Starting phenix.real_space_refine on Fri Feb 6 18:57:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lb1_62935/02_2026/9lb1_62935.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.011 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 17282 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 5 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: 27122 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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 164 Unusual residues: {'1L3': 2, 'HEM': 2, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'1L3:plan-3': 2, '1L3:plan-5': 2} Unresolved non-hydrogen planarities: 22 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: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'1L3': 2, 'HEM': 2, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'1L3:plan-3': 2, '1L3:plan-5': 2} Unresolved non-hydrogen planarities: 22 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: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'1L3': 2, 'HEM': 2, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'1L3:plan-3': 2, '1L3:plan-5': 2} Unresolved non-hydrogen planarities: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 162 40.821 55.935 70.622 1.00131.39 S ATOM 6166 SG CYS B 159 47.175 57.285 71.476 1.00129.73 S ATOM 6628 SG CYS B 224 43.339 60.776 67.654 1.00132.98 S ATOM 6199 SG CYS B 165 44.876 54.604 66.024 1.00134.15 S ATOM 5481 SG CYS B 66 33.632 54.549 76.672 1.00171.03 S ATOM 5606 SG CYS B 84 34.170 58.071 77.301 1.00148.82 S ATOM 5425 SG CYS B 58 37.062 58.039 80.896 1.00147.68 S ATOM 5463 SG CYS B 63 38.797 54.908 80.182 1.00132.47 S ATOM 6222 SG CYS B 169 44.370 52.697 57.733 1.00121.84 S ATOM 6605 SG CYS B 220 45.411 58.314 60.472 1.00132.03 S ATOM 6563 SG CYS B 214 49.634 55.586 56.534 1.00131.43 S ATOM 14988 SG CYS E 162 77.035 104.510 70.704 1.00121.66 S ATOM 15432 SG CYS E 224 79.995 99.814 67.940 1.00135.26 S ATOM 15003 SG CYS E 165 73.893 101.660 66.121 1.00128.38 S ATOM 14970 SG CYS E 159 75.032 98.304 71.600 1.00128.11 S ATOM 14229 SG CYS E 58 80.624 106.685 80.904 1.00146.07 S ATOM 14267 SG CYS E 63 77.096 106.848 80.113 1.00128.94 S ATOM 14285 SG CYS E 66 79.425 109.760 75.249 1.00146.18 S ATOM 14410 SG CYS E 84 82.364 109.273 77.468 1.00147.11 S ATOM 15026 SG CYS E 169 72.280 103.197 57.981 1.00123.53 S ATOM 15409 SG CYS E 220 75.350 100.769 60.583 1.00156.39 S ATOM 15367 SG CYS E 214 72.695 97.150 56.676 1.00141.38 S ATOM 23774 SG CYS H 159 96.711 53.655 71.553 1.00126.57 S ATOM 23792 SG CYS H 162 101.003 48.803 70.709 1.00120.68 S ATOM 23807 SG CYS H 165 100.135 53.036 66.089 1.00131.94 S ATOM 24236 SG CYS H 224 95.519 48.586 67.871 1.00128.44 S ATOM 23089 SG CYS H 66 104.283 44.154 75.251 1.00141.38 S ATOM 23214 SG CYS H 84 102.466 41.747 77.428 1.00145.38 S ATOM 23033 SG CYS H 58 101.096 44.552 80.919 1.00147.92 S ATOM 23071 SG CYS H 63 103.050 47.553 80.069 1.00134.11 S ATOM 24213 SG CYS H 220 96.926 51.695 60.800 1.00121.46 S ATOM 24171 SG CYS H 214 96.830 56.418 56.527 1.00132.23 S ATOM 23830 SG CYS H 169 102.175 53.564 57.569 1.00136.32 S Time building chain proxies: 6.80, per 1000 atoms: 0.25 Number of scatterers: 27122 At special positions: 0 Unit cell: (140.16, 147.2, 135.04, 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 17282 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: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 214 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 169 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 220 " pdb=" F3S E 303 " pdb="FE4 F3S E 303 " - pdb=" SG CYS E 214 " pdb="FE1 F3S E 303 " - pdb=" SG CYS E 169 " pdb="FE3 F3S E 303 " - pdb=" SG CYS E 220 " pdb=" F3S H 303 " pdb="FE4 F3S H 303 " - pdb=" SG CYS H 169 " pdb="FE1 F3S H 303 " - pdb=" SG CYS H 220 " pdb="FE3 F3S H 303 " - pdb=" SG CYS H 214 " 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="FE1 FES E 302 " - pdb=" SG CYS E 58 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 66 " 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="FE2 FES H 302 " - pdb=" SG CYS H 58 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 84 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 224 " 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: 124 helices and 21 sheets defined 51.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.929A pdb=" N ALA A 91 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 93 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 129 through 150 removed outlier: 3.681A pdb=" N VAL A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.822A 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: 3.797A 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: 6.664A pdb=" N ASN A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 removed outlier: 4.177A pdb=" N ASN A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 471 through 482 removed outlier: 3.524A pdb=" N THR A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 removed outlier: 4.543A 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: 3.886A pdb=" N GLU A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 removed outlier: 4.159A pdb=" N GLN A 609 " --> pdb=" O GLU A 606 " (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: 4.035A pdb=" N ASP B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 188 through 193 Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.883A pdb=" N VAL B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.745A pdb=" N ALA B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 223' Processing helix chain 'B' and resid 230 through 246 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 54 removed outlier: 3.912A pdb=" N ARG C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 98 removed outlier: 4.274A pdb=" N ALA C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 139 removed outlier: 3.831A pdb=" N ARG C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 removed outlier: 3.537A pdb=" N PHE C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 201 removed outlier: 4.818A pdb=" N TRP C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 235 removed outlier: 3.883A 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 47 through 52 removed outlier: 4.353A pdb=" N ARG D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 129 through 150 removed outlier: 3.704A pdb=" N VAL D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.863A 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: 3.806A 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 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 343 through 347 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 395 through 406 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: 4.529A pdb=" N ARG D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 533 removed outlier: 3.586A pdb=" N PHE D 521 " --> pdb=" O THR D 517 " (cutoff:3.500A) 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: 3.859A pdb=" N GLU D 574 " --> pdb=" O ASN D 570 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU D 587 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 4.074A 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: 3.682A pdb=" N SER E 90 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 removed outlier: 4.055A pdb=" N ASP E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 174 through 187 Processing helix chain 'E' and resid 188 through 193 Proline residue: E 193 - end of helix Processing helix chain 'E' and resid 194 through 210 removed outlier: 3.879A pdb=" N VAL E 200 " --> pdb=" O TYR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.521A pdb=" N ALA E 222 " --> pdb=" O GLY E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 246 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: 3.889A pdb=" N ARG F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 95 Processing helix chain 'F' and resid 116 through 139 removed outlier: 3.820A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.581A pdb=" N PHE F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 201 removed outlier: 4.830A pdb=" N TRP F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 3.814A 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 87 through 96 removed outlier: 4.038A pdb=" N ALA G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER G 93 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.663A pdb=" N VAL G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.862A 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: 3.938A 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 306 through 311 removed outlier: 3.544A pdb=" N ASP G 310 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY G 311 " --> pdb=" O ARG G 308 " (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: 3.555A pdb=" N ASN G 346 " --> pdb=" O SER G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 364 Processing helix chain 'G' and resid 378 through 385 Processing helix chain 'G' and resid 386 through 406 removed outlier: 6.621A pdb=" N ASN G 396 " --> pdb=" O GLU G 392 " (cutoff:3.500A) removed outlier: 6.254A 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 513 removed outlier: 4.558A pdb=" N ARG G 513 " --> pdb=" O LEU G 509 " (cutoff:3.500A) 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: 3.783A pdb=" N GLU G 574 " --> pdb=" O ASN G 570 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 587 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 4.020A 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: 3.801A pdb=" N SER H 90 " --> pdb=" O HIS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 126 removed outlier: 4.071A pdb=" N ASP H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 removed outlier: 4.427A 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: 3.825A pdb=" N VAL H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 224 Processing helix chain 'H' and resid 230 through 246 Processing helix chain 'I' and resid 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: 3.898A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) 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 169 removed outlier: 3.534A pdb=" N PHE I 169 " --> pdb=" O VAL I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 200 removed outlier: 4.828A pdb=" N TRP I 194 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 3.731A 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 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: 4.951A pdb=" N LEU A 214 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY A 223 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 216 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 221 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.734A pdb=" N GLN A 284 " --> pdb=" O HIS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.593A pdb=" N THR B 4 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 99 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.148A 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: 6.397A 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: 6.573A pdb=" N THR D 209 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP D 228 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET D 211 " --> pdb=" O THR D 226 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR D 226 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP D 213 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE D 224 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 215 " --> pdb=" O ARG D 222 " (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: 6.729A 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 removed outlier: 3.920A pdb=" N ARG D 312 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 377 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 24 removed outlier: 6.543A pdb=" N THR E 4 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL E 99 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 6.408A 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: 6.646A pdb=" N VAL G 79 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE G 206 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS G 81 " --> pdb=" O PHE G 206 " (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: 6.544A pdb=" N ILE G 225 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU G 214 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY G 223 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL G 216 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 6.423A 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: 6.901A pdb=" N GLN G 284 " --> pdb=" O HIS G 421 " (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: 6.337A pdb=" N THR H 4 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL H 99 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS H 6 " --> pdb=" O VAL H 99 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.77: 27464 1.77 - 2.32: 339 2.32 - 2.87: 0 2.87 - 3.42: 0 3.42 - 3.97: 9 Bond restraints: 27812 Sorted by residual: bond pdb=" S4 F3S E 303 " pdb="FE1 F3S E 303 " ideal model delta sigma weight residual 2.233 3.971 -1.738 2.00e-02 2.50e+03 7.55e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.950 -1.717 2.00e-02 2.50e+03 7.37e+03 bond pdb=" S4 F3S H 303 " pdb="FE1 F3S H 303 " ideal model delta sigma weight residual 2.233 3.948 -1.715 2.00e-02 2.50e+03 7.35e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.955 -1.655 2.00e-02 2.50e+03 6.85e+03 bond pdb=" S2 F3S H 303 " pdb="FE3 F3S H 303 " ideal model delta sigma weight residual 2.300 3.948 -1.648 2.00e-02 2.50e+03 6.79e+03 ... (remaining 27807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.08: 37762 10.08 - 20.16: 22 20.16 - 30.24: 14 30.24 - 40.32: 16 40.32 - 50.40: 6 Bond angle restraints: 37820 Sorted by residual: angle pdb=" S1 F3S H 303 " pdb="FE4 F3S H 303 " pdb=" S3 F3S H 303 " ideal model delta sigma weight residual 114.75 64.35 50.40 3.00e+00 1.11e-01 2.82e+02 angle pdb=" S1 F3S E 303 " pdb="FE4 F3S E 303 " pdb=" S3 F3S E 303 " ideal model delta sigma weight residual 114.75 64.66 50.09 3.00e+00 1.11e-01 2.79e+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 62.92 49.67 3.00e+00 1.11e-01 2.74e+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 65.12 49.63 3.00e+00 1.11e-01 2.74e+02 angle pdb=" S3 F3S H 303 " pdb="FE1 F3S H 303 " pdb=" S4 F3S H 303 " ideal model delta sigma weight residual 112.59 63.66 48.93 3.00e+00 1.11e-01 2.66e+02 ... (remaining 37815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 15998 35.43 - 70.86: 362 70.86 - 106.30: 33 106.30 - 141.73: 11 141.73 - 177.16: 2 Dihedral angle restraints: 16406 sinusoidal: 6749 harmonic: 9657 Sorted by residual: 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 0.00 -81.47 81.47 2 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" C2B HEM F 301 " pdb=" C3B HEM F 301 " pdb=" CAB HEM F 301 " pdb=" CBB HEM F 301 " ideal model delta sinusoidal sigma weight residual 0.00 -77.86 77.86 2 1.00e+01 1.00e-02 4.59e+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 -68.16 68.16 2 1.00e+01 1.00e-02 4.14e+01 ... (remaining 16403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.684: 4026 3.684 - 7.367: 0 7.367 - 11.051: 0 11.051 - 14.735: 0 14.735 - 18.418: 3 Chirality restraints: 4029 Sorted by residual: 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 -7.65 18.42 2.00e-01 2.50e+01 8.48e+03 chirality pdb=" S2 F3S H 303 " pdb="FE1 F3S H 303 " pdb="FE3 F3S H 303 " pdb="FE4 F3S H 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.61 18.37 2.00e-01 2.50e+01 8.44e+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 -7.39 18.15 2.00e-01 2.50e+01 8.24e+03 ... (remaining 4026 not shown) Planarity restraints: 4854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 1L3 C 304 " -0.120 2.00e-02 2.50e+03 2.19e-01 5.99e+02 pdb=" C15 1L3 C 304 " 0.022 2.00e-02 2.50e+03 pdb=" C16 1L3 C 304 " 0.407 2.00e-02 2.50e+03 pdb=" C17 1L3 C 304 " -0.081 2.00e-02 2.50e+03 pdb=" C18 1L3 C 304 " -0.228 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 1L3 I 304 " -0.069 2.00e-02 2.50e+03 2.04e-01 5.18e+02 pdb=" C15 1L3 I 304 " -0.040 2.00e-02 2.50e+03 pdb=" C16 1L3 I 304 " 0.395 2.00e-02 2.50e+03 pdb=" C17 1L3 I 304 " -0.101 2.00e-02 2.50e+03 pdb=" C18 1L3 I 304 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 1L3 I 305 " -0.063 2.00e-02 2.50e+03 2.03e-01 5.17e+02 pdb=" C15 1L3 I 305 " -0.047 2.00e-02 2.50e+03 pdb=" C16 1L3 I 305 " 0.396 2.00e-02 2.50e+03 pdb=" C17 1L3 I 305 " -0.106 2.00e-02 2.50e+03 pdb=" C18 1L3 I 305 " -0.180 2.00e-02 2.50e+03 ... (remaining 4851 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2504 2.74 - 3.28: 26104 3.28 - 3.82: 46906 3.82 - 4.36: 54537 4.36 - 4.90: 95264 Nonbonded interactions: 225315 Sorted by model distance: nonbonded pdb=" OG SER D 256 " pdb=" OD1 ASN D 258 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN B 171 " pdb=" OG1 THR B 215 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASN D 108 " pdb=" OH TYR G 474 " model vdw 2.220 3.040 nonbonded pdb=" S1 F3S H 303 " pdb="FE1 F3S H 303 " model vdw 2.228 2.688 nonbonded pdb=" S1 F3S E 303 " pdb="FE1 F3S E 303 " model vdw 2.228 2.688 ... (remaining 225310 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' 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)) 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.450 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 1.738 27851 Z= 1.539 Angle : 1.487 50.403 37901 Z= 0.467 Chirality : 0.501 18.418 4029 Planarity : 0.008 0.219 4854 Dihedral : 15.626 177.159 10268 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.33 % Allowed : 8.89 % Favored : 90.78 % 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: 1.47 (0.14), residues: 3363 helix: 2.04 (0.13), residues: 1581 sheet: 1.48 (0.32), residues: 261 loop : -0.24 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 208 TYR 0.009 0.001 TYR A 296 PHE 0.010 0.001 PHE I 123 TRP 0.013 0.001 TRP D 314 HIS 0.008 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.03097 (27812) covalent geometry : angle 1.28066 (37820) hydrogen bonds : bond 0.13638 ( 1326) hydrogen bonds : angle 5.12150 ( 3711) metal coordination : bond 0.00674 ( 33) metal coordination : angle 16.41613 ( 81) Misc. bond : bond 0.16566 ( 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 466 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 457 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9121 (m-30) cc_final: 0.8894 (m-30) REVERT: A 210 GLU cc_start: 0.8813 (pt0) cc_final: 0.8592 (pt0) REVERT: A 402 LYS cc_start: 0.9177 (tttp) cc_final: 0.8767 (mttt) REVERT: B 242 MET cc_start: 0.8901 (tpp) cc_final: 0.8505 (mmm) REVERT: C 55 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8853 (mt-10) REVERT: C 209 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6765 (mmm160) REVERT: C 216 ILE cc_start: 0.9250 (mt) cc_final: 0.8988 (mp) REVERT: D 86 ASP cc_start: 0.9199 (t70) cc_final: 0.8990 (t0) REVERT: D 229 MET cc_start: 0.8392 (mpp) cc_final: 0.8148 (mpp) REVERT: D 292 VAL cc_start: 0.8467 (m) cc_final: 0.8254 (m) REVERT: D 388 GLN cc_start: 0.8670 (tp40) cc_final: 0.8412 (tm130) REVERT: D 407 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8334 (mp0) REVERT: D 543 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8083 (mtt-85) REVERT: D 574 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8388 (mt-10) REVERT: E 31 MET cc_start: 0.8624 (ptp) cc_final: 0.8246 (ptm) REVERT: E 42 GLU cc_start: 0.9250 (tt0) cc_final: 0.8863 (tm-30) REVERT: E 92 LYS cc_start: 0.9012 (tppp) cc_final: 0.8660 (tppt) REVERT: E 219 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8821 (mm-30) REVERT: F 23 PHE cc_start: 0.8277 (t80) cc_final: 0.7834 (t80) REVERT: F 113 GLN cc_start: 0.9070 (mt0) cc_final: 0.8842 (mt0) REVERT: G 210 GLU cc_start: 0.9049 (pt0) cc_final: 0.8623 (pt0) REVERT: G 292 VAL cc_start: 0.8411 (m) cc_final: 0.8194 (m) REVERT: G 407 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8684 (mp0) REVERT: H 92 LYS cc_start: 0.8881 (tppp) cc_final: 0.8674 (tppt) REVERT: H 242 MET cc_start: 0.8734 (tpt) cc_final: 0.8425 (mmm) REVERT: I 9 ARG cc_start: 0.8102 (mpt-90) cc_final: 0.7824 (mtt-85) REVERT: I 23 PHE cc_start: 0.8285 (t80) cc_final: 0.7960 (t80) REVERT: I 64 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8510 (mt-10) REVERT: I 86 THR cc_start: 0.9223 (m) cc_final: 0.8963 (p) REVERT: I 209 ARG cc_start: 0.7114 (tpt170) cc_final: 0.6611 (mmm160) REVERT: I 216 ILE cc_start: 0.9356 (mt) cc_final: 0.9126 (mp) outliers start: 9 outliers final: 6 residues processed: 465 average time/residue: 0.8146 time to fit residues: 429.8869 Evaluate side-chains 281 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 275 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN C 204 ASN D 185 GLN D 279 ASN D 507 GLN F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065264 restraints weight = 66371.635| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.99 r_work: 0.2743 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 27851 Z= 0.184 Angle : 1.450 87.633 37901 Z= 0.427 Chirality : 0.080 3.267 4029 Planarity : 0.004 0.043 4854 Dihedral : 10.032 175.473 4190 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.41 % Allowed : 14.23 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.14), residues: 3363 helix: 2.37 (0.13), residues: 1542 sheet: 1.34 (0.32), residues: 264 loop : -0.35 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 90 TYR 0.024 0.001 TYR G 401 PHE 0.014 0.001 PHE D 398 TRP 0.017 0.001 TRP D 314 HIS 0.005 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00395 (27812) covalent geometry : angle 1.12003 (37820) hydrogen bonds : bond 0.04849 ( 1326) hydrogen bonds : angle 4.26253 ( 3711) metal coordination : bond 0.01084 ( 33) metal coordination : angle 19.93817 ( 81) Misc. bond : bond 0.08582 ( 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 356 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8741 (mtm) cc_final: 0.8523 (mtm) REVERT: B 69 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8524 (tpt) REVERT: B 242 MET cc_start: 0.8825 (tpp) cc_final: 0.8471 (mmm) REVERT: C 9 ARG cc_start: 0.8496 (mpt-90) cc_final: 0.8230 (mmp80) REVERT: C 55 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8963 (mt-10) REVERT: C 209 ARG cc_start: 0.7198 (tpt170) cc_final: 0.6890 (mmm160) REVERT: C 216 ILE cc_start: 0.9285 (mt) cc_final: 0.9027 (mp) REVERT: D 388 GLN cc_start: 0.8711 (tp40) cc_final: 0.8490 (tm-30) REVERT: D 402 LYS cc_start: 0.9115 (tptm) cc_final: 0.8894 (tppp) REVERT: D 543 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8200 (mtt-85) REVERT: E 31 MET cc_start: 0.8572 (ptp) cc_final: 0.8188 (ptm) REVERT: F 23 PHE cc_start: 0.8387 (t80) cc_final: 0.7978 (t80) REVERT: F 111 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8493 (mmtm) REVERT: G 210 GLU cc_start: 0.9101 (pt0) cc_final: 0.8784 (pt0) REVERT: G 285 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8474 (mm) REVERT: G 407 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8804 (mp0) REVERT: G 501 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8346 (tm-30) REVERT: H 69 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8541 (tpt) REVERT: H 249 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: I 2 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6564 (p) REVERT: I 9 ARG cc_start: 0.8363 (mpt-90) cc_final: 0.8012 (mtm-85) REVERT: I 23 PHE cc_start: 0.8418 (t80) cc_final: 0.8133 (t80) REVERT: I 64 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8588 (mt-10) REVERT: I 86 THR cc_start: 0.9214 (m) cc_final: 0.9004 (p) REVERT: I 150 GLN cc_start: 0.8954 (tp40) cc_final: 0.8748 (tp40) REVERT: I 209 ARG cc_start: 0.7162 (tpt170) cc_final: 0.6714 (mmm160) REVERT: I 216 ILE cc_start: 0.9354 (mt) cc_final: 0.9129 (mp) outliers start: 66 outliers final: 19 residues processed: 335 average time/residue: 0.7631 time to fit residues: 292.7469 Evaluate side-chains 279 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 150 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 318 optimal weight: 0.0270 chunk 289 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.060393 restraints weight = 67774.708| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.99 r_work: 0.2641 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 27851 Z= 0.259 Angle : 1.476 84.794 37901 Z= 0.413 Chirality : 0.061 1.664 4029 Planarity : 0.004 0.046 4854 Dihedral : 8.841 178.799 4188 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.00 % Allowed : 15.18 % 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: 1.51 (0.14), residues: 3363 helix: 2.24 (0.13), residues: 1560 sheet: 1.29 (0.32), residues: 258 loop : -0.34 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 9 TYR 0.014 0.001 TYR A 401 PHE 0.013 0.001 PHE B 177 TRP 0.021 0.001 TRP G 314 HIS 0.006 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00610 (27812) covalent geometry : angle 1.02649 (37820) hydrogen bonds : bond 0.05204 ( 1326) hydrogen bonds : angle 4.33169 ( 3711) metal coordination : bond 0.02173 ( 33) metal coordination : angle 22.96167 ( 81) Misc. bond : bond 0.19917 ( 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 338 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 256 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8793 (pt0) cc_final: 0.8522 (pt0) REVERT: A 303 MET cc_start: 0.8341 (tpp) cc_final: 0.8071 (mmm) REVERT: A 574 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8561 (pm20) REVERT: B 69 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8608 (tpt) REVERT: B 242 MET cc_start: 0.8850 (tpp) cc_final: 0.8526 (mmm) REVERT: C 9 ARG cc_start: 0.8472 (mpt-90) cc_final: 0.8150 (mmp-170) REVERT: D 399 ASP cc_start: 0.8509 (t0) cc_final: 0.8202 (p0) REVERT: D 543 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8240 (mtt-85) REVERT: D 574 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: E 31 MET cc_start: 0.8794 (ptp) cc_final: 0.8379 (ptm) REVERT: E 242 MET cc_start: 0.9004 (mmm) cc_final: 0.8726 (mmm) REVERT: E 249 GLU cc_start: 0.9197 (tt0) cc_final: 0.8835 (mm-30) REVERT: F 23 PHE cc_start: 0.8539 (t80) cc_final: 0.8311 (t80) REVERT: F 170 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: G 210 GLU cc_start: 0.9071 (pt0) cc_final: 0.8828 (pt0) REVERT: G 308 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6037 (mtp-110) REVERT: G 407 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8728 (mp0) REVERT: H 1 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6568 (ptm) REVERT: H 69 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8536 (tpt) REVERT: H 92 LYS cc_start: 0.8985 (tppt) cc_final: 0.8785 (ttpp) REVERT: H 242 MET cc_start: 0.9035 (mmm) cc_final: 0.8809 (mmm) REVERT: H 246 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8567 (mtt-85) REVERT: I 9 ARG cc_start: 0.8567 (mpt-90) cc_final: 0.8176 (mmp-170) REVERT: I 23 PHE cc_start: 0.8631 (t80) cc_final: 0.8365 (t80) REVERT: I 64 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8715 (mt-10) REVERT: I 86 THR cc_start: 0.9315 (m) cc_final: 0.9027 (p) REVERT: I 146 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.5104 (t80) REVERT: I 209 ARG cc_start: 0.7342 (tpt170) cc_final: 0.6959 (mmm160) REVERT: I 216 ILE cc_start: 0.9395 (mt) cc_final: 0.9179 (mp) outliers start: 82 outliers final: 31 residues processed: 311 average time/residue: 0.7617 time to fit residues: 270.9372 Evaluate side-chains 271 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 146 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 256 optimal weight: 0.0170 chunk 123 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 302 optimal weight: 0.9980 chunk 309 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 ASN F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062814 restraints weight = 67099.712| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.96 r_work: 0.2697 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 27851 Z= 0.141 Angle : 1.390 82.658 37901 Z= 0.385 Chirality : 0.057 1.557 4029 Planarity : 0.003 0.037 4854 Dihedral : 8.496 178.984 4183 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 16.28 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.14), residues: 3363 helix: 2.32 (0.13), residues: 1563 sheet: 1.30 (0.32), residues: 258 loop : -0.37 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 152 TYR 0.016 0.001 TYR A 401 PHE 0.013 0.001 PHE A 378 TRP 0.031 0.001 TRP D 314 HIS 0.009 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00316 (27812) covalent geometry : angle 0.98063 (37820) hydrogen bonds : bond 0.04511 ( 1326) hydrogen bonds : angle 4.14543 ( 3711) metal coordination : bond 0.00794 ( 33) metal coordination : angle 21.33469 ( 81) Misc. bond : bond 0.11959 ( 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 335 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8276 (tpp) cc_final: 0.8028 (mmm) REVERT: B 69 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8606 (tpt) REVERT: B 242 MET cc_start: 0.8830 (tpp) cc_final: 0.8484 (mmm) REVERT: C 9 ARG cc_start: 0.8453 (mpt-90) cc_final: 0.8168 (mmp-170) REVERT: C 86 THR cc_start: 0.9292 (m) cc_final: 0.8971 (p) REVERT: C 94 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8487 (mtp-110) REVERT: C 101 ILE cc_start: 0.9119 (tt) cc_final: 0.8765 (pt) REVERT: C 105 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7016 (ptm160) REVERT: C 109 GLN cc_start: 0.8424 (tt0) cc_final: 0.8223 (tt0) REVERT: C 112 ARG cc_start: 0.8726 (ttm170) cc_final: 0.8313 (ttm170) REVERT: C 216 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9004 (mp) REVERT: D 399 ASP cc_start: 0.8442 (t0) cc_final: 0.8148 (p0) REVERT: D 543 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8242 (mtt-85) REVERT: D 574 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: E 31 MET cc_start: 0.8803 (ptp) cc_final: 0.8397 (ptm) REVERT: E 242 MET cc_start: 0.8993 (mmm) cc_final: 0.8750 (mmm) REVERT: E 249 GLU cc_start: 0.9197 (tt0) cc_final: 0.8789 (mm-30) REVERT: F 23 PHE cc_start: 0.8524 (t80) cc_final: 0.8222 (t80) REVERT: F 170 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: F 216 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9098 (mp) REVERT: G 210 GLU cc_start: 0.9046 (pt0) cc_final: 0.8781 (pt0) REVERT: G 285 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8472 (mm) REVERT: G 308 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6013 (mtp-110) REVERT: G 407 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8661 (mp0) REVERT: H 69 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8565 (tpt) REVERT: H 92 LYS cc_start: 0.8989 (tppt) cc_final: 0.8769 (ttpp) REVERT: H 246 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8679 (mtt-85) REVERT: H 249 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8518 (mm-30) REVERT: I 9 ARG cc_start: 0.8499 (mpt-90) cc_final: 0.8168 (mmp-170) REVERT: I 23 PHE cc_start: 0.8560 (t80) cc_final: 0.8345 (t80) REVERT: I 64 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8440 (mp0) REVERT: I 86 THR cc_start: 0.9304 (m) cc_final: 0.9025 (p) REVERT: I 111 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8188 (tttp) REVERT: I 146 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5321 (t80) REVERT: I 170 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8937 (mm-40) REVERT: I 209 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6924 (mmm160) REVERT: I 216 ILE cc_start: 0.9381 (mt) cc_final: 0.9159 (mp) outliers start: 75 outliers final: 26 residues processed: 310 average time/residue: 0.7874 time to fit residues: 279.2679 Evaluate side-chains 272 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 146 TYR Chi-restraints excluded: chain I residue 170 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 123 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.060802 restraints weight = 67296.193| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.90 r_work: 0.2642 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 27851 Z= 0.221 Angle : 1.414 83.081 37901 Z= 0.400 Chirality : 0.059 1.571 4029 Planarity : 0.003 0.038 4854 Dihedral : 8.356 177.963 4183 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.93 % Allowed : 16.72 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.15), residues: 3363 helix: 2.26 (0.13), residues: 1554 sheet: 1.16 (0.32), residues: 264 loop : -0.38 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 152 TYR 0.010 0.001 TYR D 134 PHE 0.011 0.001 PHE B 177 TRP 0.024 0.001 TRP G 314 HIS 0.009 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00523 (27812) covalent geometry : angle 1.00862 (37820) hydrogen bonds : bond 0.04851 ( 1326) hydrogen bonds : angle 4.23849 ( 3711) metal coordination : bond 0.01824 ( 33) metal coordination : angle 21.45553 ( 81) Misc. bond : bond 0.16450 ( 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 324 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 244 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8413 (tttp) REVERT: B 69 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8575 (tpt) REVERT: B 242 MET cc_start: 0.8842 (tpp) cc_final: 0.8486 (mmm) REVERT: C 9 ARG cc_start: 0.8596 (mpt-90) cc_final: 0.8155 (mmp-170) REVERT: C 101 ILE cc_start: 0.9140 (tt) cc_final: 0.8740 (pt) REVERT: C 105 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7081 (ptm160) REVERT: C 216 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9048 (mp) REVERT: D 399 ASP cc_start: 0.8496 (t0) cc_final: 0.8197 (p0) REVERT: D 543 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8234 (mtt-85) REVERT: D 574 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: E 31 MET cc_start: 0.8828 (ptp) cc_final: 0.8331 (ptm) REVERT: E 88 MET cc_start: 0.9031 (mtp) cc_final: 0.8822 (mmm) REVERT: E 147 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7846 (tptm) REVERT: E 242 MET cc_start: 0.9014 (mmm) cc_final: 0.8752 (mmm) REVERT: E 249 GLU cc_start: 0.9198 (tt0) cc_final: 0.8767 (mm-30) REVERT: F 23 PHE cc_start: 0.8630 (t80) cc_final: 0.8357 (t80) REVERT: F 170 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: F 216 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9112 (mp) REVERT: G 210 GLU cc_start: 0.9011 (pt0) cc_final: 0.8674 (pt0) REVERT: G 229 MET cc_start: 0.9174 (mtm) cc_final: 0.8676 (mtp) REVERT: G 285 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (mm) REVERT: G 308 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6078 (mtp-110) REVERT: G 407 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8718 (mp0) REVERT: H 69 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8533 (tpt) REVERT: H 88 MET cc_start: 0.8855 (mtp) cc_final: 0.8609 (mmm) REVERT: H 92 LYS cc_start: 0.8986 (tppt) cc_final: 0.8739 (ttpp) REVERT: H 242 MET cc_start: 0.9036 (mmm) cc_final: 0.8814 (mmm) REVERT: H 246 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8729 (mtt-85) REVERT: I 9 ARG cc_start: 0.8547 (mpt-90) cc_final: 0.8165 (mmp-170) REVERT: I 64 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8425 (mp0) REVERT: I 209 ARG cc_start: 0.7413 (tpt170) cc_final: 0.7045 (mmm160) REVERT: I 216 ILE cc_start: 0.9387 (mt) cc_final: 0.9165 (mp) outliers start: 80 outliers final: 32 residues processed: 300 average time/residue: 0.7823 time to fit residues: 267.2560 Evaluate side-chains 270 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 74 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS C 203 ASN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS I 138 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.060100 restraints weight = 67526.278| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.94 r_work: 0.2630 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.202 27851 Z= 0.214 Angle : 1.390 83.024 37901 Z= 0.401 Chirality : 0.059 1.562 4029 Planarity : 0.003 0.038 4854 Dihedral : 8.306 177.675 4183 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.07 % Allowed : 17.12 % Favored : 79.80 % 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: 1.40 (0.14), residues: 3363 helix: 2.17 (0.13), residues: 1566 sheet: 1.14 (0.32), residues: 264 loop : -0.43 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 152 TYR 0.010 0.001 TYR D 134 PHE 0.011 0.001 PHE B 177 TRP 0.032 0.001 TRP G 314 HIS 0.016 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00507 (27812) covalent geometry : angle 1.01289 (37820) hydrogen bonds : bond 0.04903 ( 1326) hydrogen bonds : angle 4.27012 ( 3711) metal coordination : bond 0.01762 ( 33) metal coordination : angle 20.60980 ( 81) Misc. bond : bond 0.16805 ( 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 320 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8518 (mmmm) REVERT: B 69 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8588 (tpt) REVERT: B 147 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7815 (tptm) REVERT: B 242 MET cc_start: 0.8843 (tpp) cc_final: 0.8493 (mmm) REVERT: B 249 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8658 (mm-30) REVERT: C 9 ARG cc_start: 0.8572 (mpt-90) cc_final: 0.8060 (mtm-85) REVERT: C 101 ILE cc_start: 0.9126 (tt) cc_final: 0.8699 (pt) REVERT: C 105 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7093 (ptm160) REVERT: C 216 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9043 (mp) REVERT: D 229 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8457 (mtt) REVERT: D 313 ILE cc_start: 0.6693 (mm) cc_final: 0.6378 (mm) REVERT: D 399 ASP cc_start: 0.8509 (t0) cc_final: 0.8211 (p0) REVERT: D 574 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: E 31 MET cc_start: 0.8858 (ptp) cc_final: 0.8305 (ptm) REVERT: E 147 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7849 (tptm) REVERT: E 242 MET cc_start: 0.9020 (mmm) cc_final: 0.8774 (mmm) REVERT: E 249 GLU cc_start: 0.9206 (tt0) cc_final: 0.8751 (mm-30) REVERT: F 23 PHE cc_start: 0.8666 (t80) cc_final: 0.8407 (t80) REVERT: F 170 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: G 210 GLU cc_start: 0.8990 (pt0) cc_final: 0.8655 (pt0) REVERT: G 229 MET cc_start: 0.9168 (mtm) cc_final: 0.8663 (mtp) REVERT: G 285 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8488 (mm) REVERT: G 308 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6122 (mtp-110) REVERT: G 407 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8737 (mp0) REVERT: H 69 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8532 (tpt) REVERT: H 92 LYS cc_start: 0.8929 (tppt) cc_final: 0.8663 (ttpp) REVERT: H 246 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8810 (mtt-85) REVERT: H 249 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8636 (mm-30) REVERT: I 9 ARG cc_start: 0.8562 (mpt-90) cc_final: 0.8181 (mmp-170) REVERT: I 64 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8487 (mp0) REVERT: I 150 GLN cc_start: 0.8987 (tp40) cc_final: 0.8783 (tp40) REVERT: I 170 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8116 (mp10) outliers start: 84 outliers final: 35 residues processed: 293 average time/residue: 0.7691 time to fit residues: 257.1608 Evaluate side-chains 276 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 170 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 272 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 279 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.061165 restraints weight = 67180.459| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.90 r_work: 0.2645 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 27851 Z= 0.171 Angle : 1.339 83.131 37901 Z= 0.394 Chirality : 0.058 1.552 4029 Planarity : 0.003 0.039 4854 Dihedral : 8.262 176.764 4183 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.67 % Allowed : 18.26 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.14), residues: 3363 helix: 2.20 (0.13), residues: 1563 sheet: 1.17 (0.32), residues: 264 loop : -0.42 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 152 TYR 0.022 0.001 TYR A 401 PHE 0.010 0.001 PHE B 177 TRP 0.034 0.001 TRP G 314 HIS 0.011 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00401 (27812) covalent geometry : angle 1.00194 (37820) hydrogen bonds : bond 0.04676 ( 1326) hydrogen bonds : angle 4.24706 ( 3711) metal coordination : bond 0.01281 ( 33) metal coordination : angle 19.24662 ( 81) Misc. bond : bond 0.14780 ( 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 313 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 240 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8615 (mmmm) REVERT: A 372 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7911 (pp) REVERT: B 69 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8609 (tpt) REVERT: B 147 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7812 (tptm) REVERT: B 242 MET cc_start: 0.8827 (tpp) cc_final: 0.8487 (mmm) REVERT: B 249 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8655 (mm-30) REVERT: C 9 ARG cc_start: 0.8483 (mpt-90) cc_final: 0.8085 (mmp-170) REVERT: C 101 ILE cc_start: 0.9125 (tt) cc_final: 0.8693 (pt) REVERT: C 105 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7117 (ptm160) REVERT: C 155 HIS cc_start: 0.9041 (t70) cc_final: 0.8784 (p90) REVERT: C 216 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9053 (mp) REVERT: D 313 ILE cc_start: 0.6735 (mm) cc_final: 0.6416 (mm) REVERT: D 399 ASP cc_start: 0.8472 (t0) cc_final: 0.8159 (p0) REVERT: D 574 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: E 31 MET cc_start: 0.8780 (ptp) cc_final: 0.8342 (ptm) REVERT: E 249 GLU cc_start: 0.9198 (tt0) cc_final: 0.8641 (tp30) REVERT: F 23 PHE cc_start: 0.8665 (t80) cc_final: 0.8398 (t80) REVERT: F 170 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: G 210 GLU cc_start: 0.8962 (pt0) cc_final: 0.8715 (pt0) REVERT: G 402 LYS cc_start: 0.9148 (tptm) cc_final: 0.8928 (tppp) REVERT: G 407 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9005 (mp0) REVERT: H 69 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8532 (tpt) REVERT: H 92 LYS cc_start: 0.8937 (tppt) cc_final: 0.8656 (ttpp) REVERT: H 246 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (mtt-85) REVERT: H 249 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: I 9 ARG cc_start: 0.8564 (mpt-90) cc_final: 0.8199 (mmp80) REVERT: I 64 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8495 (mp0) outliers start: 73 outliers final: 35 residues processed: 289 average time/residue: 0.7744 time to fit residues: 255.3531 Evaluate side-chains 271 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 102 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 87 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS I 203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.058086 restraints weight = 67965.884| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.95 r_work: 0.2592 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 27851 Z= 0.324 Angle : 1.424 83.909 37901 Z= 0.437 Chirality : 0.062 1.576 4029 Planarity : 0.004 0.039 4854 Dihedral : 8.451 177.074 4183 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.27 % Allowed : 18.84 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3363 helix: 2.04 (0.13), residues: 1542 sheet: 1.02 (0.32), residues: 264 loop : -0.47 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.023 0.001 TYR G 401 PHE 0.015 0.002 PHE G 167 TRP 0.028 0.001 TRP G 314 HIS 0.020 0.002 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00769 (27812) covalent geometry : angle 1.07783 (37820) hydrogen bonds : bond 0.05467 ( 1326) hydrogen bonds : angle 4.48958 ( 3711) metal coordination : bond 0.02839 ( 33) metal coordination : angle 20.15516 ( 81) Misc. bond : bond 0.23033 ( 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 296 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7745 (pt) REVERT: B 69 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8645 (tpt) REVERT: B 147 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7801 (tptm) REVERT: B 242 MET cc_start: 0.8858 (tpp) cc_final: 0.8588 (mmm) REVERT: B 249 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: C 9 ARG cc_start: 0.8505 (mpt-90) cc_final: 0.8021 (mmp-170) REVERT: C 101 ILE cc_start: 0.9117 (tt) cc_final: 0.8610 (pt) REVERT: C 105 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7174 (ptm160) REVERT: C 216 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9069 (mp) REVERT: D 229 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: D 313 ILE cc_start: 0.6836 (mm) cc_final: 0.6609 (mm) REVERT: D 399 ASP cc_start: 0.8519 (t0) cc_final: 0.8205 (p0) REVERT: D 402 LYS cc_start: 0.9143 (tptm) cc_final: 0.8933 (tppp) REVERT: D 574 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: E 31 MET cc_start: 0.8873 (ptp) cc_final: 0.8420 (ptm) REVERT: E 147 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7869 (tptm) REVERT: E 242 MET cc_start: 0.8985 (mmm) cc_final: 0.8749 (tmm) REVERT: E 249 GLU cc_start: 0.9221 (tt0) cc_final: 0.8684 (tp30) REVERT: F 23 PHE cc_start: 0.8810 (t80) cc_final: 0.8567 (t80) REVERT: F 170 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: G 210 GLU cc_start: 0.8989 (pt0) cc_final: 0.8715 (pt0) REVERT: G 229 MET cc_start: 0.9178 (mtm) cc_final: 0.8751 (mtp) REVERT: H 69 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8686 (tpt) REVERT: H 92 LYS cc_start: 0.8908 (tppt) cc_final: 0.8650 (ttpp) REVERT: H 249 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8660 (mm-30) REVERT: I 9 ARG cc_start: 0.8546 (mpt-90) cc_final: 0.8145 (mmp80) REVERT: I 170 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8025 (mp10) outliers start: 62 outliers final: 33 residues processed: 281 average time/residue: 0.7262 time to fit residues: 233.8449 Evaluate side-chains 268 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 170 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 32 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 226 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.059339 restraints weight = 67625.156| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.92 r_work: 0.2620 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 27851 Z= 0.213 Angle : 1.379 83.377 37901 Z= 0.414 Chirality : 0.060 1.556 4029 Planarity : 0.004 0.042 4854 Dihedral : 8.409 176.714 4183 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.16 % Allowed : 19.21 % Favored : 78.63 % 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: 1.25 (0.14), residues: 3363 helix: 2.02 (0.13), residues: 1566 sheet: 1.06 (0.32), residues: 264 loop : -0.47 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 152 TYR 0.017 0.001 TYR G 401 PHE 0.011 0.001 PHE B 177 TRP 0.030 0.001 TRP G 314 HIS 0.008 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00502 (27812) covalent geometry : angle 1.04035 (37820) hydrogen bonds : bond 0.05058 ( 1326) hydrogen bonds : angle 4.39957 ( 3711) metal coordination : bond 0.01763 ( 33) metal coordination : angle 19.61990 ( 81) Misc. bond : bond 0.18609 ( 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 294 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8626 (pt0) cc_final: 0.8249 (pt0) REVERT: A 229 MET cc_start: 0.8958 (mtm) cc_final: 0.8588 (mtt) REVERT: A 372 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7775 (pt) REVERT: B 69 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8663 (tpt) REVERT: B 147 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7786 (tptm) REVERT: B 242 MET cc_start: 0.8842 (tpp) cc_final: 0.8513 (mmm) REVERT: B 249 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: C 9 ARG cc_start: 0.8488 (mpt-90) cc_final: 0.8046 (mmp-170) REVERT: C 101 ILE cc_start: 0.9134 (tt) cc_final: 0.8630 (pt) REVERT: C 105 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7166 (ptm160) REVERT: C 216 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 229 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: D 313 ILE cc_start: 0.6808 (mm) cc_final: 0.6589 (mm) REVERT: D 399 ASP cc_start: 0.8502 (t0) cc_final: 0.8186 (p0) REVERT: D 402 LYS cc_start: 0.9152 (tptm) cc_final: 0.8939 (tppp) REVERT: D 574 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: E 31 MET cc_start: 0.8877 (ptp) cc_final: 0.8475 (ptm) REVERT: E 147 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7829 (tptm) REVERT: E 242 MET cc_start: 0.8975 (mmm) cc_final: 0.8720 (tmm) REVERT: E 249 GLU cc_start: 0.9189 (tt0) cc_final: 0.8636 (tp30) REVERT: F 23 PHE cc_start: 0.8802 (t80) cc_final: 0.8521 (t80) REVERT: F 170 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: G 210 GLU cc_start: 0.8953 (pt0) cc_final: 0.8664 (pt0) REVERT: G 229 MET cc_start: 0.9164 (mtm) cc_final: 0.8724 (mtp) REVERT: G 402 LYS cc_start: 0.9154 (tptm) cc_final: 0.8942 (tppp) REVERT: H 69 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8657 (tpt) REVERT: H 92 LYS cc_start: 0.8905 (tppt) cc_final: 0.8652 (ttpp) REVERT: H 242 MET cc_start: 0.8923 (mmm) cc_final: 0.8655 (tmm) REVERT: H 249 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8656 (mm-30) REVERT: I 170 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8032 (mp10) outliers start: 59 outliers final: 33 residues processed: 276 average time/residue: 0.7047 time to fit residues: 222.2968 Evaluate side-chains 272 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 220 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 170 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 238 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** E 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.060215 restraints weight = 66956.535| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.90 r_work: 0.2640 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 27851 Z= 0.183 Angle : 1.362 83.350 37901 Z= 0.409 Chirality : 0.059 1.548 4029 Planarity : 0.003 0.042 4854 Dihedral : 8.343 175.472 4183 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.90 % Allowed : 19.43 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3363 helix: 2.05 (0.13), residues: 1548 sheet: 1.05 (0.32), residues: 264 loop : -0.48 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 94 TYR 0.013 0.001 TYR A 401 PHE 0.010 0.001 PHE C 23 TRP 0.042 0.001 TRP G 314 HIS 0.010 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00430 (27812) covalent geometry : angle 1.03306 (37820) hydrogen bonds : bond 0.04839 ( 1326) hydrogen bonds : angle 4.36923 ( 3711) metal coordination : bond 0.01413 ( 33) metal coordination : angle 19.21923 ( 81) Misc. bond : bond 0.16022 ( 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 284 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7793 (pt) REVERT: A 424 MET cc_start: 0.8971 (mtm) cc_final: 0.8215 (mtm) REVERT: B 69 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8659 (tpt) REVERT: B 88 MET cc_start: 0.9065 (mmm) cc_final: 0.8807 (mmm) REVERT: B 147 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7784 (tptm) REVERT: B 242 MET cc_start: 0.8848 (tpp) cc_final: 0.8475 (mmm) REVERT: B 249 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8602 (mm-30) REVERT: C 9 ARG cc_start: 0.8488 (mpt-90) cc_final: 0.8057 (mmp-170) REVERT: C 101 ILE cc_start: 0.9135 (tt) cc_final: 0.8666 (pt) REVERT: C 105 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7180 (ttm-80) REVERT: C 216 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9063 (mp) REVERT: D 229 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8357 (mtt) REVERT: D 313 ILE cc_start: 0.6810 (mm) cc_final: 0.6598 (mm) REVERT: D 399 ASP cc_start: 0.8479 (t0) cc_final: 0.8175 (p0) REVERT: D 574 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: E 31 MET cc_start: 0.8857 (ptp) cc_final: 0.8341 (ptm) REVERT: E 147 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7825 (tptm) REVERT: E 242 MET cc_start: 0.8976 (mmm) cc_final: 0.8718 (tmm) REVERT: E 249 GLU cc_start: 0.9198 (tt0) cc_final: 0.8654 (tp30) REVERT: F 23 PHE cc_start: 0.8770 (t80) cc_final: 0.8499 (t80) REVERT: F 170 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: G 210 GLU cc_start: 0.8919 (pt0) cc_final: 0.8620 (pt0) REVERT: G 229 MET cc_start: 0.9160 (mtm) cc_final: 0.8713 (mtp) REVERT: G 402 LYS cc_start: 0.9134 (tptm) cc_final: 0.8913 (tppp) REVERT: H 69 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8559 (tpt) REVERT: H 92 LYS cc_start: 0.8904 (tppt) cc_final: 0.8647 (ttpp) REVERT: H 242 MET cc_start: 0.8903 (mmm) cc_final: 0.8628 (tmm) REVERT: H 249 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: I 64 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8179 (mp0) REVERT: I 170 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: I 205 ARG cc_start: 0.8595 (ptp-170) cc_final: 0.8379 (ptp-170) outliers start: 52 outliers final: 32 residues processed: 268 average time/residue: 0.6837 time to fit residues: 209.1365 Evaluate side-chains 270 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 344 PHE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 574 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 170 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 170 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 330 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN F 203 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 HIS I 164 ASN I 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060793 restraints weight = 66778.913| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.90 r_work: 0.2651 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 27851 Z= 0.170 Angle : 1.351 83.355 37901 Z= 0.406 Chirality : 0.059 1.544 4029 Planarity : 0.003 0.042 4854 Dihedral : 8.293 174.621 4183 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.83 % Allowed : 19.65 % Favored : 78.52 % 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: 1.27 (0.14), residues: 3363 helix: 2.07 (0.13), residues: 1548 sheet: 1.07 (0.32), residues: 264 loop : -0.47 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 94 TYR 0.014 0.001 TYR A 401 PHE 0.011 0.001 PHE C 23 TRP 0.038 0.001 TRP G 314 HIS 0.005 0.001 HIS G 595 Details of bonding type rmsd covalent geometry : bond 0.00397 (27812) covalent geometry : angle 1.02832 (37820) hydrogen bonds : bond 0.04717 ( 1326) hydrogen bonds : angle 4.34874 ( 3711) metal coordination : bond 0.01196 ( 33) metal coordination : angle 18.97711 ( 81) Misc. bond : bond 0.15193 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7495.59 seconds wall clock time: 129 minutes 4.13 seconds (7744.13 seconds total)