Starting phenix.real_space_refine on Fri Aug 7 15:51:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7q_73877/08_2026/9z7q_73877.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 37 5.49 5 S 79 5.16 5 C 14001 2.51 5 N 3758 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21997 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4437 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 577} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 34, 'ASN:plan1': 11, 'ASP:plan': 29, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 266 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2697 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 19, 'TRANS': 340} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 9, 'ASN:plan1': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2403 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2401 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2425 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1057 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 131} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2311 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 283} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 811 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "I" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2424 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 16, 'ASP:plan': 13, 'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 189 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1248 SG CYS A 166 40.625 54.595 152.429 1.00 92.97 S ATOM 1268 SG CYS A 169 44.113 55.809 153.258 1.00 92.23 S ATOM 1665 SG CYS A 222 41.473 56.396 155.798 1.00 82.81 S ATOM 1682 SG CYS A 225 41.137 58.273 152.568 1.00101.22 S Time building chain proxies: 5.05, per 1000 atoms: 0.23 Number of scatterers: 21997 At special positions: 0 Unit cell: (100.464, 109.296, 189.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 79 16.00 P 37 15.00 O 4121 8.00 N 3758 7.00 C 14001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 929.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 222 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 169 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 166 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 225 " Number of angles added : 6 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 36 sheets defined 42.5% alpha, 16.7% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 104 Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.605A pdb=" N CYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.789A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 263 through 271 removed outlier: 4.115A pdb=" N THR A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.562A pdb=" N ASN A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 343 through 366 Processing helix chain 'A' and resid 389 through 406 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 514 removed outlier: 4.250A pdb=" N LYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.520A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 573 through 593 Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.650A pdb=" N HIS B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 4.689A pdb=" N LYS B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 4.353A pdb=" N ASN B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'C' and resid 43 through 58 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 175 through 189 removed outlier: 4.079A pdb=" N PHE C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 268 through 275 removed outlier: 3.580A pdb=" N GLY C 272 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 273 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 275 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'D' and resid 43 through 58 Processing helix chain 'D' and resid 73 through 82 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.651A pdb=" N CYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 4.146A pdb=" N PHE D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 268 through 275 removed outlier: 3.999A pdb=" N GLY D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 274 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 275 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'E' and resid 43 through 58 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 117 through 131 Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.770A pdb=" N PHE E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 203 removed outlier: 3.734A pdb=" N LYS E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 203 " --> pdb=" O LYS E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 221 Processing helix chain 'E' and resid 268 through 275 removed outlier: 3.518A pdb=" N LYS E 271 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE E 273 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'F' and resid 7 through 29 removed outlier: 4.059A pdb=" N ARG F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 51 Proline residue: F 44 - end of helix Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 70 through 86 removed outlier: 4.179A pdb=" N TYR F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 98 removed outlier: 4.000A pdb=" N ASN F 98 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 108 removed outlier: 3.532A pdb=" N GLU F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.794A pdb=" N TRP F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 30 removed outlier: 3.603A pdb=" N ILE G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 51 through 62 Processing helix chain 'G' and resid 71 through 88 Processing helix chain 'G' and resid 93 through 98 removed outlier: 3.774A pdb=" N ASN G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 111 through 136 removed outlier: 3.772A pdb=" N TRP G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.795A pdb=" N GLY H 83 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 95 removed outlier: 3.511A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 134 through 138 Processing helix chain 'H' and resid 141 through 161 Processing helix chain 'H' and resid 202 through 219 Processing helix chain 'H' and resid 222 through 228 Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 273 through 278 Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 320 through 325 removed outlier: 4.023A pdb=" N VAL H 324 " --> pdb=" O GLN H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 336 removed outlier: 4.161A pdb=" N SER H 334 " --> pdb=" O SER H 330 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS H 336 " --> pdb=" O LEU H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 360 Processing helix chain 'H' and resid 365 through 369 removed outlier: 3.610A pdb=" N GLY H 369 " --> pdb=" O THR H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 44 removed outlier: 3.610A pdb=" N ILE I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 60 Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.747A pdb=" N HIS I 98 " --> pdb=" O PRO I 94 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER I 101 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL I 102 " --> pdb=" O HIS I 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE I 103 " --> pdb=" O PHE I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 145 Processing helix chain 'I' and resid 150 through 154 removed outlier: 4.010A pdb=" N GLY I 154 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.676A pdb=" N ASP I 171 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP I 172 " --> pdb=" O ILE I 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 168 through 172' Processing helix chain 'I' and resid 183 through 203 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 330 through 342 removed outlier: 3.841A pdb=" N ARG I 342 " --> pdb=" O GLU I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.729A pdb=" N TYR A 177 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 219 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.800A pdb=" N LEU A 382 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 376 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA A 458 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS A 430 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.777A pdb=" N LEU B 80 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 12.597A pdb=" N ILE B 78 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE B 75 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 206 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 77 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR B 199 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA B 8 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 223 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.693A pdb=" N VAL B 191 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET B 187 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 5.639A pdb=" N LEU B 285 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 321 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 287 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 338 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 294 through 300 removed outlier: 4.981A pdb=" N GLY B 298 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP B 300 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.808A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 253 through 260 current: chain 'C' and resid 206 through 208 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.808A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 98 through 106 current: chain 'C' and resid 309 through 314 Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 152 through 154 removed outlier: 7.199A pdb=" N LYS C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 227 Processing sheet with id=AB9, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.764A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 253 through 260 current: chain 'D' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.764A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 106 current: chain 'D' and resid 309 through 314 Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 64 Processing sheet with id=AC3, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'D' and resid 152 through 154 removed outlier: 7.156A pdb=" N LYS D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 223 through 227 Processing sheet with id=AC6, first strand: chain 'E' and resid 41 through 42 removed outlier: 6.698A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 253 through 260 current: chain 'E' and resid 206 through 208 Processing sheet with id=AC7, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.698A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 98 through 106 current: chain 'E' and resid 309 through 314 Processing sheet with id=AC8, first strand: chain 'E' and resid 61 through 64 removed outlier: 3.920A pdb=" N ILE E 62 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 67 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AD1, first strand: chain 'E' and resid 157 through 160 Processing sheet with id=AD2, first strand: chain 'E' and resid 223 through 227 Processing sheet with id=AD3, first strand: chain 'H' and resid 122 through 124 removed outlier: 6.385A pdb=" N LYS H 123 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 251 through 253 removed outlier: 3.982A pdb=" N LEU H 257 " --> pdb=" O GLU H 310 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 251 through 253 removed outlier: 3.734A pdb=" N SER H 171 " --> pdb=" O GLU H 374 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 264 through 267 Processing sheet with id=AD7, first strand: chain 'I' and resid 71 through 77 removed outlier: 3.569A pdb=" N SER I 162 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR I 9 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE I 160 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 289 through 296 removed outlier: 5.948A pdb=" N TRP I 302 " --> pdb=" O GLY I 224 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG I 220 " --> pdb=" O ARG I 306 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER I 219 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 261 through 263 removed outlier: 3.704A pdb=" N VAL I 261 " --> pdb=" O VAL I 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 325 " --> pdb=" O ILE I 318 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6918 1.34 - 1.46: 5006 1.46 - 1.58: 10400 1.58 - 1.70: 74 1.70 - 1.82: 125 Bond restraints: 22523 Sorted by residual: bond pdb=" CB GLN B 114 " pdb=" CG GLN B 114 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.33e+00 bond pdb=" O4' C N 25 " pdb=" C1' C N 25 " ideal model delta sigma weight residual 1.415 1.394 0.021 1.20e-02 6.94e+03 3.09e+00 bond pdb=" CB GLU F 95 " pdb=" CG GLU F 95 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" C3' C N 25 " pdb=" C2' C N 25 " ideal model delta sigma weight residual 1.525 1.543 -0.018 1.10e-02 8.26e+03 2.76e+00 bond pdb=" C4' C N 25 " pdb=" O4' C N 25 " ideal model delta sigma weight residual 1.454 1.440 0.014 1.00e-02 1.00e+04 1.94e+00 ... (remaining 22518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 30242 2.39 - 4.77: 386 4.77 - 7.16: 36 7.16 - 9.55: 9 9.55 - 11.93: 1 Bond angle restraints: 30674 Sorted by residual: angle pdb=" N1 C N 25 " pdb=" C2 C N 25 " pdb=" O2 C N 25 " ideal model delta sigma weight residual 118.90 122.25 -3.35 6.00e-01 2.78e+00 3.12e+01 angle pdb=" C1' C N 25 " pdb=" N1 C N 25 " pdb=" C2 C N 25 " ideal model delta sigma weight residual 118.80 124.17 -5.37 1.10e+00 8.26e-01 2.39e+01 angle pdb=" O2 C N 25 " pdb=" C2 C N 25 " pdb=" N3 C N 25 " ideal model delta sigma weight residual 121.90 118.60 3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" CA MET C 108 " pdb=" CB MET C 108 " pdb=" CG MET C 108 " ideal model delta sigma weight residual 114.10 104.76 9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CB GLN B 114 " pdb=" CG GLN B 114 " pdb=" CD GLN B 114 " ideal model delta sigma weight residual 112.60 120.20 -7.60 1.70e+00 3.46e-01 2.00e+01 ... (remaining 30669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 12976 35.27 - 70.54: 496 70.54 - 105.81: 34 105.81 - 141.08: 2 141.08 - 176.34: 3 Dihedral angle restraints: 13511 sinusoidal: 5410 harmonic: 8101 Sorted by residual: dihedral pdb=" CA GLU F 88 " pdb=" C GLU F 88 " pdb=" N PRO F 89 " pdb=" CA PRO F 89 " ideal model delta harmonic sigma weight residual 180.00 81.12 98.88 0 5.00e+00 4.00e-02 3.91e+02 dihedral pdb=" O4' C N 35 " pdb=" C1' C N 35 " pdb=" N1 C N 35 " pdb=" C2 C N 35 " ideal model delta sinusoidal sigma weight residual 200.00 53.09 146.91 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' U N 20 " pdb=" C1' U N 20 " pdb=" N1 U N 20 " pdb=" C2 U N 20 " ideal model delta sinusoidal sigma weight residual -128.00 48.34 -176.34 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2676 0.046 - 0.093: 628 0.093 - 0.139: 198 0.139 - 0.186: 21 0.186 - 0.232: 4 Chirality restraints: 3527 Sorted by residual: chirality pdb=" CA ASP I 20 " pdb=" N ASP I 20 " pdb=" C ASP I 20 " pdb=" CB ASP I 20 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1' U N 18 " pdb=" O4' U N 18 " pdb=" C2' U N 18 " pdb=" N1 U N 18 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASN E 22 " pdb=" N ASN E 22 " pdb=" C ASN E 22 " pdb=" CB ASN E 22 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 3524 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 114 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C GLN B 114 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN B 114 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS B 115 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 119 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C ASN F 119 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN F 119 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU F 120 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 214 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C PHE C 214 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE C 214 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG C 215 " -0.015 2.00e-02 2.50e+03 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6882 2.83 - 3.35: 20378 3.35 - 3.86: 37655 3.86 - 4.38: 43723 4.38 - 4.90: 75571 Nonbonded interactions: 184209 Sorted by model distance: nonbonded pdb=" O ASN E 22 " pdb=" OD1 ASN E 22 " model vdw 2.310 3.040 nonbonded pdb=" O GLN B 114 " pdb=" OE1 GLN B 114 " model vdw 2.469 3.040 nonbonded pdb=" N GLU F 95 " pdb=" OE1 GLU F 95 " model vdw 2.479 3.120 nonbonded pdb=" O SER D 278 " pdb=" OG SER D 278 " model vdw 2.486 3.040 nonbonded pdb=" N GLU C 281 " pdb=" OE1 GLU C 281 " model vdw 2.488 3.120 ... (remaining 184204 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 'C' and (resid 1 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 42 or (resid 43 through \ 44 and (name N or name CA or name C or name O or name CB )) or resid 45 through \ 58 or (resid 59 through 61 and (name N or name CA or name C or name O or name CB \ )) or resid 62 through 161 or (resid 162 and (name N or name CA or name C or na \ me O or name CB )) or resid 163 through 170 or (resid 171 through 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 through 191 or (resi \ d 192 and (name N or name CA or name C or name O or name CB )) or resid 193 thro \ ugh 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) o \ r resid 196 through 199 or (resid 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 237 or (resid 238 and (name N or name CA or \ name C or name O or name CB )) or resid 239 through 266 or (resid 267 and (name \ N or name CA or name C or name O or name CB )) or resid 268 through 269 or (resi \ d 270 and (name N or name CA or name C or name O or name CB )) or resid 271 thro \ ugh 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) o \ r resid 274 through 279 or (resid 280 and (name N or name CA or name C or name O \ or name CB )) or resid 281 through 315)) selection = (chain 'D' and (resid 1 through 62 or (resid 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 83 or (resid 84 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 170 or (resid 171 through 173 and (name N or name CA or name C or name O or na \ me CB )) or resid 174 through 191 or (resid 192 and (name N or name CA or name C \ or name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 210 or (resid 211 \ through 212 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 3 through 237 or (resid 238 and (name N or name CA or name C or name O or name C \ B )) or resid 239 through 244 or (resid 245 and (name N or name CA or name C or \ name O or name CB )) or resid 246 through 266 or (resid 267 and (name N or name \ CA or name C or name O or name CB )) or resid 268 through 272 or (resid 273 and \ (name N or name CA or name C or name O or name CB )) or resid 274 through 315)) selection = (chain 'E' and (resid 1 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 42 or (resid 43 through \ 44 and (name N or name CA or name C or name O or name CB )) or resid 45 through \ 56 or (resid 57 through 61 and (name N or name CA or name C or name O or name CB \ )) or resid 62 or (resid 63 and (name N or name CA or name C or name O or name \ CB )) or resid 64 through 73 or (resid 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 137 or (resid 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 161 or (resid 162 and (na \ me N or name CA or name C or name O or name CB )) or resid 163 through 171 or (r \ esid 172 through 173 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 210 or (resid 211 through 212 and (name N or \ name CA or name C or name O or name CB )) or resid 213 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 68 or (resid 269 through 270 and (name N or name CA or name C or name O or name \ CB )) or resid 271 through 276 or (resid 277 and (name N or name CA or name C or \ name O or name CB )) or resid 278 through 279 or (resid 280 and (name N or name \ CA or name C or name O or name CB )) or resid 281 through 315)) } ncs_group { reference = (chain 'F' and (resid 8 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 136 or \ (resid 137 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 8)) selection = (chain 'G' and (resid 8 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 78 or (resid 79 and (name N or name \ CA or name C or name O or name CB )) or resid 80 through 89 or (resid 90 and (n \ ame N or name CA or name C or name O or name CB )) or resid 91 through 138)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.590 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.003 0.055 22527 Z= 0.152 Angle : 0.644 11.931 30680 Z= 0.370 Chirality : 0.045 0.232 3527 Planarity : 0.004 0.046 3769 Dihedral : 17.082 176.344 8291 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 0.90 % Allowed : 24.79 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2784 helix: 1.22 (0.16), residues: 1049 sheet: 0.21 (0.25), residues: 404 loop : -0.77 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 215 TYR 0.020 0.001 TYR G 39 PHE 0.024 0.001 PHE A 55 TRP 0.011 0.001 TRP I 302 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (22523) covalent geometry : angle 0.64176 / 0.37 (30674) hydrogen bonds : bond 0.15863 / 11.04 ( 989) hydrogen bonds : angle 7.07049 / 5.13 ( 2808) metal coordination : bond 0.00241 / 0.12 ( 4) metal coordination : angle 3.78312 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 312 TYR cc_start: 0.8102 (m-80) cc_final: 0.7884 (m-80) REVERT: A 447 GLN cc_start: 0.8829 (tp40) cc_final: 0.8433 (tm-30) REVERT: B 109 MET cc_start: 0.8825 (mpp) cc_final: 0.8598 (mpp) REVERT: B 132 GLN cc_start: 0.8827 (mt0) cc_final: 0.8616 (pm20) REVERT: B 230 ILE cc_start: 0.8434 (mm) cc_final: 0.8153 (mt) REVERT: B 343 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.8013 (mtp-110) REVERT: B 346 ASP cc_start: 0.8778 (m-30) cc_final: 0.8336 (m-30) REVERT: C 28 ASP cc_start: 0.8789 (m-30) cc_final: 0.8404 (m-30) REVERT: C 247 TYR cc_start: 0.9508 (m-80) cc_final: 0.9277 (m-80) REVERT: D 127 ASP cc_start: 0.8451 (m-30) cc_final: 0.8154 (m-30) REVERT: D 216 ASP cc_start: 0.8455 (m-30) cc_final: 0.8057 (m-30) REVERT: D 245 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7787 (mt-10) REVERT: E 57 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7248 (pt0) REVERT: F 42 ASN cc_start: 0.9139 (t0) cc_final: 0.8841 (t0) REVERT: F 64 GLU cc_start: 0.8462 (tp30) cc_final: 0.7816 (mm-30) REVERT: F 120 GLU cc_start: 0.8658 (tp30) cc_final: 0.8187 (tm-30) REVERT: F 126 VAL cc_start: 0.9159 (p) cc_final: 0.8827 (m) REVERT: G 83 GLU cc_start: 0.8294 (tp30) cc_final: 0.8013 (tp30) REVERT: H 211 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8403 (mtp180) REVERT: H 273 TYR cc_start: 0.7884 (m-80) cc_final: 0.6787 (m-80) REVERT: H 320 GLN cc_start: 0.9205 (mt0) cc_final: 0.8683 (mt0) REVERT: I 117 ASN cc_start: 0.7761 (t0) cc_final: 0.7425 (m-40) REVERT: I 176 ASP cc_start: 0.8337 (t0) cc_final: 0.7851 (t0) outliers start: 19 outliers final: 8 residues processed: 246 average time/residue: 0.6776 time to fit residues: 189.9852 Evaluate side-chains 209 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain I residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 497 ASN B 328 ASN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN E 154 ASN G 99 ASN I 57 GLN I 98 HIS I 126 GLN I 194 ASN I 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.067465 restraints weight = 42269.440| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.82 r_work: 0.2721 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22527 Z= 0.121 Angle : 0.529 8.052 30680 Z= 0.286 Chirality : 0.041 0.179 3527 Planarity : 0.004 0.048 3769 Dihedral : 12.074 175.966 3585 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 2.87 % Allowed : 22.10 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2784 helix: 1.75 (0.16), residues: 1061 sheet: 0.46 (0.25), residues: 402 loop : -0.64 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 303 TYR 0.015 0.001 TYR F 94 PHE 0.028 0.001 PHE A 325 TRP 0.017 0.001 TRP I 336 HIS 0.003 0.001 HIS I 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22523) covalent geometry : angle 0.52687 / 0.29 (30674) hydrogen bonds : bond 0.03938 / 2.61 ( 989) hydrogen bonds : angle 5.26428 / 3.84 ( 2808) metal coordination : bond 0.00388 / 0.19 ( 4) metal coordination : angle 3.37025 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.080 Fit side-chains REVERT: A 312 TYR cc_start: 0.8021 (m-80) cc_final: 0.7698 (m-80) REVERT: A 323 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8606 (ttt) REVERT: B 109 MET cc_start: 0.8742 (mpp) cc_final: 0.8504 (mpp) REVERT: B 132 GLN cc_start: 0.8876 (mt0) cc_final: 0.8629 (pm20) REVERT: B 230 ILE cc_start: 0.8106 (mm) cc_final: 0.7888 (tt) REVERT: B 346 ASP cc_start: 0.8670 (m-30) cc_final: 0.8317 (m-30) REVERT: C 28 ASP cc_start: 0.8729 (m-30) cc_final: 0.8196 (m-30) REVERT: C 35 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8434 (tpp-160) REVERT: C 141 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: C 247 TYR cc_start: 0.9326 (m-80) cc_final: 0.8899 (m-80) REVERT: D 127 ASP cc_start: 0.8379 (m-30) cc_final: 0.8150 (m-30) REVERT: D 216 ASP cc_start: 0.8481 (m-30) cc_final: 0.8052 (m-30) REVERT: D 245 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7890 (mt-10) REVERT: D 255 TYR cc_start: 0.9186 (p90) cc_final: 0.8966 (p90) REVERT: E 34 GLU cc_start: 0.8421 (tt0) cc_final: 0.8007 (tt0) REVERT: E 57 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7072 (tm-30) REVERT: F 42 ASN cc_start: 0.9099 (t0) cc_final: 0.8800 (t0) REVERT: F 50 ASN cc_start: 0.8746 (m110) cc_final: 0.8436 (m-40) REVERT: F 64 GLU cc_start: 0.8336 (tp30) cc_final: 0.7710 (mm-30) REVERT: F 120 GLU cc_start: 0.8550 (tp30) cc_final: 0.8187 (tm-30) REVERT: F 126 VAL cc_start: 0.9084 (p) cc_final: 0.8745 (m) REVERT: G 34 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8746 (ttmm) REVERT: G 35 GLU cc_start: 0.8961 (mp0) cc_final: 0.8563 (mp0) REVERT: G 83 GLU cc_start: 0.8417 (tp30) cc_final: 0.7854 (tp30) REVERT: H 137 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8165 (ttp80) REVERT: H 273 TYR cc_start: 0.7548 (m-80) cc_final: 0.6505 (m-80) REVERT: I 117 ASN cc_start: 0.7375 (t0) cc_final: 0.7018 (m-40) REVERT: I 176 ASP cc_start: 0.8129 (t0) cc_final: 0.7518 (t0) REVERT: I 212 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: I 302 TRP cc_start: 0.8430 (p-90) cc_final: 0.8200 (p-90) outliers start: 61 outliers final: 13 residues processed: 267 average time/residue: 0.6382 time to fit residues: 195.3587 Evaluate side-chains 207 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 263 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 20 optimal weight: 0.0170 chunk 182 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 7 ASN B 325 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN E 154 ASN G 99 ASN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.068008 restraints weight = 42360.415| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.78 r_work: 0.2744 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 22527 Z= 0.108 Angle : 0.499 11.531 30680 Z= 0.267 Chirality : 0.041 0.326 3527 Planarity : 0.004 0.049 3769 Dihedral : 11.885 176.360 3569 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.50 % Allowed : 23.09 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 2784 helix: 1.89 (0.16), residues: 1064 sheet: 0.45 (0.24), residues: 404 loop : -0.56 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.017 0.001 TYR E 247 PHE 0.027 0.001 PHE A 325 TRP 0.017 0.001 TRP I 336 HIS 0.007 0.001 HIS I 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22523) covalent geometry : angle 0.49681 / 0.27 (30674) hydrogen bonds : bond 0.03572 / 2.35 ( 989) hydrogen bonds : angle 4.94208 / 3.60 ( 2808) metal coordination : bond 0.00285 / 0.14 ( 4) metal coordination : angle 3.16959 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 1.068 Fit side-chains REVERT: A 62 SER cc_start: 0.9213 (m) cc_final: 0.8961 (p) REVERT: A 149 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7957 (mptp) REVERT: A 312 TYR cc_start: 0.7914 (m-80) cc_final: 0.7552 (m-80) REVERT: A 323 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8579 (ttt) REVERT: B 132 GLN cc_start: 0.8862 (mt0) cc_final: 0.8551 (pm20) REVERT: B 346 ASP cc_start: 0.8670 (m-30) cc_final: 0.8307 (m-30) REVERT: C 28 ASP cc_start: 0.8733 (m-30) cc_final: 0.8193 (m-30) REVERT: C 141 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8227 (mm-40) REVERT: C 247 TYR cc_start: 0.9326 (m-80) cc_final: 0.8927 (m-80) REVERT: D 216 ASP cc_start: 0.8505 (m-30) cc_final: 0.8042 (m-30) REVERT: D 245 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7859 (mt-10) REVERT: E 34 GLU cc_start: 0.8396 (tt0) cc_final: 0.8175 (tt0) REVERT: E 57 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7096 (tm-30) REVERT: E 173 GLU cc_start: 0.8965 (tp30) cc_final: 0.8407 (tp30) REVERT: F 35 GLU cc_start: 0.9094 (mp0) cc_final: 0.8834 (mm-30) REVERT: F 42 ASN cc_start: 0.9059 (t0) cc_final: 0.8741 (t0) REVERT: F 64 GLU cc_start: 0.8303 (tp30) cc_final: 0.7717 (mm-30) REVERT: F 120 GLU cc_start: 0.8543 (tp30) cc_final: 0.8150 (tm-30) REVERT: F 126 VAL cc_start: 0.9055 (p) cc_final: 0.8720 (m) REVERT: G 34 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8720 (ttmm) REVERT: G 35 GLU cc_start: 0.8936 (mp0) cc_final: 0.8645 (mp0) REVERT: G 83 GLU cc_start: 0.8403 (tp30) cc_final: 0.7796 (tp30) REVERT: H 100 GLN cc_start: 0.9187 (mt0) cc_final: 0.8400 (mp10) REVERT: H 137 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8185 (ttp80) REVERT: H 260 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8989 (p) REVERT: H 273 TYR cc_start: 0.7452 (m-80) cc_final: 0.6480 (m-80) REVERT: I 117 ASN cc_start: 0.7372 (t0) cc_final: 0.7001 (m-40) REVERT: I 157 ASN cc_start: 0.6251 (m-40) cc_final: 0.5715 (m110) REVERT: I 176 ASP cc_start: 0.8081 (t0) cc_final: 0.7467 (t0) REVERT: I 212 GLU cc_start: 0.8020 (tp30) cc_final: 0.7309 (tm-30) REVERT: I 290 ILE cc_start: 0.8400 (mt) cc_final: 0.8157 (tp) REVERT: I 302 TRP cc_start: 0.8562 (p-90) cc_final: 0.8281 (p-90) outliers start: 53 outliers final: 12 residues processed: 250 average time/residue: 0.6033 time to fit residues: 174.5784 Evaluate side-chains 207 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 39 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 277 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 151 ASN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN I 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.088275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.063734 restraints weight = 42872.090| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.81 r_work: 0.2645 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22527 Z= 0.227 Angle : 0.553 9.124 30680 Z= 0.293 Chirality : 0.043 0.194 3527 Planarity : 0.004 0.048 3769 Dihedral : 11.784 175.711 3569 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.96 % Allowed : 22.05 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2784 helix: 1.83 (0.16), residues: 1066 sheet: 0.40 (0.24), residues: 408 loop : -0.59 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 147 TYR 0.019 0.001 TYR F 94 PHE 0.031 0.002 PHE A 325 TRP 0.019 0.001 TRP I 336 HIS 0.006 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (22523) covalent geometry : angle 0.55113 / 0.29 (30674) hydrogen bonds : bond 0.03859 / 2.54 ( 989) hydrogen bonds : angle 4.77878 / 3.50 ( 2808) metal coordination : bond 0.00822 / 0.41 ( 4) metal coordination : angle 3.64045 / 2.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 196 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9268 (m) cc_final: 0.8944 (p) REVERT: A 312 TYR cc_start: 0.8005 (m-80) cc_final: 0.7672 (m-80) REVERT: A 323 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8779 (ttt) REVERT: A 395 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (tttp) REVERT: B 132 GLN cc_start: 0.8914 (mt0) cc_final: 0.8546 (pm20) REVERT: B 230 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7935 (pt) REVERT: B 310 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8573 (mtt180) REVERT: B 346 ASP cc_start: 0.8763 (m-30) cc_final: 0.8354 (m-30) REVERT: C 28 ASP cc_start: 0.8641 (m-30) cc_final: 0.8108 (m-30) REVERT: C 247 TYR cc_start: 0.9370 (m-80) cc_final: 0.9053 (m-80) REVERT: C 295 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: D 245 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7972 (mt-10) REVERT: E 3 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: E 57 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7215 (tm-30) REVERT: E 169 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8234 (ttt90) REVERT: F 42 ASN cc_start: 0.9126 (t0) cc_final: 0.8863 (t0) REVERT: F 120 GLU cc_start: 0.8616 (tp30) cc_final: 0.8228 (tm-30) REVERT: G 34 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8783 (ttmm) REVERT: G 35 GLU cc_start: 0.8919 (mp0) cc_final: 0.8614 (mp0) REVERT: G 83 GLU cc_start: 0.8540 (tp30) cc_final: 0.8129 (tm-30) REVERT: H 137 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8209 (ttp80) REVERT: H 211 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7994 (ttp-170) REVERT: H 260 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9012 (p) REVERT: H 273 TYR cc_start: 0.7725 (m-80) cc_final: 0.6623 (m-80) REVERT: I 117 ASN cc_start: 0.7376 (t0) cc_final: 0.7008 (m-40) REVERT: I 157 ASN cc_start: 0.6521 (m-40) cc_final: 0.5976 (m110) REVERT: I 176 ASP cc_start: 0.8098 (t0) cc_final: 0.7484 (t0) REVERT: I 212 GLU cc_start: 0.8197 (tp30) cc_final: 0.7485 (tm-30) REVERT: I 290 ILE cc_start: 0.8504 (mt) cc_final: 0.8192 (tp) REVERT: I 302 TRP cc_start: 0.8516 (p-90) cc_final: 0.8300 (p-90) outliers start: 84 outliers final: 24 residues processed: 264 average time/residue: 0.6506 time to fit residues: 196.3996 Evaluate side-chains 209 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 340 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 225 optimal weight: 0.1980 chunk 251 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 325 GLN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN I 57 GLN I 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.065425 restraints weight = 42493.883| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.77 r_work: 0.2682 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22527 Z= 0.125 Angle : 0.502 8.412 30680 Z= 0.265 Chirality : 0.041 0.179 3527 Planarity : 0.003 0.048 3769 Dihedral : 11.767 175.998 3569 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.73 % Allowed : 23.70 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2784 helix: 1.90 (0.16), residues: 1068 sheet: 0.55 (0.24), residues: 398 loop : -0.54 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.022 0.001 TYR E 247 PHE 0.029 0.001 PHE A 325 TRP 0.011 0.001 TRP G 84 HIS 0.004 0.001 HIS I 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22523) covalent geometry : angle 0.50041 / 0.27 (30674) hydrogen bonds : bond 0.03397 / 2.23 ( 989) hydrogen bonds : angle 4.62036 / 3.38 ( 2808) metal coordination : bond 0.00464 / 0.23 ( 4) metal coordination : angle 2.91985 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9230 (m) cc_final: 0.8893 (p) REVERT: A 312 TYR cc_start: 0.7889 (m-80) cc_final: 0.7523 (m-80) REVERT: A 323 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8773 (ttt) REVERT: B 132 GLN cc_start: 0.8878 (mt0) cc_final: 0.8611 (pm20) REVERT: B 230 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7785 (pt) REVERT: B 310 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.7957 (mtm180) REVERT: B 346 ASP cc_start: 0.8730 (m-30) cc_final: 0.8372 (m-30) REVERT: C 28 ASP cc_start: 0.8626 (m-30) cc_final: 0.8060 (m-30) REVERT: C 99 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8205 (mpt-90) REVERT: C 141 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8199 (mm110) REVERT: C 247 TYR cc_start: 0.9366 (m-80) cc_final: 0.9083 (m-80) REVERT: D 63 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8656 (tttm) REVERT: D 245 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7989 (mt-10) REVERT: E 3 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: E 38 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: E 57 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7182 (tm-30) REVERT: E 169 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8357 (ttt90) REVERT: E 173 GLU cc_start: 0.8995 (tp30) cc_final: 0.8376 (tp30) REVERT: F 42 ASN cc_start: 0.9077 (t0) cc_final: 0.8803 (t0) REVERT: F 120 GLU cc_start: 0.8569 (tp30) cc_final: 0.8178 (tm-30) REVERT: G 34 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8754 (ttmm) REVERT: G 35 GLU cc_start: 0.8902 (mp0) cc_final: 0.8627 (mp0) REVERT: G 83 GLU cc_start: 0.8585 (tp30) cc_final: 0.7967 (tp30) REVERT: G 120 GLU cc_start: 0.8986 (tp30) cc_final: 0.8750 (tp30) REVERT: H 100 GLN cc_start: 0.9186 (mt0) cc_final: 0.8403 (mp10) REVERT: H 137 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8250 (ttp80) REVERT: H 211 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: H 260 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9048 (p) REVERT: H 273 TYR cc_start: 0.7618 (m-80) cc_final: 0.6571 (m-80) REVERT: I 117 ASN cc_start: 0.7381 (t0) cc_final: 0.6992 (m-40) REVERT: I 157 ASN cc_start: 0.6437 (m-40) cc_final: 0.5908 (m110) REVERT: I 176 ASP cc_start: 0.8073 (t0) cc_final: 0.7449 (t0) REVERT: I 212 GLU cc_start: 0.8195 (tp30) cc_final: 0.7550 (tm-30) REVERT: I 290 ILE cc_start: 0.8563 (mt) cc_final: 0.8279 (tp) REVERT: I 302 TRP cc_start: 0.8536 (p-90) cc_final: 0.8262 (p-90) outliers start: 58 outliers final: 22 residues processed: 245 average time/residue: 0.6058 time to fit residues: 170.9665 Evaluate side-chains 229 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 261 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 210 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 277 optimal weight: 0.2980 chunk 9 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS I 203 ASN I 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.064717 restraints weight = 42667.903| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.78 r_work: 0.2667 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22527 Z= 0.153 Angle : 0.500 7.339 30680 Z= 0.264 Chirality : 0.041 0.179 3527 Planarity : 0.003 0.048 3769 Dihedral : 11.724 175.953 3569 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.78 % Allowed : 23.85 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2784 helix: 1.92 (0.16), residues: 1067 sheet: 0.58 (0.24), residues: 401 loop : -0.54 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 331 TYR 0.015 0.001 TYR F 94 PHE 0.028 0.001 PHE A 325 TRP 0.010 0.001 TRP G 84 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (22523) covalent geometry : angle 0.49843 / 0.26 (30674) hydrogen bonds : bond 0.03404 / 2.23 ( 989) hydrogen bonds : angle 4.55324 / 3.33 ( 2808) metal coordination : bond 0.00578 / 0.29 ( 4) metal coordination : angle 3.04469 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9246 (m) cc_final: 0.8881 (p) REVERT: A 312 TYR cc_start: 0.7899 (m-80) cc_final: 0.7568 (m-80) REVERT: A 323 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (ttt) REVERT: B 132 GLN cc_start: 0.8886 (mt0) cc_final: 0.8605 (pm20) REVERT: B 230 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7779 (pt) REVERT: B 310 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.7914 (mtm180) REVERT: B 346 ASP cc_start: 0.8792 (m-30) cc_final: 0.8432 (m-30) REVERT: C 6 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8593 (mtp85) REVERT: C 33 ARG cc_start: 0.9005 (mtt-85) cc_final: 0.8619 (mtt-85) REVERT: C 99 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8315 (mtt-85) REVERT: C 247 TYR cc_start: 0.9368 (m-80) cc_final: 0.9071 (m-80) REVERT: D 63 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8627 (tttm) REVERT: D 245 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7963 (mt-10) REVERT: E 3 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8770 (mttt) REVERT: E 57 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7201 (tm-30) REVERT: E 169 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (ttt90) REVERT: F 42 ASN cc_start: 0.9077 (t0) cc_final: 0.8800 (t0) REVERT: F 83 GLU cc_start: 0.8680 (tt0) cc_final: 0.8083 (tp30) REVERT: F 87 GLN cc_start: 0.8163 (pt0) cc_final: 0.7627 (pt0) REVERT: F 120 GLU cc_start: 0.8635 (tp30) cc_final: 0.8393 (tt0) REVERT: G 34 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: G 35 GLU cc_start: 0.8895 (mp0) cc_final: 0.8605 (mp0) REVERT: G 83 GLU cc_start: 0.8571 (tp30) cc_final: 0.7940 (tp30) REVERT: G 120 GLU cc_start: 0.8957 (tp30) cc_final: 0.8695 (tp30) REVERT: H 100 GLN cc_start: 0.9182 (mt0) cc_final: 0.8389 (mp10) REVERT: H 137 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8264 (ttp80) REVERT: H 211 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7944 (ttp-170) REVERT: H 260 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9051 (p) REVERT: H 273 TYR cc_start: 0.7627 (m-80) cc_final: 0.6727 (m-80) REVERT: I 117 ASN cc_start: 0.7373 (t0) cc_final: 0.6991 (m-40) REVERT: I 157 ASN cc_start: 0.6409 (m-40) cc_final: 0.5934 (m110) REVERT: I 176 ASP cc_start: 0.8064 (t0) cc_final: 0.7431 (t0) REVERT: I 212 GLU cc_start: 0.8272 (tp30) cc_final: 0.7606 (tm-30) REVERT: I 290 ILE cc_start: 0.8505 (mt) cc_final: 0.8277 (tp) REVERT: I 302 TRP cc_start: 0.8582 (p-90) cc_final: 0.8342 (p-90) outliers start: 59 outliers final: 24 residues processed: 244 average time/residue: 0.6304 time to fit residues: 176.1777 Evaluate side-chains 213 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 25 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 325 GLN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN I 57 GLN I 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.065097 restraints weight = 42435.516| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.78 r_work: 0.2675 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22527 Z= 0.131 Angle : 0.494 7.410 30680 Z= 0.262 Chirality : 0.041 0.177 3527 Planarity : 0.003 0.056 3769 Dihedral : 11.676 176.128 3568 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.69 % Allowed : 24.60 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2784 helix: 1.94 (0.16), residues: 1068 sheet: 0.59 (0.24), residues: 405 loop : -0.52 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 66 TYR 0.016 0.001 TYR E 247 PHE 0.027 0.001 PHE A 325 TRP 0.010 0.001 TRP G 84 HIS 0.003 0.001 HIS I 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22523) covalent geometry : angle 0.49260 / 0.26 (30674) hydrogen bonds : bond 0.03287 / 2.16 ( 989) hydrogen bonds : angle 4.50233 / 3.29 ( 2808) metal coordination : bond 0.00493 / 0.25 ( 4) metal coordination : angle 2.94299 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9192 (m) cc_final: 0.8846 (p) REVERT: A 312 TYR cc_start: 0.7865 (m-80) cc_final: 0.7505 (m-80) REVERT: A 323 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8772 (ttt) REVERT: B 132 GLN cc_start: 0.8899 (mt0) cc_final: 0.8605 (pm20) REVERT: B 230 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7813 (pt) REVERT: B 310 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.7956 (mtm180) REVERT: B 346 ASP cc_start: 0.8777 (m-30) cc_final: 0.8439 (m-30) REVERT: C 99 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8180 (mpt-90) REVERT: C 141 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: C 247 TYR cc_start: 0.9332 (m-80) cc_final: 0.9051 (m-80) REVERT: D 63 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8636 (tttm) REVERT: D 245 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 3 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8764 (mttt) REVERT: E 57 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7190 (tm-30) REVERT: E 122 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: E 169 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8322 (ttt90) REVERT: E 173 GLU cc_start: 0.8990 (tp30) cc_final: 0.8346 (tp30) REVERT: F 42 ASN cc_start: 0.9066 (t0) cc_final: 0.8772 (t0) REVERT: F 83 GLU cc_start: 0.8651 (tt0) cc_final: 0.8086 (tp30) REVERT: F 87 GLN cc_start: 0.8163 (pt0) cc_final: 0.7622 (pt0) REVERT: F 120 GLU cc_start: 0.8692 (tp30) cc_final: 0.8432 (tt0) REVERT: G 34 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (ttmm) REVERT: G 35 GLU cc_start: 0.8885 (mp0) cc_final: 0.8598 (mp0) REVERT: G 83 GLU cc_start: 0.8560 (tp30) cc_final: 0.7925 (tp30) REVERT: G 108 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: G 120 GLU cc_start: 0.8945 (tp30) cc_final: 0.8698 (tp30) REVERT: H 100 GLN cc_start: 0.9182 (mt0) cc_final: 0.8391 (mp10) REVERT: H 137 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8273 (ttp80) REVERT: H 211 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: H 260 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9061 (p) REVERT: H 273 TYR cc_start: 0.7623 (m-80) cc_final: 0.6615 (m-80) REVERT: I 117 ASN cc_start: 0.7393 (t0) cc_final: 0.7012 (m-40) REVERT: I 157 ASN cc_start: 0.6457 (m-40) cc_final: 0.5996 (m110) REVERT: I 176 ASP cc_start: 0.8054 (t0) cc_final: 0.7425 (t0) REVERT: I 212 GLU cc_start: 0.8379 (tp30) cc_final: 0.7679 (tm-30) REVERT: I 290 ILE cc_start: 0.8513 (mt) cc_final: 0.8279 (tp) REVERT: I 302 TRP cc_start: 0.8589 (p-90) cc_final: 0.8334 (p-90) outliers start: 57 outliers final: 27 residues processed: 236 average time/residue: 0.6303 time to fit residues: 170.3306 Evaluate side-chains 229 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 218 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN H 263 GLN I 203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.065892 restraints weight = 42378.408| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.77 r_work: 0.2671 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22527 Z= 0.146 Angle : 0.500 8.425 30680 Z= 0.265 Chirality : 0.041 0.180 3527 Planarity : 0.004 0.053 3769 Dihedral : 11.654 176.112 3568 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.69 % Allowed : 24.74 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 2784 helix: 1.94 (0.16), residues: 1067 sheet: 0.62 (0.24), residues: 405 loop : -0.51 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 66 TYR 0.024 0.001 TYR E 247 PHE 0.028 0.001 PHE A 325 TRP 0.010 0.001 TRP G 84 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22523) covalent geometry : angle 0.49835 / 0.27 (30674) hydrogen bonds : bond 0.03292 / 2.16 ( 989) hydrogen bonds : angle 4.48395 / 3.27 ( 2808) metal coordination : bond 0.00561 / 0.28 ( 4) metal coordination : angle 2.99309 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9188 (m) cc_final: 0.8834 (p) REVERT: A 312 TYR cc_start: 0.7871 (m-80) cc_final: 0.7504 (m-80) REVERT: A 323 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8746 (ttt) REVERT: B 132 GLN cc_start: 0.8880 (mt0) cc_final: 0.8595 (pm20) REVERT: B 230 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7787 (pt) REVERT: B 346 ASP cc_start: 0.8785 (m-30) cc_final: 0.8464 (m-30) REVERT: C 6 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8612 (mtp85) REVERT: C 33 ARG cc_start: 0.9016 (mtt-85) cc_final: 0.8654 (mtt-85) REVERT: C 99 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: C 141 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8173 (mm-40) REVERT: C 247 TYR cc_start: 0.9339 (m-80) cc_final: 0.9047 (m-80) REVERT: D 63 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (tttm) REVERT: D 245 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7984 (mt-10) REVERT: E 57 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7199 (tm-30) REVERT: E 122 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 169 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (ttt90) REVERT: E 173 GLU cc_start: 0.8993 (tp30) cc_final: 0.8349 (tp30) REVERT: F 42 ASN cc_start: 0.9077 (t0) cc_final: 0.8802 (t0) REVERT: F 83 GLU cc_start: 0.8643 (tt0) cc_final: 0.8072 (tp30) REVERT: F 87 GLN cc_start: 0.8242 (pt0) cc_final: 0.7551 (pt0) REVERT: F 120 GLU cc_start: 0.8684 (tp30) cc_final: 0.8395 (tt0) REVERT: G 34 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8750 (ttmm) REVERT: G 35 GLU cc_start: 0.8887 (mp0) cc_final: 0.8601 (mp0) REVERT: G 70 SER cc_start: 0.9167 (p) cc_final: 0.8804 (m) REVERT: G 83 GLU cc_start: 0.8558 (tp30) cc_final: 0.7920 (tp30) REVERT: G 108 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: G 120 GLU cc_start: 0.8970 (tp30) cc_final: 0.8727 (tp30) REVERT: H 100 GLN cc_start: 0.9178 (mt0) cc_final: 0.8386 (mp10) REVERT: H 137 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8291 (ttp80) REVERT: H 211 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7945 (ttp-170) REVERT: H 260 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9065 (p) REVERT: H 273 TYR cc_start: 0.7606 (m-80) cc_final: 0.6773 (m-80) REVERT: I 117 ASN cc_start: 0.7396 (t0) cc_final: 0.7012 (m-40) REVERT: I 157 ASN cc_start: 0.6461 (m-40) cc_final: 0.6018 (m110) REVERT: I 176 ASP cc_start: 0.8032 (t0) cc_final: 0.7385 (t0) REVERT: I 212 GLU cc_start: 0.8331 (tp30) cc_final: 0.7653 (tm-30) REVERT: I 247 ASN cc_start: 0.8619 (m-40) cc_final: 0.8121 (t0) REVERT: I 290 ILE cc_start: 0.8505 (mt) cc_final: 0.8277 (tp) REVERT: I 302 TRP cc_start: 0.8580 (p-90) cc_final: 0.8349 (p-90) outliers start: 57 outliers final: 30 residues processed: 241 average time/residue: 0.6777 time to fit residues: 185.7626 Evaluate side-chains 226 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 131 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 497 ASN B 325 GLN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN I 57 GLN I 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.063384 restraints weight = 42816.333| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.77 r_work: 0.2648 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22527 Z= 0.207 Angle : 0.533 7.076 30680 Z= 0.282 Chirality : 0.043 0.186 3527 Planarity : 0.004 0.049 3769 Dihedral : 11.656 175.697 3568 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.31 % Allowed : 25.49 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2784 helix: 1.86 (0.16), residues: 1068 sheet: 0.60 (0.24), residues: 406 loop : -0.54 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 66 TYR 0.021 0.001 TYR G 39 PHE 0.030 0.002 PHE A 325 TRP 0.009 0.001 TRP G 84 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (22523) covalent geometry : angle 0.53128 / 0.28 (30674) hydrogen bonds : bond 0.03548 / 2.34 ( 989) hydrogen bonds : angle 4.52986 / 3.31 ( 2808) metal coordination : bond 0.00817 / 0.41 ( 4) metal coordination : angle 3.20491 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9217 (m) cc_final: 0.8832 (p) REVERT: A 312 TYR cc_start: 0.7941 (m-80) cc_final: 0.7579 (m-80) REVERT: A 323 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8842 (ttt) REVERT: A 395 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8535 (tttp) REVERT: B 132 GLN cc_start: 0.8890 (mt0) cc_final: 0.8603 (pm20) REVERT: B 230 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (pt) REVERT: B 346 ASP cc_start: 0.8810 (m-30) cc_final: 0.8467 (m-30) REVERT: C 99 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8394 (mtt-85) REVERT: C 247 TYR cc_start: 0.9389 (m-80) cc_final: 0.9132 (m-80) REVERT: D 63 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8640 (tttm) REVERT: D 245 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8124 (mt-10) REVERT: E 57 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7215 (tm-30) REVERT: E 169 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8276 (ttt90) REVERT: F 42 ASN cc_start: 0.9079 (t0) cc_final: 0.8799 (t0) REVERT: F 64 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: F 83 GLU cc_start: 0.8680 (tt0) cc_final: 0.8119 (tp30) REVERT: F 87 GLN cc_start: 0.8250 (pt0) cc_final: 0.7582 (pt0) REVERT: F 120 GLU cc_start: 0.8706 (tp30) cc_final: 0.8372 (tt0) REVERT: F 133 GLU cc_start: 0.8640 (mp0) cc_final: 0.8287 (mp0) REVERT: G 34 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8796 (ttmm) REVERT: G 35 GLU cc_start: 0.8899 (mp0) cc_final: 0.8598 (mp0) REVERT: G 70 SER cc_start: 0.9149 (p) cc_final: 0.8798 (m) REVERT: G 83 GLU cc_start: 0.8575 (tp30) cc_final: 0.8087 (tm-30) REVERT: G 120 GLU cc_start: 0.8986 (tp30) cc_final: 0.8746 (tp30) REVERT: H 100 GLN cc_start: 0.9189 (mt0) cc_final: 0.8384 (mp10) REVERT: H 137 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8305 (ttp80) REVERT: H 211 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7932 (ttp-170) REVERT: H 260 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9060 (p) REVERT: H 273 TYR cc_start: 0.7728 (m-80) cc_final: 0.6842 (m-80) REVERT: I 117 ASN cc_start: 0.7427 (t0) cc_final: 0.7042 (m-40) REVERT: I 157 ASN cc_start: 0.6532 (m-40) cc_final: 0.5967 (m110) REVERT: I 176 ASP cc_start: 0.8028 (t0) cc_final: 0.7374 (t0) REVERT: I 212 GLU cc_start: 0.8397 (tp30) cc_final: 0.7625 (tm-30) REVERT: I 247 ASN cc_start: 0.8623 (m-40) cc_final: 0.8156 (t0) REVERT: I 290 ILE cc_start: 0.8518 (mt) cc_final: 0.8298 (tp) REVERT: I 302 TRP cc_start: 0.8585 (p-90) cc_final: 0.8332 (p-90) outliers start: 49 outliers final: 28 residues processed: 228 average time/residue: 0.6242 time to fit residues: 163.7580 Evaluate side-chains 223 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 267 optimal weight: 8.9990 chunk 208 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 225 optimal weight: 0.0670 chunk 190 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 497 ASN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 99 ASN H 263 GLN I 57 GLN I 203 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.065292 restraints weight = 42516.841| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.79 r_work: 0.2679 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22527 Z= 0.115 Angle : 0.500 7.409 30680 Z= 0.266 Chirality : 0.041 0.171 3527 Planarity : 0.003 0.048 3769 Dihedral : 11.618 176.102 3568 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.84 % Allowed : 26.20 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2784 helix: 1.95 (0.16), residues: 1064 sheet: 0.62 (0.24), residues: 406 loop : -0.49 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 66 TYR 0.022 0.001 TYR G 39 PHE 0.028 0.001 PHE A 325 TRP 0.012 0.001 TRP G 84 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22523) covalent geometry : angle 0.49860 / 0.27 (30674) hydrogen bonds : bond 0.03217 / 2.12 ( 989) hydrogen bonds : angle 4.43207 / 3.23 ( 2808) metal coordination : bond 0.00452 / 0.23 ( 4) metal coordination : angle 2.89596 / 1.64 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 62 SER cc_start: 0.9162 (m) cc_final: 0.8794 (p) REVERT: A 312 TYR cc_start: 0.7848 (m-80) cc_final: 0.7437 (m-80) REVERT: A 323 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8787 (ttt) REVERT: B 132 GLN cc_start: 0.8859 (mt0) cc_final: 0.8576 (pm20) REVERT: B 230 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7776 (pt) REVERT: B 346 ASP cc_start: 0.8801 (m-30) cc_final: 0.8473 (m-30) REVERT: C 6 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8647 (mtp85) REVERT: C 33 ARG cc_start: 0.8945 (mtt-85) cc_final: 0.8595 (mtt-85) REVERT: C 99 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8361 (mtt-85) REVERT: C 247 TYR cc_start: 0.9326 (m-80) cc_final: 0.9049 (m-80) REVERT: D 63 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8604 (tttm) REVERT: D 245 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8006 (mt-10) REVERT: E 57 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7194 (tm-30) REVERT: E 173 GLU cc_start: 0.8984 (tp30) cc_final: 0.8355 (tp30) REVERT: F 42 ASN cc_start: 0.9040 (t0) cc_final: 0.8711 (t0) REVERT: F 83 GLU cc_start: 0.8644 (tt0) cc_final: 0.8219 (tp30) REVERT: F 120 GLU cc_start: 0.8685 (tp30) cc_final: 0.8371 (tt0) REVERT: F 133 GLU cc_start: 0.8587 (mp0) cc_final: 0.8375 (mp0) REVERT: G 34 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8735 (ttmm) REVERT: G 35 GLU cc_start: 0.8885 (mp0) cc_final: 0.8613 (mp0) REVERT: G 70 SER cc_start: 0.9133 (p) cc_final: 0.8794 (m) REVERT: G 83 GLU cc_start: 0.8533 (tp30) cc_final: 0.7895 (tp30) REVERT: G 120 GLU cc_start: 0.8949 (tp30) cc_final: 0.8705 (tp30) REVERT: H 100 GLN cc_start: 0.9176 (mt0) cc_final: 0.8392 (mp10) REVERT: H 137 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8287 (ttp80) REVERT: H 211 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7923 (ttp-170) REVERT: H 260 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9077 (p) REVERT: H 273 TYR cc_start: 0.7592 (m-80) cc_final: 0.6831 (m-80) REVERT: I 117 ASN cc_start: 0.7426 (t0) cc_final: 0.7032 (m-40) REVERT: I 157 ASN cc_start: 0.6451 (m-40) cc_final: 0.5882 (m110) REVERT: I 176 ASP cc_start: 0.7986 (t0) cc_final: 0.7317 (t0) REVERT: I 212 GLU cc_start: 0.8404 (tp30) cc_final: 0.7803 (tm-30) REVERT: I 247 ASN cc_start: 0.8570 (m-40) cc_final: 0.8084 (t0) REVERT: I 290 ILE cc_start: 0.8494 (mt) cc_final: 0.8283 (tp) REVERT: I 302 TRP cc_start: 0.8572 (p-90) cc_final: 0.8359 (p-90) outliers start: 39 outliers final: 24 residues processed: 232 average time/residue: 0.6576 time to fit residues: 174.0214 Evaluate side-chains 218 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 221 optimal weight: 1.9990 chunk 214 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 497 ASN B 325 GLN B 330 GLN B 333 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN I 57 GLN I 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.088962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.064744 restraints weight = 43152.972| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.79 r_work: 0.2650 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22527 Z= 0.184 Angle : 0.524 10.198 30680 Z= 0.276 Chirality : 0.042 0.188 3527 Planarity : 0.004 0.050 3769 Dihedral : 11.596 175.913 3568 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.03 % Allowed : 25.92 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2784 helix: 1.87 (0.16), residues: 1072 sheet: 0.60 (0.24), residues: 406 loop : -0.51 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 331 TYR 0.023 0.001 TYR G 39 PHE 0.030 0.001 PHE A 325 TRP 0.010 0.001 TRP G 84 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (22523) covalent geometry : angle 0.52244 / 0.28 (30674) hydrogen bonds : bond 0.03426 / 2.26 ( 989) hydrogen bonds : angle 4.46575 / 3.26 ( 2808) metal coordination : bond 0.00695 / 0.35 ( 4) metal coordination : angle 3.17211 / 1.81 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.87 seconds wall clock time: 99 minutes 38.88 seconds (5978.88 seconds total)