pdb=" N ALA B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 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: 3.870A pdb=" N ARG C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 96 removed outlier: 3.617A pdb=" N LEU C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 171 through 201 removed outlier: 4.909A pdb=" N TRP C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 235 removed outlier: 4.500A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C 229 " --> pdb=" O GLY C 225 " (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 50 through 53 Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 129 through 150 removed outlier: 3.627A pdb=" N VAL D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.987A 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: 3.612A 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 305 through 309 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 342 through 347 removed outlier: 4.252A pdb=" N GLY D 345 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN D 346 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 378 through 385 Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 459 through 470 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 492 through 513 removed outlier: 4.603A pdb=" N ARG D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 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: 3.677A pdb=" N GLU D 574 " --> pdb=" O ASN D 570 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU D 587 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 3.988A 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 removed outlier: 3.538A pdb=" N SER E 90 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 91 " --> pdb=" O MET E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 117 through 126 removed outlier: 4.087A pdb=" N ASP E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.419A pdb=" N ILE E 143 " --> pdb=" O ALA E 140 " (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 193 Proline residue: E 193 - end of helix Processing helix chain 'E' and resid 194 through 210 removed outlier: 3.959A pdb=" N VAL E 200 " --> pdb=" O TYR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.655A pdb=" N ALA E 222 " --> pdb=" O GLY E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 246 removed outlier: 3.564A pdb=" N ALA E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 9 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: 3.915A pdb=" N ARG F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 98 removed outlier: 4.173A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 140 removed outlier: 3.935A pdb=" N LEU F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.512A pdb=" N PHE F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 201 removed outlier: 4.836A pdb=" N TRP F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE F 197 " --> pdb=" O VAL F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 235 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 91 through 96 removed outlier: 3.702A pdb=" N ALA G 96 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 129 through 150 removed outlier: 3.627A pdb=" N VAL G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.999A 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: 3.903A 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 305 through 309 removed outlier: 3.720A pdb=" N ARG G 308 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 328 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 343 through 347 removed outlier: 3.640A pdb=" N ASN G 346 " --> pdb=" O SER G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 364 removed outlier: 3.517A pdb=" N GLY G 364 " --> pdb=" O VAL G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 385 Processing helix chain 'G' and resid 386 through 406 removed outlier: 6.796A pdb=" N ASN G 396 " --> pdb=" O GLU G 392 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU G 397 " --> pdb=" O ARG G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 470 Processing helix chain 'G' and resid 471 through 481 Processing helix chain 'G' and resid 492 through 512 Processing helix chain 'G' and resid 517 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: 3.677A pdb=" N GLU G 574 " --> pdb=" O ASN G 570 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 587 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 3.981A 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 removed outlier: 3.558A pdb=" N SER H 90 " --> pdb=" O HIS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 126 removed outlier: 4.108A pdb=" N ASP H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 removed outlier: 4.434A pdb=" N ILE H 143 " --> pdb=" O ALA H 140 " (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 193 Proline residue: H 193 - end of helix Processing helix chain 'H' and resid 194 through 210 removed outlier: 3.908A pdb=" N VAL H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 224 removed outlier: 3.606A pdb=" N ALA H 222 " --> pdb=" O GLY H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 246 Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 10 through 37 Processing helix chain 'I' and resid 38 through 41 Processing helix chain 'I' and resid 42 through 55 removed outlier: 4.039A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 64 through 95 Processing helix chain 'I' and resid 116 through 140 Processing helix chain 'I' and resid 160 through 167 Processing helix chain 'I' and resid 171 through 200 removed outlier: 4.855A pdb=" N TRP I 194 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE I 197 " --> pdb=" O VAL I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 235 Proline residue: I 230 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 206 removed outlier: 6.564A pdb=" N VAL A 79 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 206 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 81 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 241 " --> pdb=" O THR A 55 " (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: 6.550A pdb=" N ILE A 225 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 214 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY A 223 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 216 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.400A 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: 5.757A pdb=" N HIS A 286 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 420 " --> pdb=" O HIS A 286 " (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 'B' and resid 18 through 24 removed outlier: 6.599A pdb=" N THR B 4 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 99 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS B 6 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 203 through 206 removed outlier: 6.598A pdb=" N VAL D 79 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE D 206 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS D 81 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 241 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 242 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'D' and resid 209 through 217 removed outlier: 6.528A pdb=" N ILE D 225 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU D 214 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY D 223 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 216 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA D 221 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AB3, first strand: chain 'D' and resid 283 through 286 removed outlier: 6.728A pdb=" N GLN D 284 " --> pdb=" O HIS D 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 24 removed outlier: 6.570A pdb=" N THR E 4 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL E 99 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS E 6 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 203 through 206 removed outlier: 6.580A pdb=" N VAL G 79 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE G 206 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS G 81 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 241 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AB8, first strand: chain 'G' and resid 209 through 217 removed outlier: 6.543A pdb=" N ILE G 225 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU G 214 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY G 223 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL G 216 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA G 221 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 426 through 427 Processing sheet with id=AC1, first strand: chain 'G' and resid 283 through 286 removed outlier: 5.525A pdb=" N HIS G 286 " --> pdb=" O VAL G 420 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL G 420 " --> pdb=" O HIS G 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'H' and resid 18 through 24 removed outlier: 6.381A pdb=" N THR H 4 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL H 99 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS H 6 " --> pdb=" O VAL H 99 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.76: 27500 1.76 - 2.31: 336 2.31 - 2.86: 3 2.86 - 3.41: 0 3.41 - 3.96: 9 Bond restraints: 27848 Sorted by residual: bond pdb=" S4 F3S E 303 " pdb="FE1 F3S E 303 " ideal model delta sigma weight residual 2.233 3.957 -1.724 2.00e-02 2.50e+03 7.43e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.937 -1.704 2.00e-02 2.50e+03 7.26e+03 bond pdb=" S4 F3S H 303 " pdb="FE1 F3S H 303 " ideal model delta sigma weight residual 2.233 3.908 -1.675 2.00e-02 2.50e+03 7.01e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.943 -1.643 2.00e-02 2.50e+03 6.75e+03 bond pdb=" S1 F3S H 303 " pdb="FE4 F3S H 303 " ideal model delta sigma weight residual 2.258 3.900 -1.642 2.00e-02 2.50e+03 6.74e+03 ... (remaining 27843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.22: 37838 10.22 - 20.43: 0 20.43 - 30.65: 9 30.65 - 40.87: 15 40.87 - 51.09: 6 Bond angle restraints: 37868 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 63.66 51.09 3.00e+00 1.11e-01 2.90e+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 65.08 49.67 3.00e+00 1.11e-01 2.74e+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 65.17 49.58 3.00e+00 1.11e-01 2.73e+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 63.36 49.23 3.00e+00 1.11e-01 2.69e+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 64.19 48.40 3.00e+00 1.11e-01 2.60e+02 ... (remaining 37863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 16006 34.98 - 69.96: 343 69.96 - 104.95: 49 104.95 - 139.93: 13 139.93 - 174.91: 1 Dihedral angle restraints: 16412 sinusoidal: 6755 harmonic: 9657 Sorted by residual: dihedral pdb=" C2C HEM I 302 " pdb=" C3C HEM I 302 " pdb=" CAC HEM I 302 " pdb=" CBC HEM I 302 " ideal model delta sinusoidal sigma weight residual 0.00 88.67 -88.67 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2B HEM C 301 " pdb=" C3B HEM C 301 " pdb=" CAB HEM C 301 " pdb=" CBB HEM C 301 " ideal model delta sinusoidal sigma weight residual 180.00 -92.17 -87.83 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEM I 301 " pdb=" C3B HEM I 301 " pdb=" CAB HEM I 301 " pdb=" CBB HEM I 301 " ideal model delta sinusoidal sigma weight residual -0.00 -87.67 87.67 2 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.695: 4026 3.695 - 7.391: 0 7.391 - 11.086: 0 11.086 - 14.781: 0 14.781 - 18.476: 3 Chirality restraints: 4029 Sorted by residual: 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 -7.71 18.48 2.00e-01 2.50e+01 8.53e+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 -7.31 18.08 2.00e-01 2.50e+01 8.17e+03 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 -7.23 17.99 2.00e-01 2.50e+01 8.10e+03 ... (remaining 4026 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 200 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL E 200 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL E 200 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN E 201 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 201 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ASN B 201 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN B 201 " -0.012 2.00e-02 2.50e+03 pdb=" N MET B 202 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 200 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C VAL H 200 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL H 200 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN H 201 " 0.011 2.00e-02 2.50e+03 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 243 2.65 - 3.21: 24395 3.21 - 3.77: 42712 3.77 - 4.34: 60008 4.34 - 4.90: 100244 Nonbonded interactions: 227602 Sorted by model distance: nonbonded pdb=" OG SER G 449 " pdb=" OD1 ASP G 450 " model vdw 2.082 3.040 nonbonded pdb=" O GLY C 3 " pdb=" OG1 THR C 6 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR D 191 " pdb=" OD1 ASP E 121 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR G 288 " pdb=" O SER G 304 " model vdw 2.214 3.040 nonbonded pdb=" O ARG I 9 " pdb=" O3B LMT I 303 " model vdw 2.218 3.040 ... (remaining 227597 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' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 1 through 303 or (resid 304 through 305 and (name C1 or na \ me C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C19 or name C2 or name C20 or name C2M or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 or \ name O4 )))) selection = (chain 'F' and (resid 1 through 302 or (resid 303 and (name C1 or name C1' or na \ me C10 or name C11 or name C1B or name C2 or name C2' or name C2B or name C3 or \ name C3' or name C3B or name C4 or name C4' or name C4B or name C5 or name C5' o \ r name C5B or name C6 or name C6' or name C6B or name C7 or name C8 or name C9 o \ r name O1' or name O1B or name O2' or name O2B or name O3' or name O3B or name O \ 4' or name O5' or name O5B or name O6' or name O6B)) or (resid 304 through 305 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C2M or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 or name O1 or name O4 )))) selection = (chain 'I' and (resid 1 through 302 or (resid 303 and (name C1 or name C1' or na \ me C10 or name C11 or name C1B or name C2 or name C2' or name C2B or name C3 or \ name C3' or name C3B or name C4 or name C4' or name C4B or name C5 or name C5' o \ r name C5B or name C6 or name C6' or name C6B or name C7 or name C8 or name C9 o \ r name O1' or name O1B or name O2' or name O2B or name O3' or name O3B or name O \ 4' or name O5' or name O5B or name O6' or name O6B)) or (resid 304 through 305 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C2M or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 or name O1 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 30.910 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 1.724 27887 Z= 1.550 Angle : 1.377 51.085 37949 Z= 0.465 Chirality : 0.498 18.476 4029 Planarity : 0.004 0.041 4860 Dihedral : 15.854 174.911 10274 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.51 % Allowed : 6.18 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3363 helix: 1.45 (0.13), residues: 1560 sheet: 1.50 (0.33), residues: 237 loop : -0.64 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.012 0.001 TYR I 107 PHE 0.013 0.001 PHE C 229 TRP 0.012 0.001 TRP G 314 HIS 0.009 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.03037 (27848) covalent geometry : angle 1.21469 (37868) hydrogen bonds : bond 0.13617 ( 1312) hydrogen bonds : angle 5.49708 ( 3693) metal coordination : bond 0.17360 ( 33) metal coordination : angle 14.11144 ( 81) Misc. bond : bond 0.14049 ( 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 380 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 0.889 Fit side-chains REVERT: A 344 PHE cc_start: 0.7821 (m-80) cc_final: 0.7595 (m-80) REVERT: A 347 LEU cc_start: 0.8605 (mm) cc_final: 0.8347 (mm) REVERT: A 504 GLN cc_start: 0.8487 (tp40) cc_final: 0.8021 (tp40) REVERT: A 620 GLU cc_start: 0.8390 (pp20) cc_final: 0.8055 (pp20) REVERT: B 95 ASP cc_start: 0.8552 (t0) cc_final: 0.8093 (t0) REVERT: B 139 ASP cc_start: 0.8429 (t70) cc_final: 0.8068 (t0) REVERT: B 231 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 249 GLU cc_start: 0.8283 (tp30) cc_final: 0.7976 (mm-30) REVERT: C 1 MET cc_start: 0.6772 (mmp) cc_final: 0.6061 (mmp) REVERT: C 8 THR cc_start: 0.8996 (m) cc_final: 0.8655 (p) REVERT: C 9 ARG cc_start: 0.8131 (mpt-90) cc_final: 0.7819 (mpt-90) REVERT: C 44 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8240 (mm-30) REVERT: C 160 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 205 ARG cc_start: 0.7833 (mpt-90) cc_final: 0.7542 (mtt-85) REVERT: D 52 ARG cc_start: 0.8260 (ptm-80) cc_final: 0.7963 (ptm-80) REVERT: D 61 SER cc_start: 0.9482 (t) cc_final: 0.9258 (t) REVERT: D 288 THR cc_start: 0.8898 (m) cc_final: 0.8642 (p) REVERT: D 323 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8375 (mtp180) REVERT: D 339 GLU cc_start: 0.8674 (tt0) cc_final: 0.8279 (pt0) REVERT: D 405 THR cc_start: 0.9087 (m) cc_final: 0.8885 (p) REVERT: D 504 GLN cc_start: 0.8432 (tp40) cc_final: 0.8127 (tp40) REVERT: D 636 LYS cc_start: 0.8728 (mttt) cc_final: 0.8376 (mmtm) REVERT: E 116 ASP cc_start: 0.8304 (t0) cc_final: 0.7999 (t0) REVERT: F 1 MET cc_start: 0.5269 (ppp) cc_final: 0.4505 (ppp) REVERT: F 41 GLN cc_start: 0.8448 (mm110) cc_final: 0.8213 (mt0) REVERT: F 171 ASN cc_start: 0.8077 (t0) cc_final: 0.7744 (t0) REVERT: G 339 GLU cc_start: 0.8671 (tt0) cc_final: 0.8143 (pt0) REVERT: G 389 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7742 (mppt) REVERT: G 405 THR cc_start: 0.9050 (m) cc_final: 0.8779 (p) REVERT: G 504 GLN cc_start: 0.8526 (tp40) cc_final: 0.8117 (tp40) REVERT: H 28 ASN cc_start: 0.8979 (t0) cc_final: 0.8678 (t0) REVERT: H 116 ASP cc_start: 0.8414 (t0) cc_final: 0.8167 (t0) REVERT: H 231 GLU cc_start: 0.8128 (mp0) cc_final: 0.7921 (mp0) REVERT: I 41 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7533 (mt0) REVERT: I 119 TYR cc_start: 0.8092 (m-80) cc_final: 0.7824 (m-80) REVERT: I 205 ARG cc_start: 0.8094 (mpt-90) cc_final: 0.7529 (mtt-85) outliers start: 14 outliers final: 9 residues processed: 378 average time/residue: 0.8318 time to fit residues: 354.7958 Evaluate side-chains 262 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 253 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN C 91 GLN C 109 GLN C 170 GLN C 226 ASN D 284 GLN F 113 GLN F 226 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN I 138 HIS I 164 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.073831 restraints weight = 48357.281| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.50 r_work: 0.2772 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 27887 Z= 0.221 Angle : 1.408 67.141 37949 Z= 0.414 Chirality : 0.080 2.630 4029 Planarity : 0.004 0.040 4860 Dihedral : 10.755 172.861 4200 Min Nonbonded Distance : 1.510 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.20 % Allowed : 11.67 % Favored : 86.13 % 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: 0.94 (0.14), residues: 3363 helix: 1.65 (0.13), residues: 1575 sheet: 1.51 (0.32), residues: 240 loop : -0.59 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 513 TYR 0.015 0.001 TYR G 84 PHE 0.017 0.001 PHE G 344 TRP 0.012 0.001 TRP G 314 HIS 0.005 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00481 (27848) covalent geometry : angle 1.05858 (37868) hydrogen bonds : bond 0.05656 ( 1312) hydrogen bonds : angle 4.61099 ( 3693) metal coordination : bond 0.01525 ( 33) metal coordination : angle 20.12645 ( 81) Misc. bond : bond 0.12795 ( 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 335 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 1.145 Fit side-chains REVERT: A 97 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 295 GLU cc_start: 0.8562 (mp0) cc_final: 0.8144 (tt0) REVERT: A 344 PHE cc_start: 0.7845 (m-80) cc_final: 0.7491 (m-80) REVERT: A 347 LEU cc_start: 0.8659 (mm) cc_final: 0.8359 (mm) REVERT: A 504 GLN cc_start: 0.8576 (tp40) cc_final: 0.8134 (tp40) REVERT: A 620 GLU cc_start: 0.8525 (pp20) cc_final: 0.8219 (pp20) REVERT: B 97 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8962 (mt) REVERT: B 249 GLU cc_start: 0.8454 (tp30) cc_final: 0.8067 (mm-30) REVERT: C 1 MET cc_start: 0.7026 (mmp) cc_final: 0.6204 (mmp) REVERT: C 205 ARG cc_start: 0.8220 (mpt-90) cc_final: 0.7877 (mtt-85) REVERT: D 52 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.8215 (ptm-80) REVERT: D 61 SER cc_start: 0.9491 (t) cc_final: 0.9281 (t) REVERT: D 324 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7581 (mtm110) REVERT: D 504 GLN cc_start: 0.8536 (tp40) cc_final: 0.8271 (tp40) REVERT: E 11 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (tttp) REVERT: E 35 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: E 36 MET cc_start: 0.9324 (ttp) cc_final: 0.9118 (ttp) REVERT: E 116 ASP cc_start: 0.8153 (t0) cc_final: 0.7873 (t0) REVERT: F 1 MET cc_start: 0.5556 (ppp) cc_final: 0.4727 (ppp) REVERT: F 41 GLN cc_start: 0.8448 (mm110) cc_final: 0.8145 (mt0) REVERT: F 105 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6673 (mtm180) REVERT: F 171 ASN cc_start: 0.7839 (t0) cc_final: 0.7628 (t0) REVERT: G 61 SER cc_start: 0.9437 (t) cc_final: 0.9176 (t) REVERT: G 324 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7889 (mtm110) REVERT: G 332 GLU cc_start: 0.8429 (mp0) cc_final: 0.8205 (mp0) REVERT: G 405 THR cc_start: 0.9129 (m) cc_final: 0.8836 (p) REVERT: G 504 GLN cc_start: 0.8592 (tp40) cc_final: 0.8206 (tp40) REVERT: G 620 GLU cc_start: 0.8466 (tt0) cc_final: 0.8213 (tm-30) REVERT: H 28 ASN cc_start: 0.9050 (t0) cc_final: 0.8680 (t0) REVERT: H 116 ASP cc_start: 0.8331 (t0) cc_final: 0.8068 (t0) REVERT: H 231 GLU cc_start: 0.8373 (mp0) cc_final: 0.8112 (mp0) REVERT: I 111 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7737 (mttm) REVERT: I 164 ASN cc_start: 0.8333 (m110) cc_final: 0.8035 (m-40) REVERT: I 205 ARG cc_start: 0.8207 (mpt-90) cc_final: 0.7576 (mtt-85) outliers start: 60 outliers final: 17 residues processed: 314 average time/residue: 0.8474 time to fit residues: 300.9260 Evaluate side-chains 273 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 93 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 317 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 463 GLN C 226 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS F 113 GLN F 226 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.073315 restraints weight = 48850.928| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.49 r_work: 0.2760 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 27887 Z= 0.186 Angle : 1.387 85.470 37949 Z= 0.396 Chirality : 0.058 1.601 4029 Planarity : 0.004 0.038 4860 Dihedral : 9.257 171.487 4193 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.74 % Allowed : 12.59 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3363 helix: 1.79 (0.13), residues: 1572 sheet: 1.46 (0.32), residues: 240 loop : -0.66 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 152 TYR 0.013 0.001 TYR G 84 PHE 0.019 0.001 PHE G 344 TRP 0.011 0.001 TRP G 314 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00436 (27848) covalent geometry : angle 1.00658 (37868) hydrogen bonds : bond 0.05290 ( 1312) hydrogen bonds : angle 4.41617 ( 3693) metal coordination : bond 0.00922 ( 33) metal coordination : angle 20.68052 ( 81) Misc. bond : bond 0.12439 ( 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 341 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 1.080 Fit side-chains REVERT: A 97 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: A 295 GLU cc_start: 0.8592 (mp0) cc_final: 0.8103 (tt0) REVERT: A 344 PHE cc_start: 0.7828 (m-80) cc_final: 0.7527 (m-80) REVERT: A 347 LEU cc_start: 0.8651 (mm) cc_final: 0.8315 (mm) REVERT: A 504 GLN cc_start: 0.8556 (tp40) cc_final: 0.8132 (tp40) REVERT: A 620 GLU cc_start: 0.8535 (pp20) cc_final: 0.8216 (pp20) REVERT: B 69 MET cc_start: 0.9022 (tpp) cc_final: 0.8776 (tpt) REVERT: B 97 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8933 (mt) REVERT: B 116 ASP cc_start: 0.8220 (t0) cc_final: 0.7908 (t0) REVERT: B 249 GLU cc_start: 0.8506 (tp30) cc_final: 0.8287 (tp30) REVERT: C 1 MET cc_start: 0.7064 (mmp) cc_final: 0.6780 (mmp) REVERT: C 41 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: C 205 ARG cc_start: 0.8234 (mpt-90) cc_final: 0.8018 (mtt-85) REVERT: D 52 ARG cc_start: 0.8492 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: D 61 SER cc_start: 0.9504 (t) cc_final: 0.9290 (t) REVERT: D 324 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7595 (mtm110) REVERT: D 411 GLU cc_start: 0.8207 (mp0) cc_final: 0.7983 (mp0) REVERT: D 504 GLN cc_start: 0.8516 (tp40) cc_final: 0.8045 (tp40) REVERT: E 35 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: E 36 MET cc_start: 0.9279 (ttp) cc_final: 0.9070 (ttp) REVERT: E 116 ASP cc_start: 0.8124 (t0) cc_final: 0.7874 (t0) REVERT: F 1 MET cc_start: 0.5585 (ppp) cc_final: 0.4685 (ppp) REVERT: F 41 GLN cc_start: 0.8340 (mm110) cc_final: 0.7999 (mt0) REVERT: F 105 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6629 (mtm180) REVERT: G 61 SER cc_start: 0.9442 (t) cc_final: 0.9163 (t) REVERT: G 324 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7904 (mtm110) REVERT: G 332 GLU cc_start: 0.8503 (mp0) cc_final: 0.8221 (mp0) REVERT: G 339 GLU cc_start: 0.8805 (tt0) cc_final: 0.8435 (pm20) REVERT: G 385 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (tt) REVERT: G 405 THR cc_start: 0.9156 (m) cc_final: 0.8868 (p) REVERT: G 504 GLN cc_start: 0.8565 (tp40) cc_final: 0.8193 (tp40) REVERT: G 620 GLU cc_start: 0.8429 (tt0) cc_final: 0.8156 (tm-30) REVERT: H 2 LYS cc_start: 0.8160 (tptp) cc_final: 0.7833 (tppp) REVERT: H 28 ASN cc_start: 0.9031 (t0) cc_final: 0.8676 (t0) REVERT: H 116 ASP cc_start: 0.8321 (t0) cc_final: 0.7975 (t0) REVERT: H 231 GLU cc_start: 0.8374 (mp0) cc_final: 0.8139 (mp0) REVERT: I 111 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7792 (mttm) REVERT: I 205 ARG cc_start: 0.8167 (mpt-90) cc_final: 0.7714 (mtt-85) outliers start: 75 outliers final: 27 residues processed: 310 average time/residue: 0.8371 time to fit residues: 294.7036 Evaluate side-chains 276 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN C 226 ASN D 284 GLN D 432 ASN F 113 GLN F 226 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.072328 restraints weight = 48432.050| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.48 r_work: 0.2731 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 27887 Z= 0.212 Angle : 1.373 82.742 37949 Z= 0.400 Chirality : 0.060 1.561 4029 Planarity : 0.004 0.038 4860 Dihedral : 8.814 171.078 4191 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 13.72 % Favored : 83.75 % 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: 0.98 (0.14), residues: 3363 helix: 1.86 (0.13), residues: 1551 sheet: 1.43 (0.32), residues: 240 loop : -0.73 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 513 TYR 0.015 0.001 TYR A 422 PHE 0.020 0.001 PHE G 344 TRP 0.010 0.001 TRP G 314 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00503 (27848) covalent geometry : angle 1.00898 (37868) hydrogen bonds : bond 0.05417 ( 1312) hydrogen bonds : angle 4.41329 ( 3693) metal coordination : bond 0.01046 ( 33) metal coordination : angle 20.17221 ( 81) Misc. bond : bond 0.14174 ( 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 329 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 1.187 Fit side-chains REVERT: A 97 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8583 (mt0) REVERT: A 295 GLU cc_start: 0.8558 (mp0) cc_final: 0.8195 (tt0) REVERT: A 344 PHE cc_start: 0.7842 (m-80) cc_final: 0.7548 (m-80) REVERT: A 347 LEU cc_start: 0.8715 (mm) cc_final: 0.8375 (mm) REVERT: A 504 GLN cc_start: 0.8534 (tp40) cc_final: 0.8065 (tp40) REVERT: A 620 GLU cc_start: 0.8528 (pp20) cc_final: 0.8268 (pp20) REVERT: B 97 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (mt) REVERT: B 116 ASP cc_start: 0.8256 (t0) cc_final: 0.7704 (t0) REVERT: B 249 GLU cc_start: 0.8559 (tp30) cc_final: 0.8293 (tp30) REVERT: C 1 MET cc_start: 0.7075 (mmp) cc_final: 0.6833 (mmp) REVERT: C 148 PRO cc_start: 0.9260 (Cg_exo) cc_final: 0.9052 (Cg_endo) REVERT: D 52 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8209 (ptm-80) REVERT: D 61 SER cc_start: 0.9537 (t) cc_final: 0.9326 (t) REVERT: D 324 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7610 (mtm110) REVERT: D 411 GLU cc_start: 0.8261 (mp0) cc_final: 0.8033 (mp0) REVERT: D 504 GLN cc_start: 0.8524 (tp40) cc_final: 0.8059 (tp40) REVERT: E 35 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: E 36 MET cc_start: 0.9287 (ttp) cc_final: 0.9067 (ttp) REVERT: E 116 ASP cc_start: 0.8118 (t0) cc_final: 0.7856 (t0) REVERT: F 1 MET cc_start: 0.5652 (ppp) cc_final: 0.4668 (ppp) REVERT: F 41 GLN cc_start: 0.8380 (mm110) cc_final: 0.8053 (mt0) REVERT: F 105 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6659 (mtm180) REVERT: G 61 SER cc_start: 0.9462 (t) cc_final: 0.9186 (t) REVERT: G 324 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (mtm110) REVERT: G 332 GLU cc_start: 0.8542 (mp0) cc_final: 0.8222 (mp0) REVERT: G 339 GLU cc_start: 0.8774 (tt0) cc_final: 0.8413 (pm20) REVERT: G 385 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7849 (tt) REVERT: G 405 THR cc_start: 0.9171 (m) cc_final: 0.8873 (p) REVERT: G 411 GLU cc_start: 0.8282 (mp0) cc_final: 0.8039 (mp0) REVERT: G 504 GLN cc_start: 0.8556 (tp40) cc_final: 0.8187 (tp40) REVERT: G 620 GLU cc_start: 0.8435 (tt0) cc_final: 0.8166 (tm-30) REVERT: H 2 LYS cc_start: 0.8208 (tptp) cc_final: 0.7866 (tppp) REVERT: H 24 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: H 28 ASN cc_start: 0.9011 (t0) cc_final: 0.8623 (t0) REVERT: H 35 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: H 116 ASP cc_start: 0.8341 (t0) cc_final: 0.7991 (t0) REVERT: H 231 GLU cc_start: 0.8387 (mp0) cc_final: 0.8129 (mp0) REVERT: I 111 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7786 (mttm) REVERT: I 205 ARG cc_start: 0.8172 (mpt-90) cc_final: 0.7599 (mtt-85) outliers start: 69 outliers final: 31 residues processed: 304 average time/residue: 0.8326 time to fit residues: 287.4893 Evaluate side-chains 282 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN C 113 GLN C 226 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN F 164 ASN F 226 ASN G 185 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.071599 restraints weight = 48180.883| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.47 r_work: 0.2736 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.221 27887 Z= 0.227 Angle : 1.343 82.981 37949 Z= 0.403 Chirality : 0.060 1.581 4029 Planarity : 0.004 0.037 4860 Dihedral : 8.648 170.518 4191 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 14.01 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3363 helix: 1.69 (0.13), residues: 1578 sheet: 1.36 (0.32), residues: 237 loop : -0.71 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.014 0.001 TYR D 422 PHE 0.024 0.001 PHE D 344 TRP 0.009 0.001 TRP G 314 HIS 0.014 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00540 (27848) covalent geometry : angle 1.01291 (37868) hydrogen bonds : bond 0.05538 ( 1312) hydrogen bonds : angle 4.43104 ( 3693) metal coordination : bond 0.01116 ( 33) metal coordination : angle 19.11580 ( 81) Misc. bond : bond 0.16043 ( 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 335 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: A 295 GLU cc_start: 0.8603 (mp0) cc_final: 0.8093 (tt0) REVERT: A 344 PHE cc_start: 0.7850 (m-80) cc_final: 0.7549 (m-80) REVERT: A 347 LEU cc_start: 0.8727 (mm) cc_final: 0.8411 (mm) REVERT: A 411 GLU cc_start: 0.8597 (mp0) cc_final: 0.8265 (mp0) REVERT: A 504 GLN cc_start: 0.8543 (tp40) cc_final: 0.8093 (tp40) REVERT: A 620 GLU cc_start: 0.8502 (pp20) cc_final: 0.8243 (pp20) REVERT: B 2 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7867 (ttmt) REVERT: B 116 ASP cc_start: 0.8246 (t0) cc_final: 0.7696 (t0) REVERT: C 41 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: C 147 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 148 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.9062 (Cg_endo) REVERT: D 52 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.8233 (ptm-80) REVERT: D 61 SER cc_start: 0.9554 (t) cc_final: 0.9340 (t) REVERT: D 324 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7644 (mtm110) REVERT: D 337 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7466 (mp) REVERT: D 411 GLU cc_start: 0.8293 (mp0) cc_final: 0.8054 (mp0) REVERT: D 504 GLN cc_start: 0.8513 (tp40) cc_final: 0.8070 (tp40) REVERT: E 116 ASP cc_start: 0.8120 (t0) cc_final: 0.7874 (t0) REVERT: E 249 GLU cc_start: 0.8966 (tt0) cc_final: 0.8648 (tt0) REVERT: F 1 MET cc_start: 0.5656 (ppp) cc_final: 0.4503 (ppp) REVERT: G 61 SER cc_start: 0.9481 (t) cc_final: 0.9214 (t) REVERT: G 324 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7962 (mtm110) REVERT: G 332 GLU cc_start: 0.8569 (mp0) cc_final: 0.8226 (mp0) REVERT: G 339 GLU cc_start: 0.8791 (tt0) cc_final: 0.8423 (pm20) REVERT: G 385 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7939 (tt) REVERT: G 405 THR cc_start: 0.9153 (m) cc_final: 0.8871 (p) REVERT: G 411 GLU cc_start: 0.8365 (mp0) cc_final: 0.8085 (mp0) REVERT: G 504 GLN cc_start: 0.8535 (tp40) cc_final: 0.8179 (tp40) REVERT: G 620 GLU cc_start: 0.8453 (tt0) cc_final: 0.8149 (tm-30) REVERT: H 2 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7887 (tppp) REVERT: H 24 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: H 35 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: H 47 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8428 (ttm-80) REVERT: H 116 ASP cc_start: 0.8340 (t0) cc_final: 0.8005 (t0) REVERT: H 231 GLU cc_start: 0.8402 (mp0) cc_final: 0.8146 (mp0) REVERT: I 111 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7759 (mttm) REVERT: I 205 ARG cc_start: 0.8187 (mpt-90) cc_final: 0.7742 (mtt-85) outliers start: 79 outliers final: 36 residues processed: 306 average time/residue: 0.7852 time to fit residues: 273.0437 Evaluate side-chains 291 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 169 CYS Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 25 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 chunk 284 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 301 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN C 164 ASN C 226 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.072900 restraints weight = 48236.503| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.44 r_work: 0.2741 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 27887 Z= 0.188 Angle : 1.321 82.599 37949 Z= 0.393 Chirality : 0.060 1.573 4029 Planarity : 0.004 0.037 4860 Dihedral : 8.459 170.123 4191 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.78 % Allowed : 14.75 % Favored : 82.47 % 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: 0.97 (0.14), residues: 3363 helix: 1.78 (0.13), residues: 1581 sheet: 1.36 (0.32), residues: 237 loop : -0.68 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 152 TYR 0.012 0.001 TYR D 422 PHE 0.025 0.001 PHE D 344 TRP 0.010 0.001 TRP G 314 HIS 0.011 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00440 (27848) covalent geometry : angle 0.99824 (37868) hydrogen bonds : bond 0.05192 ( 1312) hydrogen bonds : angle 4.34523 ( 3693) metal coordination : bond 0.00890 ( 33) metal coordination : angle 18.74933 ( 81) Misc. bond : bond 0.13773 ( 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 333 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 257 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: A 295 GLU cc_start: 0.8550 (mp0) cc_final: 0.8213 (tt0) REVERT: A 344 PHE cc_start: 0.7827 (m-80) cc_final: 0.7523 (m-80) REVERT: A 347 LEU cc_start: 0.8766 (mm) cc_final: 0.8429 (mm) REVERT: A 411 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: A 504 GLN cc_start: 0.8541 (tp40) cc_final: 0.8090 (tp40) REVERT: A 620 GLU cc_start: 0.8504 (pp20) cc_final: 0.8236 (pp20) REVERT: B 2 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7889 (ttmt) REVERT: B 116 ASP cc_start: 0.8252 (t0) cc_final: 0.7719 (t0) REVERT: C 41 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: C 147 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 148 PRO cc_start: 0.9300 (Cg_exo) cc_final: 0.9052 (Cg_endo) REVERT: D 52 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.8214 (ptm-80) REVERT: D 61 SER cc_start: 0.9555 (t) cc_final: 0.9333 (t) REVERT: D 324 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7665 (mtm110) REVERT: D 339 GLU cc_start: 0.8758 (tt0) cc_final: 0.8322 (pt0) REVERT: D 400 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7837 (ttm) REVERT: D 411 GLU cc_start: 0.8321 (mp0) cc_final: 0.8078 (mp0) REVERT: D 504 GLN cc_start: 0.8512 (tp40) cc_final: 0.8070 (tp40) REVERT: E 116 ASP cc_start: 0.8108 (t0) cc_final: 0.7868 (t0) REVERT: E 249 GLU cc_start: 0.8978 (tt0) cc_final: 0.8662 (tt0) REVERT: F 1 MET cc_start: 0.5666 (ppp) cc_final: 0.4560 (ppp) REVERT: F 41 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: F 105 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6696 (mtm180) REVERT: G 61 SER cc_start: 0.9491 (t) cc_final: 0.9219 (t) REVERT: G 167 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: G 324 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7863 (mtm110) REVERT: G 332 GLU cc_start: 0.8598 (mp0) cc_final: 0.8251 (mp0) REVERT: G 339 GLU cc_start: 0.8790 (tt0) cc_final: 0.8435 (pm20) REVERT: G 344 PHE cc_start: 0.6546 (m-80) cc_final: 0.6335 (m-80) REVERT: G 385 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7972 (tt) REVERT: G 405 THR cc_start: 0.9156 (m) cc_final: 0.8864 (p) REVERT: G 411 GLU cc_start: 0.8426 (mp0) cc_final: 0.8118 (mp0) REVERT: G 504 GLN cc_start: 0.8521 (tp40) cc_final: 0.8172 (tp40) REVERT: G 620 GLU cc_start: 0.8438 (tt0) cc_final: 0.8164 (tm-30) REVERT: H 2 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7916 (tppp) REVERT: H 24 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: H 28 ASN cc_start: 0.9041 (t0) cc_final: 0.8709 (t0) REVERT: H 47 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8372 (ttm-80) REVERT: H 116 ASP cc_start: 0.8305 (t0) cc_final: 0.7945 (t0) REVERT: H 231 GLU cc_start: 0.8403 (mp0) cc_final: 0.8140 (mp0) REVERT: I 111 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7735 (mttm) REVERT: I 205 ARG cc_start: 0.8191 (mpt-90) cc_final: 0.7730 (mtt-85) outliers start: 76 outliers final: 39 residues processed: 305 average time/residue: 0.7429 time to fit residues: 257.4777 Evaluate side-chains 294 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 169 CYS Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 242 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 292 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 226 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.071797 restraints weight = 47878.431| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.44 r_work: 0.2716 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 27887 Z= 0.229 Angle : 1.335 82.686 37949 Z= 0.405 Chirality : 0.061 1.583 4029 Planarity : 0.004 0.037 4860 Dihedral : 8.506 169.876 4191 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.71 % Allowed : 14.97 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3363 helix: 1.73 (0.13), residues: 1578 sheet: 1.31 (0.32), residues: 237 loop : -0.75 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 152 TYR 0.016 0.001 TYR D 336 PHE 0.019 0.001 PHE G 344 TRP 0.009 0.001 TRP G 314 HIS 0.016 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00547 (27848) covalent geometry : angle 1.01722 (37868) hydrogen bonds : bond 0.05468 ( 1312) hydrogen bonds : angle 4.40292 ( 3693) metal coordination : bond 0.01121 ( 33) metal coordination : angle 18.74433 ( 81) Misc. bond : bond 0.15004 ( 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 324 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 250 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: A 295 GLU cc_start: 0.8595 (mp0) cc_final: 0.8162 (tt0) REVERT: A 344 PHE cc_start: 0.7825 (m-80) cc_final: 0.7516 (m-80) REVERT: A 347 LEU cc_start: 0.8758 (mm) cc_final: 0.8432 (mm) REVERT: A 411 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: A 504 GLN cc_start: 0.8537 (tp40) cc_final: 0.8093 (tp40) REVERT: A 620 GLU cc_start: 0.8486 (pp20) cc_final: 0.8268 (pp20) REVERT: B 2 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (ttmt) REVERT: B 116 ASP cc_start: 0.8230 (t0) cc_final: 0.7703 (t0) REVERT: C 41 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: C 111 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7757 (mttp) REVERT: C 147 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 148 PRO cc_start: 0.9303 (Cg_exo) cc_final: 0.9068 (Cg_endo) REVERT: D 52 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.8225 (ptm-80) REVERT: D 61 SER cc_start: 0.9563 (t) cc_final: 0.9346 (t) REVERT: D 324 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7635 (mtm110) REVERT: D 339 GLU cc_start: 0.8770 (tt0) cc_final: 0.8529 (pm20) REVERT: D 400 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7854 (ttm) REVERT: D 411 GLU cc_start: 0.8316 (mp0) cc_final: 0.8062 (mp0) REVERT: D 504 GLN cc_start: 0.8488 (tp40) cc_final: 0.8058 (tp40) REVERT: E 116 ASP cc_start: 0.8098 (t0) cc_final: 0.7858 (t0) REVERT: E 249 GLU cc_start: 0.8959 (tt0) cc_final: 0.8627 (tt0) REVERT: F 1 MET cc_start: 0.5670 (ppp) cc_final: 0.4573 (ppp) REVERT: F 41 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7556 (mp10) REVERT: G 61 SER cc_start: 0.9497 (t) cc_final: 0.9224 (t) REVERT: G 167 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: G 324 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7926 (mtm110) REVERT: G 332 GLU cc_start: 0.8615 (mp0) cc_final: 0.8266 (mp0) REVERT: G 339 GLU cc_start: 0.8795 (tt0) cc_final: 0.8423 (pm20) REVERT: G 385 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (tt) REVERT: G 405 THR cc_start: 0.9160 (m) cc_final: 0.8866 (p) REVERT: G 411 GLU cc_start: 0.8418 (mp0) cc_final: 0.8160 (mp0) REVERT: G 504 GLN cc_start: 0.8518 (tp40) cc_final: 0.8180 (tp40) REVERT: G 620 GLU cc_start: 0.8441 (tt0) cc_final: 0.8155 (tm-30) REVERT: H 2 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7923 (tppp) REVERT: H 24 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: H 116 ASP cc_start: 0.8317 (t0) cc_final: 0.7986 (t0) REVERT: H 231 GLU cc_start: 0.8417 (mp0) cc_final: 0.8148 (mp0) REVERT: I 111 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7743 (mttm) REVERT: I 205 ARG cc_start: 0.8193 (mpt-90) cc_final: 0.7725 (mtt-85) outliers start: 74 outliers final: 35 residues processed: 291 average time/residue: 0.8389 time to fit residues: 277.3453 Evaluate side-chains 289 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 169 CYS Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 242 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 235 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 303 optimal weight: 0.5980 chunk 239 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 254 optimal weight: 0.1980 chunk 270 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN C 36 ASN C 164 ASN F 164 ASN G 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075673 restraints weight = 47826.178| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.45 r_work: 0.2791 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 27887 Z= 0.139 Angle : 1.289 82.165 37949 Z= 0.383 Chirality : 0.058 1.529 4029 Planarity : 0.003 0.035 4860 Dihedral : 8.136 167.971 4190 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 16.10 % Favored : 81.92 % 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: 1.16 (0.14), residues: 3363 helix: 1.95 (0.13), residues: 1581 sheet: 1.39 (0.32), residues: 237 loop : -0.59 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.018 0.001 TYR D 336 PHE 0.026 0.001 PHE D 344 TRP 0.011 0.001 TRP G 314 HIS 0.011 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00304 (27848) covalent geometry : angle 0.97851 (37868) hydrogen bonds : bond 0.04525 ( 1312) hydrogen bonds : angle 4.20896 ( 3693) metal coordination : bond 0.00436 ( 33) metal coordination : angle 18.20087 ( 81) Misc. bond : bond 0.07748 ( 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 325 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 271 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8638 (mt0) REVERT: A 295 GLU cc_start: 0.8535 (mp0) cc_final: 0.8210 (tt0) REVERT: A 344 PHE cc_start: 0.7795 (m-80) cc_final: 0.7482 (m-80) REVERT: A 347 LEU cc_start: 0.8708 (mm) cc_final: 0.8332 (mm) REVERT: A 411 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: A 504 GLN cc_start: 0.8502 (tp40) cc_final: 0.8119 (tp40) REVERT: A 620 GLU cc_start: 0.8493 (pp20) cc_final: 0.8221 (pp20) REVERT: B 116 ASP cc_start: 0.8257 (t0) cc_final: 0.7731 (t0) REVERT: C 41 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: C 111 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7709 (mttm) REVERT: D 52 ARG cc_start: 0.8455 (ptm-80) cc_final: 0.8199 (ptm-80) REVERT: D 61 SER cc_start: 0.9559 (t) cc_final: 0.9337 (t) REVERT: D 295 GLU cc_start: 0.8481 (mp0) cc_final: 0.7828 (pp20) REVERT: D 324 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7560 (mtm110) REVERT: D 350 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6852 (ptt90) REVERT: D 400 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7885 (ttm) REVERT: D 411 GLU cc_start: 0.8323 (mp0) cc_final: 0.8079 (mp0) REVERT: D 504 GLN cc_start: 0.8479 (tp40) cc_final: 0.7993 (tp40) REVERT: E 116 ASP cc_start: 0.8071 (t0) cc_final: 0.7851 (t0) REVERT: E 249 GLU cc_start: 0.8958 (tt0) cc_final: 0.8644 (tt0) REVERT: F 1 MET cc_start: 0.5687 (ppp) cc_final: 0.4642 (ppp) REVERT: F 41 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: G 61 SER cc_start: 0.9476 (t) cc_final: 0.9183 (t) REVERT: G 167 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: G 295 GLU cc_start: 0.8468 (mp0) cc_final: 0.7392 (tt0) REVERT: G 324 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: G 332 GLU cc_start: 0.8664 (mp0) cc_final: 0.8288 (mp0) REVERT: G 339 GLU cc_start: 0.8788 (tt0) cc_final: 0.8514 (pm20) REVERT: G 385 LEU cc_start: 0.8184 (mp) cc_final: 0.7970 (tt) REVERT: G 405 THR cc_start: 0.9169 (m) cc_final: 0.8874 (p) REVERT: G 411 GLU cc_start: 0.8488 (mp0) cc_final: 0.8165 (mp0) REVERT: G 504 GLN cc_start: 0.8514 (tp40) cc_final: 0.8177 (tp40) REVERT: G 558 GLU cc_start: 0.8805 (tp30) cc_final: 0.8513 (tp30) REVERT: G 620 GLU cc_start: 0.8461 (tt0) cc_final: 0.8193 (tm-30) REVERT: H 2 LYS cc_start: 0.8293 (tptp) cc_final: 0.7961 (tppp) REVERT: H 24 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: H 28 ASN cc_start: 0.9045 (t0) cc_final: 0.8720 (t0) REVERT: H 116 ASP cc_start: 0.8280 (t0) cc_final: 0.7702 (t0) REVERT: H 231 GLU cc_start: 0.8390 (mp0) cc_final: 0.8136 (mp0) REVERT: I 111 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7700 (mttm) REVERT: I 205 ARG cc_start: 0.8205 (mpt-90) cc_final: 0.7709 (mtt-85) outliers start: 54 outliers final: 18 residues processed: 303 average time/residue: 0.8543 time to fit residues: 293.6125 Evaluate side-chains 278 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 242 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 111 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN C 226 ASN F 164 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.074360 restraints weight = 47748.114| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.45 r_work: 0.2758 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 27887 Z= 0.163 Angle : 1.299 82.468 37949 Z= 0.390 Chirality : 0.059 1.551 4029 Planarity : 0.004 0.045 4860 Dihedral : 8.144 168.541 4189 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.61 % Allowed : 16.58 % Favored : 81.81 % 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: 1.14 (0.14), residues: 3363 helix: 1.95 (0.13), residues: 1581 sheet: 1.44 (0.32), residues: 240 loop : -0.64 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.017 0.001 TYR D 336 PHE 0.027 0.001 PHE D 344 TRP 0.009 0.001 TRP G 314 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00375 (27848) covalent geometry : angle 0.99018 (37868) hydrogen bonds : bond 0.04733 ( 1312) hydrogen bonds : angle 4.21207 ( 3693) metal coordination : bond 0.00693 ( 33) metal coordination : angle 18.22296 ( 81) Misc. bond : bond 0.07806 ( 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 296 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8660 (mt0) REVERT: A 295 GLU cc_start: 0.8592 (mp0) cc_final: 0.8154 (tt0) REVERT: A 344 PHE cc_start: 0.7796 (m-80) cc_final: 0.7485 (m-80) REVERT: A 347 LEU cc_start: 0.8704 (mm) cc_final: 0.8343 (mm) REVERT: A 411 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 504 GLN cc_start: 0.8480 (tp40) cc_final: 0.8089 (tp40) REVERT: A 620 GLU cc_start: 0.8479 (pp20) cc_final: 0.8205 (pp20) REVERT: B 116 ASP cc_start: 0.8234 (t0) cc_final: 0.7708 (t0) REVERT: C 41 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: C 111 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7701 (mttm) REVERT: D 52 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.8179 (ptm-80) REVERT: D 61 SER cc_start: 0.9558 (t) cc_final: 0.9334 (t) REVERT: D 86 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8360 (p0) REVERT: D 295 GLU cc_start: 0.8500 (mp0) cc_final: 0.7872 (pp20) REVERT: D 324 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7598 (mtm110) REVERT: D 350 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6785 (ptt90) REVERT: D 400 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7848 (ttm) REVERT: D 411 GLU cc_start: 0.8304 (mp0) cc_final: 0.8059 (mp0) REVERT: D 504 GLN cc_start: 0.8474 (tp40) cc_final: 0.8033 (tp40) REVERT: E 116 ASP cc_start: 0.8074 (t0) cc_final: 0.7844 (t0) REVERT: E 249 GLU cc_start: 0.8943 (tt0) cc_final: 0.8622 (tt0) REVERT: F 1 MET cc_start: 0.5671 (ppp) cc_final: 0.4626 (ppp) REVERT: F 41 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: G 61 SER cc_start: 0.9492 (t) cc_final: 0.9199 (t) REVERT: G 167 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: G 324 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7835 (mtm110) REVERT: G 332 GLU cc_start: 0.8652 (mp0) cc_final: 0.8265 (mp0) REVERT: G 339 GLU cc_start: 0.8784 (tt0) cc_final: 0.8506 (pm20) REVERT: G 405 THR cc_start: 0.9160 (m) cc_final: 0.8861 (p) REVERT: G 411 GLU cc_start: 0.8474 (mp0) cc_final: 0.8091 (mp0) REVERT: G 504 GLN cc_start: 0.8503 (tp40) cc_final: 0.8166 (tp40) REVERT: G 620 GLU cc_start: 0.8449 (tt0) cc_final: 0.8174 (tm-30) REVERT: H 2 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7932 (tppp) REVERT: H 24 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7642 (mtp) REVERT: H 28 ASN cc_start: 0.9016 (t0) cc_final: 0.8723 (t0) REVERT: H 116 ASP cc_start: 0.8271 (t0) cc_final: 0.7701 (t0) REVERT: H 231 GLU cc_start: 0.8403 (mp0) cc_final: 0.8134 (mp0) REVERT: I 111 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7695 (mttm) REVERT: I 205 ARG cc_start: 0.8185 (mpt-90) cc_final: 0.7707 (mtt-85) outliers start: 44 outliers final: 24 residues processed: 279 average time/residue: 0.8311 time to fit residues: 261.5879 Evaluate side-chains 277 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 169 CYS Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 242 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 210 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN C 36 ASN C 226 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN F 164 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.071565 restraints weight = 48261.571| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.42 r_work: 0.2726 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 27887 Z= 0.244 Angle : 1.347 82.693 37949 Z= 0.417 Chirality : 0.061 1.574 4029 Planarity : 0.004 0.037 4860 Dihedral : 8.365 167.817 4189 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.68 % Allowed : 16.83 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3363 helix: 1.74 (0.13), residues: 1581 sheet: 1.24 (0.33), residues: 243 loop : -0.75 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.014 0.001 TYR A 422 PHE 0.027 0.001 PHE D 344 TRP 0.007 0.001 TRP E 102 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00583 (27848) covalent geometry : angle 1.03703 (37868) hydrogen bonds : bond 0.05568 ( 1312) hydrogen bonds : angle 4.41610 ( 3693) metal coordination : bond 0.01207 ( 33) metal coordination : angle 18.64515 ( 81) Misc. bond : bond 0.12473 ( 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 286 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 97 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8681 (mt0) REVERT: A 295 GLU cc_start: 0.8538 (mp0) cc_final: 0.8220 (tt0) REVERT: A 344 PHE cc_start: 0.7839 (m-80) cc_final: 0.7533 (m-80) REVERT: A 347 LEU cc_start: 0.8806 (mm) cc_final: 0.8483 (mm) REVERT: A 411 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: A 504 GLN cc_start: 0.8508 (tp40) cc_final: 0.8041 (tp40) REVERT: A 620 GLU cc_start: 0.8465 (pp20) cc_final: 0.8164 (pp20) REVERT: B 116 ASP cc_start: 0.8242 (t0) cc_final: 0.7700 (t0) REVERT: B 139 ASP cc_start: 0.8472 (t70) cc_final: 0.8165 (t70) REVERT: C 41 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: C 111 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7804 (mttm) REVERT: D 52 ARG cc_start: 0.8438 (ptm-80) cc_final: 0.8197 (ptm-80) REVERT: D 61 SER cc_start: 0.9573 (t) cc_final: 0.9360 (t) REVERT: D 295 GLU cc_start: 0.8525 (mp0) cc_final: 0.7933 (pp20) REVERT: D 324 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7620 (mtm110) REVERT: D 350 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6952 (ptt90) REVERT: D 400 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7888 (ttm) REVERT: D 411 GLU cc_start: 0.8321 (mp0) cc_final: 0.8068 (mp0) REVERT: D 504 GLN cc_start: 0.8509 (tp40) cc_final: 0.8073 (tp40) REVERT: E 116 ASP cc_start: 0.8097 (t0) cc_final: 0.7869 (t0) REVERT: F 1 MET cc_start: 0.5624 (ppp) cc_final: 0.4663 (ppp) REVERT: F 41 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: G 61 SER cc_start: 0.9509 (t) cc_final: 0.9240 (t) REVERT: G 167 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: G 295 GLU cc_start: 0.8541 (mp0) cc_final: 0.7560 (tt0) REVERT: G 324 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7935 (mtm110) REVERT: G 332 GLU cc_start: 0.8651 (mp0) cc_final: 0.8275 (mp0) REVERT: G 339 GLU cc_start: 0.8779 (tt0) cc_final: 0.8518 (pm20) REVERT: G 411 GLU cc_start: 0.8450 (mp0) cc_final: 0.8185 (mp0) REVERT: G 504 GLN cc_start: 0.8496 (tp40) cc_final: 0.8153 (tp40) REVERT: G 620 GLU cc_start: 0.8438 (tt0) cc_final: 0.8141 (tm-30) REVERT: H 2 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7961 (tppp) REVERT: H 24 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7649 (mtp) REVERT: H 116 ASP cc_start: 0.8284 (t0) cc_final: 0.7751 (t0) REVERT: H 231 GLU cc_start: 0.8448 (mp0) cc_final: 0.8173 (mp0) REVERT: I 111 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7733 (mttm) REVERT: I 205 ARG cc_start: 0.8184 (mpt-90) cc_final: 0.7709 (mtt-85) outliers start: 46 outliers final: 26 residues processed: 269 average time/residue: 0.8529 time to fit residues: 258.7257 Evaluate side-chains 271 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 169 CYS Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 242 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.072824 restraints weight = 47807.241| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.44 r_work: 0.2749 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 27887 Z= 0.185 Angle : 1.323 82.459 37949 Z= 0.403 Chirality : 0.060 1.550 4029 Planarity : 0.004 0.045 4860 Dihedral : 8.299 168.551 4189 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 16.94 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3363 helix: 1.80 (0.13), residues: 1578 sheet: 1.33 (0.33), residues: 237 loop : -0.70 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.016 0.001 TYR A 336 PHE 0.028 0.001 PHE D 344 TRP 0.009 0.001 TRP G 314 HIS 0.008 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00432 (27848) covalent geometry : angle 1.01438 (37868) hydrogen bonds : bond 0.05149 ( 1312) hydrogen bonds : angle 4.34764 ( 3693) metal coordination : bond 0.00856 ( 33) metal coordination : angle 18.42382 ( 81) Misc. bond : bond 0.09878 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9657.43 seconds wall clock time: 165 minutes 9.20 seconds (9909.20 seconds total)