Starting phenix.real_space_refine on Fri Feb 6 19:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.map" model { file = "/net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9laz_62933/02_2026/9laz_62933.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 33 7.16 5 P 15 5.49 5 S 186 5.16 5 C 17503 2.51 5 N 4722 2.21 5 O 5010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27469 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "C" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "D" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "E" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "F" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4948 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 28, 'TRANS': 602} Chain: "H" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1929 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain: "I" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1927 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'HEM': 2, 'LMT': 2, 'PEV': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 272 Unusual residues: {'HEM': 2, 'LMT': 2, 'PEV': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SIN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 276 Unusual residues: {'HEM': 2, 'LMT': 2, 'PEV': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 162 40.081 49.257 62.304 1.00 14.04 S ATOM 6166 SG CYS B 159 44.777 53.781 61.528 1.00 14.93 S ATOM 6628 SG CYS B 224 45.481 48.510 65.265 1.00 5.30 S ATOM 6199 SG CYS B 165 41.176 53.313 66.832 1.00 7.56 S ATOM 5481 SG CYS B 66 35.362 44.278 56.517 1.00 42.16 S ATOM 5606 SG CYS B 84 38.209 42.491 55.812 1.00 14.04 S ATOM 5425 SG CYS B 58 39.608 45.508 52.200 1.00 11.44 S ATOM 5463 SG CYS B 63 37.850 48.570 53.107 1.00 16.85 S ATOM 6222 SG CYS B 169 39.086 54.245 74.861 1.00 17.01 S ATOM 6605 SG CYS B 220 44.132 51.592 72.275 1.00 13.99 S ATOM 6563 SG CYS B 214 45.054 56.301 76.189 1.00 9.64 S ATOM 14988 SG CYS E 162 99.348 52.310 62.333 1.00 15.58 S ATOM 15432 SG CYS E 224 97.146 57.423 65.243 1.00 10.61 S ATOM 15003 SG CYS E 165 95.261 51.244 66.861 1.00 9.02 S ATOM 14970 SG CYS E 159 93.087 54.098 61.526 1.00 19.17 S ATOM 14229 SG CYS E 58 102.908 53.924 52.342 1.00 13.76 S ATOM 14267 SG CYS E 63 101.161 50.902 53.018 1.00 14.62 S ATOM 14285 SG CYS E 66 104.979 51.588 58.001 1.00 21.18 S ATOM 14410 SG CYS E 84 106.116 54.035 55.801 1.00 14.19 S ATOM 15026 SG CYS E 169 95.517 48.999 74.803 1.00 18.30 S ATOM 15409 SG CYS E 220 95.166 54.937 72.469 1.00 17.58 S ATOM 15367 SG CYS E 214 90.756 53.108 76.241 1.00 10.21 S ATOM 23774 SG CYS H 159 68.615 95.771 61.519 1.00 16.21 S ATOM 23792 SG CYS H 162 67.055 102.108 62.306 1.00 10.87 S ATOM 23807 SG CYS H 165 69.998 99.123 66.872 1.00 9.94 S ATOM 24236 SG CYS H 224 63.751 97.661 65.255 1.00 7.35 S ATOM 23089 SG CYS H 66 64.952 107.336 57.883 1.00 20.21 S ATOM 23214 SG CYS H 84 62.185 107.116 55.799 1.00 15.59 S ATOM 23033 SG CYS H 58 64.068 104.338 52.324 1.00 14.44 S ATOM 23071 SG CYS H 63 67.554 104.338 52.980 1.00 11.90 S ATOM 24213 SG CYS H 220 66.932 97.140 72.390 1.00 19.16 S ATOM 24171 SG CYS H 214 70.656 94.226 76.316 1.00 12.85 S ATOM 23830 SG CYS H 169 71.772 100.438 74.815 1.00 20.26 S Time building chain proxies: 6.75, per 1000 atoms: 0.25 Number of scatterers: 27469 At special positions: 0 Unit cell: (142.29, 143.22, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 33 26.01 S 186 16.00 P 15 15.00 O 5010 8.00 N 4722 7.00 C 17503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 169 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 214 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 220 " pdb=" F3S E 303 " pdb="FE1 F3S E 303 " - pdb=" SG CYS E 169 " pdb="FE3 F3S E 303 " - pdb=" SG CYS E 220 " pdb="FE4 F3S E 303 " - pdb=" SG CYS E 214 " pdb=" F3S H 303 " pdb="FE4 F3S H 303 " - pdb=" SG CYS H 169 " pdb="FE3 F3S H 303 " - pdb=" SG CYS H 214 " pdb="FE1 F3S H 303 " - pdb=" SG CYS H 220 " pdb=" FES B 302 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 66 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 63 " pdb="FE2 FES B 302 " - pdb=" SG CYS B 58 " pdb="FE1 FES B 302 " - pdb=" SG CYS B 84 " pdb=" FES E 302 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 63 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 66 " pdb="FE1 FES E 302 " - pdb=" SG CYS E 58 " pdb="FE2 FES E 302 " - pdb=" SG CYS E 84 " pdb=" FES H 302 " pdb="FE2 FES H 302 " - pdb=" SG CYS H 63 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 66 " pdb="FE2 FES H 302 " - pdb=" SG CYS H 58 " pdb="FE1 FES H 302 " - pdb=" SG CYS H 84 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 159 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 165 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 224 " pdb=" SF4 E 301 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 162 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 159 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 224 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 165 " pdb=" SF4 H 301 " pdb="FE2 SF4 H 301 " - pdb=" SG CYS H 162 " pdb="FE3 SF4 H 301 " - pdb=" SG CYS H 165 " pdb="FE1 SF4 H 301 " - pdb=" SG CYS H 159 " pdb="FE4 SF4 H 301 " - pdb=" SG CYS H 224 " Number of angles added : 81 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6138 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 51.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.915A pdb=" N ARG A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 87 through 96 removed outlier: 6.248A pdb=" N HIS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER A 93 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 129 through 150 removed outlier: 4.710A pdb=" N VAL A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.729A pdb=" N PHE A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.838A pdb=" N LEU A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 386 through 406 removed outlier: 7.080A pdb=" N ASN A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 removed outlier: 3.862A pdb=" N ASN A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.927A pdb=" N HIS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 452 " --> pdb=" O SER A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.791A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 492 through 512 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 538 through 559 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.681A pdb=" N GLU A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 117 through 126 removed outlier: 3.894A pdb=" N ASP B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.779A pdb=" N VAL B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'C' and resid 2 through 9 removed outlier: 4.172A pdb=" N LEU C 5 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 8 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.832A pdb=" N ARG C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 98 removed outlier: 4.169A pdb=" N ALA C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 171 through 200 removed outlier: 4.853A pdb=" N TRP C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 235 removed outlier: 4.496A pdb=" N ARG C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 49 through 53 removed outlier: 3.880A pdb=" N ARG D 52 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 129 through 150 removed outlier: 4.697A pdb=" N VAL D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 200 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.710A pdb=" N PHE D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.741A pdb=" N ARG D 308 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 349 through 364 Processing helix chain 'D' and resid 378 through 385 Processing helix chain 'D' and resid 386 through 406 removed outlier: 7.025A pdb=" N ASN D 396 " --> pdb=" O GLU D 392 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 447 removed outlier: 3.868A pdb=" N ASN D 447 " --> pdb=" O GLY D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 458 through 471 removed outlier: 3.882A pdb=" N MET D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 482 removed outlier: 3.665A pdb=" N ALA D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 512 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 538 through 559 Proline residue: D 550 - end of helix Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.709A pdb=" N GLU D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU D 587 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 48 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.913A pdb=" N ASP E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 174 through 187 Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 194 through 210 removed outlier: 3.833A pdb=" N VAL E 200 " --> pdb=" O TYR E 196 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 230 through 246 Processing helix chain 'F' and resid 2 through 9 removed outlier: 4.053A pdb=" N LEU F 5 " --> pdb=" O THR F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 37 Processing helix chain 'F' and resid 38 through 41 Processing helix chain 'F' and resid 42 through 55 removed outlier: 3.772A pdb=" N ARG F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 98 removed outlier: 3.732A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 139 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 171 through 200 removed outlier: 4.852A pdb=" N TRP F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE F 197 " --> pdb=" O VAL F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 235 removed outlier: 4.515A pdb=" N ARG F 209 " --> pdb=" O ARG F 205 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU F 210 " --> pdb=" O THR F 206 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'G' and resid 34 through 43 Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.883A pdb=" N ARG G 52 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 Processing helix chain 'G' and resid 87 through 96 removed outlier: 3.730A pdb=" N ALA G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER G 93 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 129 through 150 removed outlier: 4.714A pdb=" N VAL G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 200 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.723A pdb=" N PHE G 253 " --> pdb=" O GLY G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 304 through 310 removed outlier: 3.704A pdb=" N ARG G 308 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP G 310 " --> pdb=" O LEU G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 349 through 364 removed outlier: 3.516A pdb=" N GLY G 364 " --> pdb=" O VAL G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 385 Processing helix chain 'G' and resid 386 through 406 removed outlier: 6.931A pdb=" N ASN G 396 " --> pdb=" O GLU G 392 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU G 397 " --> pdb=" O ARG G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 447 removed outlier: 3.857A pdb=" N ASN G 447 " --> pdb=" O GLY G 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 444 through 447' Processing helix chain 'G' and resid 448 through 452 removed outlier: 3.940A pdb=" N HIS G 451 " --> pdb=" O PHE G 448 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY G 452 " --> pdb=" O SER G 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 448 through 452' Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.763A pdb=" N MET G 462 " --> pdb=" O ALA G 458 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 482 removed outlier: 3.671A pdb=" N ALA G 477 " --> pdb=" O PRO G 473 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 512 Processing helix chain 'G' and resid 518 through 533 Processing helix chain 'G' and resid 538 through 559 Proline residue: G 550 - end of helix Processing helix chain 'G' and resid 570 through 596 removed outlier: 3.674A pdb=" N GLU G 584 " --> pdb=" O ALA G 580 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU G 587 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 48 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 117 through 126 removed outlier: 3.992A pdb=" N ASP H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 158 Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 174 through 187 Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'H' and resid 194 through 210 removed outlier: 3.815A pdb=" N VAL H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 224 Processing helix chain 'H' and resid 230 through 246 Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.008A pdb=" N LEU I 5 " --> pdb=" O THR I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 37 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.745A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 98 removed outlier: 3.741A pdb=" N LEU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 139 removed outlier: 3.552A pdb=" N ARG I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.511A pdb=" N PHE I 169 " --> pdb=" O VAL I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 200 removed outlier: 4.922A pdb=" N TRP I 194 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE I 197 " --> pdb=" O VAL I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 235 removed outlier: 4.618A pdb=" N ARG I 209 " --> pdb=" O ARG I 205 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU I 210 " --> pdb=" O THR I 206 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 206 removed outlier: 6.567A pdb=" N VAL A 79 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 206 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS A 81 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 217 removed outlier: 6.492A pdb=" N ILE A 225 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 214 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A 223 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 216 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA A 221 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.652A pdb=" N GLN A 284 " --> pdb=" O HIS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517 removed outlier: 6.455A pdb=" N ARG A 516 " --> pdb=" O ASN A 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.533A pdb=" N THR B 4 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B 99 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 6 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 203 through 206 removed outlier: 6.602A pdb=" N VAL D 79 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE D 206 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS D 81 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 242 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AB2, first strand: chain 'D' and resid 209 through 217 removed outlier: 6.495A pdb=" N ILE D 225 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU D 214 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY D 223 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 216 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA D 221 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AB4, first strand: chain 'D' and resid 283 through 286 removed outlier: 5.590A pdb=" N HIS D 286 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL D 420 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB6, first strand: chain 'D' and resid 516 through 517 removed outlier: 6.592A pdb=" N ARG D 516 " --> pdb=" O ASN D 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 24 removed outlier: 6.604A pdb=" N THR E 4 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 99 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS E 6 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 203 through 206 removed outlier: 6.630A pdb=" N VAL G 79 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE G 206 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS G 81 " --> pdb=" O PHE G 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'G' and resid 209 through 217 removed outlier: 6.482A pdb=" N ILE G 225 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU G 214 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY G 223 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL G 216 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA G 221 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 426 through 427 Processing sheet with id=AC3, first strand: chain 'G' and resid 283 through 286 removed outlier: 6.698A pdb=" N GLN G 284 " --> pdb=" O HIS G 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 333 through 334 Processing sheet with id=AC5, first strand: chain 'G' and resid 516 through 517 removed outlier: 6.432A pdb=" N ARG G 516 " --> pdb=" O ASN G 561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 24 removed outlier: 6.525A pdb=" N THR H 4 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL H 99 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS H 6 " --> pdb=" O VAL H 99 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.76: 27796 1.76 - 2.31: 336 2.31 - 2.87: 3 2.87 - 3.42: 0 3.42 - 3.98: 9 Bond restraints: 28144 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.945 -1.712 2.00e-02 2.50e+03 7.33e+03 bond pdb=" S4 F3S H 303 " pdb="FE1 F3S H 303 " ideal model delta sigma weight residual 2.233 3.923 -1.690 2.00e-02 2.50e+03 7.14e+03 bond pdb=" S4 F3S E 303 " pdb="FE1 F3S E 303 " ideal model delta sigma weight residual 2.233 3.911 -1.678 2.00e-02 2.50e+03 7.04e+03 bond pdb=" S2 F3S H 303 " pdb="FE3 F3S H 303 " ideal model delta sigma weight residual 2.300 3.976 -1.676 2.00e-02 2.50e+03 7.02e+03 bond pdb=" S2 F3S E 303 " pdb="FE3 F3S E 303 " ideal model delta sigma weight residual 2.300 3.972 -1.672 2.00e-02 2.50e+03 6.99e+03 ... (remaining 28139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.01: 38156 10.01 - 20.01: 2 20.01 - 30.02: 3 30.02 - 40.03: 21 40.03 - 50.03: 6 Bond angle restraints: 38188 Sorted by residual: angle pdb=" S1 F3S H 303 " pdb="FE4 F3S H 303 " pdb=" S3 F3S H 303 " ideal model delta sigma weight residual 114.75 64.72 50.03 3.00e+00 1.11e-01 2.78e+02 angle pdb=" S1 F3S E 303 " pdb="FE4 F3S E 303 " pdb=" S3 F3S E 303 " ideal model delta sigma weight residual 114.75 64.80 49.95 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.95 49.80 3.00e+00 1.11e-01 2.76e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 63.92 48.67 3.00e+00 1.11e-01 2.63e+02 angle pdb=" S3 F3S H 303 " pdb="FE1 F3S H 303 " pdb=" S4 F3S H 303 " ideal model delta sigma weight residual 112.59 64.51 48.08 3.00e+00 1.11e-01 2.57e+02 ... (remaining 38183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 16068 34.38 - 68.75: 694 68.75 - 103.13: 75 103.13 - 137.51: 29 137.51 - 171.88: 7 Dihedral angle restraints: 16873 sinusoidal: 7216 harmonic: 9657 Sorted by residual: dihedral pdb=" C2B HEM C 301 " pdb=" C3B HEM C 301 " pdb=" CAB HEM C 301 " pdb=" CBB HEM C 301 " ideal model delta sinusoidal sigma weight residual 0.00 -71.55 71.55 2 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" C2B HEM C 302 " pdb=" C3B HEM C 302 " pdb=" CAB HEM C 302 " pdb=" CBB HEM C 302 " ideal model delta sinusoidal sigma weight residual -0.00 63.37 -63.37 2 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" C2C HEM C 302 " pdb=" C3C HEM C 302 " pdb=" CAC HEM C 302 " pdb=" CBC HEM C 302 " ideal model delta sinusoidal sigma weight residual 0.00 62.74 -62.74 2 1.00e+01 1.00e-02 3.79e+01 ... (remaining 16870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.619: 4068 3.619 - 7.239: 0 7.239 - 10.858: 0 10.858 - 14.478: 0 14.478 - 18.097: 3 Chirality restraints: 4071 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.33 18.10 2.00e-01 2.50e+01 8.19e+03 chirality pdb=" S2 F3S H 303 " pdb="FE1 F3S H 303 " pdb="FE3 F3S H 303 " pdb="FE4 F3S H 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.31 18.08 2.00e-01 2.50e+01 8.17e+03 chirality pdb=" S2 F3S E 303 " pdb="FE1 F3S E 303 " pdb="FE3 F3S E 303 " pdb="FE4 F3S E 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.21 17.98 2.00e-01 2.50e+01 8.08e+03 ... (remaining 4068 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 200 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C VAL B 200 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL B 200 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 201 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 200 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C VAL H 200 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL H 200 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN H 201 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 199 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C VAL B 199 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B 199 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL B 200 " -0.012 2.00e-02 2.50e+03 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1984 2.74 - 3.28: 27182 3.28 - 3.82: 50822 3.82 - 4.36: 63896 4.36 - 4.90: 104731 Nonbonded interactions: 248615 Sorted by model distance: nonbonded pdb=" OD1 ASN E 213 " pdb=" OG SER F 92 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN D 101 " pdb=" OG1 THR D 175 " model vdw 2.197 3.040 nonbonded pdb=" O LEU D 63 " pdb=" OG SER D 67 " model vdw 2.205 3.040 nonbonded pdb=" O LEU G 63 " pdb=" OG SER G 67 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG D 90 " pdb=" O GLY E 161 " model vdw 2.208 3.120 ... (remaining 248610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 1 through 239 or resid 302 or resid 307)) selection = (chain 'F' and (resid 1 through 239 or resid 302 or (resid 307 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or \ name C44 or name C45 or name C5 or name N6 or name O11 or name O1P or name O2 or \ name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'I' and (resid 1 through 239 or resid 302 or (resid 307 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or \ name C44 or name C45 or name C5 or name N6 or name O11 or name O1P or name O2 or \ name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.500 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.030 1.712 28183 Z= 1.496 Angle : 1.314 50.033 38269 Z= 0.450 Chirality : 0.492 18.097 4071 Planarity : 0.004 0.039 4860 Dihedral : 19.329 171.883 10735 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.10 % Allowed : 16.90 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3363 helix: 0.68 (0.12), residues: 1650 sheet: 0.98 (0.31), residues: 225 loop : -0.31 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 112 TYR 0.019 0.001 TYR I 107 PHE 0.012 0.001 PHE A 117 TRP 0.013 0.001 TRP B 102 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.03011 (28144) covalent geometry : angle 1.20401 (38188) hydrogen bonds : bond 0.12066 ( 1344) hydrogen bonds : angle 5.68386 ( 3753) metal coordination : bond 0.00969 ( 33) metal coordination : angle 11.52457 ( 81) Misc. bond : bond 0.14460 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 448 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7856 (mtt180) REVERT: A 312 ARG cc_start: 0.7155 (mtp85) cc_final: 0.6951 (mtp180) REVERT: A 359 GLN cc_start: 0.7680 (tp40) cc_final: 0.6743 (tm-30) REVERT: A 402 LYS cc_start: 0.7739 (tttm) cc_final: 0.7402 (ttpt) REVERT: B 35 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 42 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7439 (mp0) REVERT: C 9 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6623 (mmm-85) REVERT: C 206 THR cc_start: 0.7835 (p) cc_final: 0.7542 (t) REVERT: C 209 ARG cc_start: 0.7055 (tpt170) cc_final: 0.5808 (tmm160) REVERT: C 234 TYR cc_start: 0.8192 (t80) cc_final: 0.7938 (t80) REVERT: D 372 LEU cc_start: 0.8504 (mt) cc_final: 0.8249 (mt) REVERT: D 377 ASP cc_start: 0.6891 (p0) cc_final: 0.6645 (t70) REVERT: D 402 LYS cc_start: 0.7750 (tttm) cc_final: 0.7356 (ttpp) REVERT: E 30 ASP cc_start: 0.8041 (m-30) cc_final: 0.7835 (m-30) REVERT: E 42 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7584 (mp0) REVERT: E 151 ASP cc_start: 0.8438 (m-30) cc_final: 0.8075 (m-30) REVERT: E 242 MET cc_start: 0.8564 (tpp) cc_final: 0.8334 (tpp) REVERT: F 209 ARG cc_start: 0.7061 (tpt170) cc_final: 0.5742 (tmm160) REVERT: F 234 TYR cc_start: 0.8271 (t80) cc_final: 0.7973 (t80) REVERT: G 52 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7770 (mtt180) REVERT: G 332 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7366 (mt-10) REVERT: G 338 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5845 (mm-30) REVERT: G 402 LYS cc_start: 0.7717 (tttm) cc_final: 0.7430 (ttmt) REVERT: G 515 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7879 (mmmt) REVERT: G 529 MET cc_start: 0.8347 (mmm) cc_final: 0.8108 (mmm) REVERT: G 543 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7197 (mtm-85) REVERT: I 33 MET cc_start: 0.8737 (tmm) cc_final: 0.8416 (tmm) REVERT: I 209 ARG cc_start: 0.7058 (tpt170) cc_final: 0.6810 (tpt170) REVERT: I 234 TYR cc_start: 0.8129 (t80) cc_final: 0.7831 (t80) outliers start: 30 outliers final: 22 residues processed: 475 average time/residue: 0.9077 time to fit residues: 485.6812 Evaluate side-chains 370 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 348 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 478 ASN A 547 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 50 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN E 79 ASN F 226 ASN H 79 ASN I 110 HIS I 138 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.109262 restraints weight = 27044.978| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.11 r_work: 0.3043 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 28183 Z= 0.201 Angle : 1.367 80.041 38269 Z= 0.423 Chirality : 0.063 2.185 4071 Planarity : 0.004 0.047 4860 Dihedral : 15.702 168.267 4676 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.60 % Allowed : 17.78 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3363 helix: 1.04 (0.12), residues: 1659 sheet: 0.67 (0.31), residues: 237 loop : -0.28 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 93 TYR 0.013 0.001 TYR C 119 PHE 0.011 0.001 PHE G 117 TRP 0.011 0.001 TRP B 102 HIS 0.005 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00424 (28144) covalent geometry : angle 1.10916 (38188) hydrogen bonds : bond 0.04923 ( 1344) hydrogen bonds : angle 4.87462 ( 3753) metal coordination : bond 0.01161 ( 33) metal coordination : angle 17.38908 ( 81) Misc. bond : bond 0.12980 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 355 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 303 MET cc_start: 0.7985 (mtm) cc_final: 0.7528 (mtp) REVERT: A 307 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6595 (pp) REVERT: A 312 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6802 (mtp180) REVERT: A 350 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7935 (tmm160) REVERT: A 402 LYS cc_start: 0.7690 (tttm) cc_final: 0.7295 (ttpt) REVERT: A 565 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: C 9 ARG cc_start: 0.7518 (mtt90) cc_final: 0.6822 (mtp180) REVERT: C 63 HIS cc_start: 0.7768 (m-70) cc_final: 0.7462 (t-90) REVERT: C 209 ARG cc_start: 0.7008 (tpt170) cc_final: 0.5566 (tmm160) REVERT: C 234 TYR cc_start: 0.8194 (t80) cc_final: 0.7894 (t80) REVERT: D 372 LEU cc_start: 0.8436 (mt) cc_final: 0.8164 (mt) REVERT: D 377 ASP cc_start: 0.7028 (p0) cc_final: 0.6824 (t70) REVERT: D 402 LYS cc_start: 0.7705 (tttm) cc_final: 0.7247 (ttpp) REVERT: D 462 MET cc_start: 0.8284 (ttm) cc_final: 0.7997 (ttm) REVERT: D 515 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8041 (mmpt) REVERT: D 565 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: D 647 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: E 151 ASP cc_start: 0.8341 (m-30) cc_final: 0.8015 (m-30) REVERT: E 242 MET cc_start: 0.8464 (tpp) cc_final: 0.8163 (tpp) REVERT: F 209 ARG cc_start: 0.7080 (tpt170) cc_final: 0.5574 (tmm160) REVERT: F 234 TYR cc_start: 0.8252 (t80) cc_final: 0.7932 (t80) REVERT: G 52 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7857 (mtt180) REVERT: G 338 GLU cc_start: 0.6701 (mt-10) cc_final: 0.5722 (mm-30) REVERT: G 347 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.3906 (pp) REVERT: G 402 LYS cc_start: 0.7649 (tttm) cc_final: 0.7313 (ttmt) REVERT: G 450 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: G 504 GLN cc_start: 0.7714 (mt0) cc_final: 0.7503 (mt0) REVERT: G 515 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7744 (mmmt) REVERT: G 523 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7813 (ttp-110) REVERT: G 529 MET cc_start: 0.8271 (mmm) cc_final: 0.7934 (mmm) REVERT: G 543 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.7017 (mtm-85) REVERT: I 33 MET cc_start: 0.8646 (tmm) cc_final: 0.8306 (tmm) REVERT: I 44 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: I 209 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6714 (tpt170) outliers start: 71 outliers final: 30 residues processed: 399 average time/residue: 0.8070 time to fit residues: 365.5289 Evaluate side-chains 370 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 330 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 306 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 478 ASN A 547 GLN C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN E 251 ASN G 432 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN H 235 GLN I 150 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105379 restraints weight = 27137.797| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.11 r_work: 0.2982 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 28183 Z= 0.248 Angle : 1.415 85.282 38269 Z= 0.431 Chirality : 0.056 1.485 4071 Planarity : 0.004 0.043 4860 Dihedral : 13.910 179.341 4665 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.40 % Allowed : 17.71 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3363 helix: 0.95 (0.12), residues: 1641 sheet: 0.73 (0.31), residues: 237 loop : -0.38 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 93 TYR 0.016 0.002 TYR E 196 PHE 0.014 0.002 PHE G 117 TRP 0.016 0.002 TRP B 102 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00576 (28144) covalent geometry : angle 1.09124 (38188) hydrogen bonds : bond 0.05244 ( 1344) hydrogen bonds : angle 4.95078 ( 3753) metal coordination : bond 0.01513 ( 33) metal coordination : angle 19.61590 ( 81) Misc. bond : bond 0.17850 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 338 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6800 (pp) REVERT: A 312 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6699 (mtp180) REVERT: A 339 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: A 350 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7888 (tmm160) REVERT: A 402 LYS cc_start: 0.7600 (tttm) cc_final: 0.7112 (ttpt) REVERT: A 565 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: B 35 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: C 9 ARG cc_start: 0.7483 (mtt90) cc_final: 0.6738 (mtp180) REVERT: C 63 HIS cc_start: 0.7752 (m-70) cc_final: 0.7385 (t-90) REVERT: C 209 ARG cc_start: 0.6979 (tpt170) cc_final: 0.5486 (tmm160) REVERT: C 234 TYR cc_start: 0.8193 (t80) cc_final: 0.7862 (t80) REVERT: D 303 MET cc_start: 0.7961 (mtm) cc_final: 0.7758 (mtt) REVERT: D 372 LEU cc_start: 0.8417 (mt) cc_final: 0.8151 (mt) REVERT: D 402 LYS cc_start: 0.7551 (tttm) cc_final: 0.7124 (ttpt) REVERT: D 515 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (mmpt) REVERT: D 565 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: E 151 ASP cc_start: 0.8302 (m-30) cc_final: 0.7922 (m-30) REVERT: F 209 ARG cc_start: 0.7094 (tpt170) cc_final: 0.5489 (tmm160) REVERT: F 234 TYR cc_start: 0.8192 (t80) cc_final: 0.7885 (t80) REVERT: G 125 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8344 (t0) REVERT: G 277 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: G 308 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7738 (mtp-110) REVERT: G 338 GLU cc_start: 0.6753 (mt-10) cc_final: 0.5960 (mm-30) REVERT: G 347 LEU cc_start: 0.4303 (OUTLIER) cc_final: 0.3740 (pp) REVERT: G 402 LYS cc_start: 0.7561 (tttm) cc_final: 0.7118 (ttmt) REVERT: G 504 GLN cc_start: 0.7674 (mt0) cc_final: 0.7463 (mt0) REVERT: G 515 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7658 (mmmt) REVERT: G 523 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7687 (ttp-110) REVERT: G 543 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6877 (mtm-85) REVERT: G 544 GLU cc_start: 0.7358 (tt0) cc_final: 0.6921 (pt0) REVERT: G 565 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: I 33 MET cc_start: 0.8621 (tmm) cc_final: 0.8239 (tmm) REVERT: I 44 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: I 209 ARG cc_start: 0.7076 (tpt170) cc_final: 0.5694 (tmm160) outliers start: 93 outliers final: 38 residues processed: 405 average time/residue: 0.7830 time to fit residues: 360.6789 Evaluate side-chains 372 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 64 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 63 HIS C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN G 403 GLN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN I 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110237 restraints weight = 27178.948| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.10 r_work: 0.3060 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 28183 Z= 0.161 Angle : 1.325 81.620 38269 Z= 0.377 Chirality : 0.064 2.312 4071 Planarity : 0.003 0.043 4860 Dihedral : 12.902 174.518 4661 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.04 % Allowed : 18.37 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3363 helix: 1.23 (0.12), residues: 1662 sheet: 0.72 (0.31), residues: 237 loop : -0.28 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 638 TYR 0.013 0.001 TYR I 107 PHE 0.015 0.001 PHE F 31 TRP 0.009 0.001 TRP B 102 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00345 (28144) covalent geometry : angle 0.96371 (38188) hydrogen bonds : bond 0.04364 ( 1344) hydrogen bonds : angle 4.58162 ( 3753) metal coordination : bond 0.01300 ( 33) metal coordination : angle 19.79455 ( 81) Misc. bond : bond 0.11628 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 353 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 THR cc_start: 0.9178 (m) cc_final: 0.8898 (m) REVERT: A 303 MET cc_start: 0.7819 (mtm) cc_final: 0.7437 (mtp) REVERT: A 307 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6834 (pp) REVERT: A 312 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6885 (mtp180) REVERT: A 317 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7677 (mmmt) REVERT: A 350 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7797 (tmm160) REVERT: A 402 LYS cc_start: 0.7648 (tttm) cc_final: 0.7164 (ttpp) REVERT: A 403 GLN cc_start: 0.7811 (tp40) cc_final: 0.7600 (tp-100) REVERT: A 565 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: B 35 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 9 ARG cc_start: 0.7387 (mtt90) cc_final: 0.6563 (mmm-85) REVERT: C 63 HIS cc_start: 0.7744 (m170) cc_final: 0.7444 (t-90) REVERT: C 206 THR cc_start: 0.7721 (p) cc_final: 0.7486 (t) REVERT: C 209 ARG cc_start: 0.6956 (tpt170) cc_final: 0.5593 (tmm160) REVERT: C 234 TYR cc_start: 0.8189 (t80) cc_final: 0.7891 (t80) REVERT: D 402 LYS cc_start: 0.7706 (tttm) cc_final: 0.7195 (ttpp) REVERT: D 515 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7957 (mmpt) REVERT: D 565 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7677 (mm-30) REVERT: E 13 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6696 (mtp-110) REVERT: E 151 ASP cc_start: 0.8345 (m-30) cc_final: 0.8008 (m-30) REVERT: E 152 ARG cc_start: 0.7509 (mtp180) cc_final: 0.7263 (mtp180) REVERT: F 205 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6583 (ptt180) REVERT: F 209 ARG cc_start: 0.7133 (tpt170) cc_final: 0.5584 (tmm160) REVERT: F 234 TYR cc_start: 0.8243 (t80) cc_final: 0.7948 (t80) REVERT: G 308 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7792 (mtp-110) REVERT: G 309 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: G 338 GLU cc_start: 0.6620 (mt-10) cc_final: 0.5579 (mm-30) REVERT: G 402 LYS cc_start: 0.7585 (tttm) cc_final: 0.7185 (ttmt) REVERT: G 450 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: G 515 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7593 (mmmt) REVERT: G 523 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7873 (ttp-110) REVERT: G 543 ARG cc_start: 0.7337 (mtt-85) cc_final: 0.7058 (mtm-85) REVERT: G 544 GLU cc_start: 0.7427 (tt0) cc_final: 0.7043 (pt0) REVERT: G 565 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: I 33 MET cc_start: 0.8628 (tmm) cc_final: 0.8368 (tmm) REVERT: I 44 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: I 93 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7799 (mtp85) REVERT: I 209 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6745 (tpt170) outliers start: 83 outliers final: 29 residues processed: 408 average time/residue: 0.8055 time to fit residues: 374.5067 Evaluate side-chains 372 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 309 ASN Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 612 ASP Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 44 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 173 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 547 GLN C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 403 GLN E 79 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106906 restraints weight = 27044.869| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.10 r_work: 0.3024 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 28183 Z= 0.178 Angle : 1.332 81.921 38269 Z= 0.388 Chirality : 0.059 1.522 4071 Planarity : 0.004 0.035 4860 Dihedral : 12.793 178.541 4657 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.60 % Allowed : 19.65 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3363 helix: 1.19 (0.12), residues: 1662 sheet: 0.79 (0.31), residues: 237 loop : -0.27 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 638 TYR 0.012 0.001 TYR E 196 PHE 0.012 0.001 PHE G 117 TRP 0.012 0.002 TRP H 102 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00403 (28144) covalent geometry : angle 0.98577 (38188) hydrogen bonds : bond 0.04629 ( 1344) hydrogen bonds : angle 4.62834 ( 3753) metal coordination : bond 0.01048 ( 33) metal coordination : angle 19.49122 ( 81) Misc. bond : bond 0.14307 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6826 (pp) REVERT: A 317 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7554 (mmmt) REVERT: A 339 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: A 350 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7803 (tmm160) REVERT: A 402 LYS cc_start: 0.7511 (tttm) cc_final: 0.7007 (ttpt) REVERT: A 565 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: B 35 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 9 ARG cc_start: 0.7383 (mtt90) cc_final: 0.6657 (mtp180) REVERT: C 63 HIS cc_start: 0.7736 (m170) cc_final: 0.7408 (t-90) REVERT: C 206 THR cc_start: 0.7660 (p) cc_final: 0.7411 (t) REVERT: C 209 ARG cc_start: 0.6917 (tpt170) cc_final: 0.5484 (tmm160) REVERT: C 234 TYR cc_start: 0.8142 (t80) cc_final: 0.7844 (t80) REVERT: D 402 LYS cc_start: 0.7534 (tttm) cc_final: 0.6977 (ttpp) REVERT: D 565 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: E 151 ASP cc_start: 0.8322 (m-30) cc_final: 0.7903 (m-30) REVERT: E 152 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7138 (mtp180) REVERT: F 205 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6595 (ptt180) REVERT: F 209 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6648 (tpt170) REVERT: F 234 TYR cc_start: 0.8209 (t80) cc_final: 0.7912 (t80) REVERT: G 125 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8288 (t0) REVERT: G 167 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.4714 (m-80) REVERT: G 338 GLU cc_start: 0.6719 (mt-10) cc_final: 0.5693 (mm-30) REVERT: G 402 LYS cc_start: 0.7517 (tttm) cc_final: 0.7030 (ttmt) REVERT: G 450 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: G 515 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7520 (mmmt) REVERT: G 523 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7761 (ttp-110) REVERT: G 543 ARG cc_start: 0.7220 (mtt-85) cc_final: 0.6910 (mtm-85) REVERT: G 544 GLU cc_start: 0.7366 (tt0) cc_final: 0.6956 (pt0) REVERT: G 565 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: I 33 MET cc_start: 0.8588 (tmm) cc_final: 0.8199 (tmm) REVERT: I 44 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: I 93 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7742 (mtp85) REVERT: I 114 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8189 (t) REVERT: I 209 ARG cc_start: 0.7097 (tpt170) cc_final: 0.6689 (tpt170) outliers start: 71 outliers final: 35 residues processed: 383 average time/residue: 0.8294 time to fit residues: 361.1992 Evaluate side-chains 376 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 326 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 79 ASN G 297 GLN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.134355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107994 restraints weight = 26963.787| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.11 r_work: 0.3026 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 28183 Z= 0.176 Angle : 1.317 81.276 38269 Z= 0.385 Chirality : 0.060 1.642 4071 Planarity : 0.004 0.036 4860 Dihedral : 12.582 178.504 4657 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.85 % Allowed : 19.72 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3363 helix: 1.27 (0.12), residues: 1644 sheet: 0.78 (0.31), residues: 237 loop : -0.26 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 638 TYR 0.017 0.001 TYR A 254 PHE 0.013 0.001 PHE G 117 TRP 0.012 0.001 TRP H 102 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00397 (28144) covalent geometry : angle 0.97943 (38188) hydrogen bonds : bond 0.04600 ( 1344) hydrogen bonds : angle 4.62455 ( 3753) metal coordination : bond 0.01016 ( 33) metal coordination : angle 19.17664 ( 81) Misc. bond : bond 0.13927 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 338 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6877 (pp) REVERT: A 317 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7632 (mmmt) REVERT: A 339 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: A 350 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7869 (tmm160) REVERT: A 402 LYS cc_start: 0.7597 (tttm) cc_final: 0.7125 (ttpt) REVERT: A 565 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: A 569 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 35 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 9 ARG cc_start: 0.7416 (mtt90) cc_final: 0.6739 (mtp180) REVERT: C 63 HIS cc_start: 0.7764 (m170) cc_final: 0.7507 (t-90) REVERT: C 206 THR cc_start: 0.7693 (p) cc_final: 0.7447 (t) REVERT: C 209 ARG cc_start: 0.6950 (tpt170) cc_final: 0.5512 (tmm160) REVERT: C 234 TYR cc_start: 0.8207 (t80) cc_final: 0.7861 (t80) REVERT: D 97 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: D 303 MET cc_start: 0.7684 (mtm) cc_final: 0.7479 (mtt) REVERT: D 402 LYS cc_start: 0.7646 (tttm) cc_final: 0.7215 (ttpt) REVERT: D 565 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: E 151 ASP cc_start: 0.8345 (m-30) cc_final: 0.8009 (m-30) REVERT: E 152 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7244 (mtp180) REVERT: F 205 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6655 (ptt180) REVERT: F 209 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6737 (tpt170) REVERT: F 234 TYR cc_start: 0.8269 (t80) cc_final: 0.7969 (t80) REVERT: G 125 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (t0) REVERT: G 167 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.4794 (m-80) REVERT: G 338 GLU cc_start: 0.6728 (mt-10) cc_final: 0.5737 (mm-30) REVERT: G 402 LYS cc_start: 0.7626 (tttm) cc_final: 0.7197 (ttmt) REVERT: G 450 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: G 515 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7624 (mmmt) REVERT: G 523 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7849 (ttp-110) REVERT: G 543 ARG cc_start: 0.7322 (mtt-85) cc_final: 0.7039 (mtm-85) REVERT: G 544 GLU cc_start: 0.7415 (tt0) cc_final: 0.7037 (pt0) REVERT: G 565 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: I 33 MET cc_start: 0.8636 (tmm) cc_final: 0.8381 (tmm) REVERT: I 44 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: I 93 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7845 (mtp85) REVERT: I 114 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8207 (t) REVERT: I 209 ARG cc_start: 0.7109 (tpt170) cc_final: 0.6747 (tpt170) outliers start: 78 outliers final: 38 residues processed: 389 average time/residue: 0.7955 time to fit residues: 352.4048 Evaluate side-chains 380 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 325 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 612 ASP Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 156 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 251 optimal weight: 0.0070 chunk 208 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108609 restraints weight = 26908.573| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.11 r_work: 0.3033 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 28183 Z= 0.166 Angle : 1.310 81.247 38269 Z= 0.383 Chirality : 0.060 1.616 4071 Planarity : 0.003 0.036 4860 Dihedral : 12.304 178.259 4657 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.82 % Allowed : 19.87 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3363 helix: 1.24 (0.12), residues: 1662 sheet: 0.80 (0.32), residues: 237 loop : -0.26 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.013 0.001 TYR A 254 PHE 0.012 0.001 PHE G 117 TRP 0.013 0.001 TRP B 102 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00374 (28144) covalent geometry : angle 0.97546 (38188) hydrogen bonds : bond 0.04518 ( 1344) hydrogen bonds : angle 4.58863 ( 3753) metal coordination : bond 0.00905 ( 33) metal coordination : angle 19.03892 ( 81) Misc. bond : bond 0.13119 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 334 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6895 (pp) REVERT: A 317 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7621 (mmmt) REVERT: A 350 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7866 (tmm160) REVERT: A 402 LYS cc_start: 0.7595 (tttm) cc_final: 0.7120 (ttpt) REVERT: A 565 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: B 35 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 100 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: C 9 ARG cc_start: 0.7324 (mtt90) cc_final: 0.6681 (mtp180) REVERT: C 63 HIS cc_start: 0.7742 (m170) cc_final: 0.7499 (t-90) REVERT: C 209 ARG cc_start: 0.6949 (tpt170) cc_final: 0.5523 (tmm160) REVERT: C 234 TYR cc_start: 0.8210 (t80) cc_final: 0.7871 (t80) REVERT: D 303 MET cc_start: 0.7693 (mtm) cc_final: 0.7467 (mtt) REVERT: D 402 LYS cc_start: 0.7628 (tttm) cc_final: 0.7178 (ttpt) REVERT: E 13 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6890 (mtp-110) REVERT: E 151 ASP cc_start: 0.8351 (m-30) cc_final: 0.7924 (m-30) REVERT: E 152 ARG cc_start: 0.7513 (mtp180) cc_final: 0.7256 (mtp180) REVERT: F 205 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6601 (ptt180) REVERT: F 209 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6731 (tpt170) REVERT: F 234 TYR cc_start: 0.8269 (t80) cc_final: 0.7966 (t80) REVERT: G 125 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8284 (t0) REVERT: G 167 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: G 338 GLU cc_start: 0.6721 (mt-10) cc_final: 0.5660 (mm-30) REVERT: G 402 LYS cc_start: 0.7641 (tttm) cc_final: 0.7192 (ttmt) REVERT: G 450 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: G 515 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7602 (mmmt) REVERT: G 523 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7862 (ttp-110) REVERT: G 543 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.7035 (mtm-85) REVERT: G 544 GLU cc_start: 0.7434 (tt0) cc_final: 0.7051 (pt0) REVERT: G 565 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: G 597 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: I 33 MET cc_start: 0.8647 (tmm) cc_final: 0.8384 (tmm) REVERT: I 44 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: I 93 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7826 (mtp85) REVERT: I 114 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8215 (t) REVERT: I 209 ARG cc_start: 0.7120 (tpt170) cc_final: 0.6748 (tpt170) outliers start: 77 outliers final: 36 residues processed: 383 average time/residue: 0.8686 time to fit residues: 377.3007 Evaluate side-chains 370 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 318 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 26 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 317 optimal weight: 0.7980 chunk 299 optimal weight: 0.0770 chunk 191 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 79 ASN G 297 GLN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.111497 restraints weight = 27072.484| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.10 r_work: 0.3070 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 28183 Z= 0.139 Angle : 1.282 81.392 38269 Z= 0.372 Chirality : 0.058 1.572 4071 Planarity : 0.003 0.037 4860 Dihedral : 11.824 177.503 4657 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 20.67 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.14), residues: 3363 helix: 1.43 (0.12), residues: 1659 sheet: 0.77 (0.31), residues: 237 loop : -0.23 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 638 TYR 0.011 0.001 TYR I 107 PHE 0.011 0.001 PHE G 117 TRP 0.013 0.001 TRP B 102 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00303 (28144) covalent geometry : angle 0.95835 (38188) hydrogen bonds : bond 0.04203 ( 1344) hydrogen bonds : angle 4.44161 ( 3753) metal coordination : bond 0.00689 ( 33) metal coordination : angle 18.52774 ( 81) Misc. bond : bond 0.10189 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 343 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7779 (mtm) cc_final: 0.7381 (mtp) REVERT: A 307 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6895 (pp) REVERT: A 317 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7580 (mmmt) REVERT: A 339 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6613 (mm-30) REVERT: A 350 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7822 (tmm160) REVERT: A 402 LYS cc_start: 0.7587 (tttm) cc_final: 0.7118 (ttpt) REVERT: A 565 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: B 35 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: C 9 ARG cc_start: 0.7305 (mtt90) cc_final: 0.6491 (mmm-85) REVERT: C 63 HIS cc_start: 0.7735 (m170) cc_final: 0.7480 (t-90) REVERT: C 209 ARG cc_start: 0.6928 (tpt170) cc_final: 0.5497 (tmm160) REVERT: C 234 TYR cc_start: 0.8194 (t80) cc_final: 0.7858 (t80) REVERT: D 402 LYS cc_start: 0.7794 (tttm) cc_final: 0.7242 (ttpp) REVERT: D 519 ASP cc_start: 0.7984 (m-30) cc_final: 0.7637 (m-30) REVERT: D 520 SER cc_start: 0.8766 (t) cc_final: 0.8458 (p) REVERT: E 13 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6836 (mtp-110) REVERT: E 151 ASP cc_start: 0.8395 (m-30) cc_final: 0.7967 (m-30) REVERT: E 152 ARG cc_start: 0.7503 (mtp180) cc_final: 0.7265 (mtp180) REVERT: F 209 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6673 (tpt170) REVERT: F 234 TYR cc_start: 0.8262 (t80) cc_final: 0.7950 (t80) REVERT: G 167 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.4693 (m-80) REVERT: G 338 GLU cc_start: 0.6685 (mt-10) cc_final: 0.5618 (mm-30) REVERT: G 402 LYS cc_start: 0.7591 (tttm) cc_final: 0.7116 (ttmt) REVERT: G 450 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: G 515 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7512 (mmmt) REVERT: G 523 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7860 (ttp-110) REVERT: G 543 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.7021 (mtm-85) REVERT: G 544 GLU cc_start: 0.7487 (tt0) cc_final: 0.7148 (pt0) REVERT: G 565 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: G 597 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: I 33 MET cc_start: 0.8578 (tmm) cc_final: 0.8320 (tmm) REVERT: I 44 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: I 114 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8173 (t) REVERT: I 209 ARG cc_start: 0.7096 (tpt170) cc_final: 0.6722 (tpt170) outliers start: 58 outliers final: 27 residues processed: 381 average time/residue: 0.8622 time to fit residues: 372.9157 Evaluate side-chains 367 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain G residue 597 GLU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 11 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN C 203 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106718 restraints weight = 26788.893| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.13 r_work: 0.2998 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 28183 Z= 0.210 Angle : 1.336 81.041 38269 Z= 0.401 Chirality : 0.061 1.646 4071 Planarity : 0.004 0.035 4860 Dihedral : 11.978 172.675 4656 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.38 % Allowed : 20.64 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3363 helix: 1.24 (0.12), residues: 1644 sheet: 0.79 (0.32), residues: 237 loop : -0.26 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.016 0.002 TYR A 254 PHE 0.014 0.002 PHE C 184 TRP 0.014 0.002 TRP H 102 HIS 0.005 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00484 (28144) covalent geometry : angle 1.00676 (38188) hydrogen bonds : bond 0.04831 ( 1344) hydrogen bonds : angle 4.69119 ( 3753) metal coordination : bond 0.01150 ( 33) metal coordination : angle 19.11649 ( 81) Misc. bond : bond 0.15075 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 1.225 Fit side-chains REVERT: A 307 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6862 (pp) REVERT: A 317 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7592 (mmmt) REVERT: A 339 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6561 (mm-30) REVERT: A 350 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7870 (tmm160) REVERT: A 402 LYS cc_start: 0.7550 (tttm) cc_final: 0.7034 (ttpt) REVERT: A 565 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: B 151 ASP cc_start: 0.8256 (m-30) cc_final: 0.8040 (m-30) REVERT: C 9 ARG cc_start: 0.7374 (mtt90) cc_final: 0.6718 (mtp180) REVERT: C 63 HIS cc_start: 0.7740 (m170) cc_final: 0.7466 (t-90) REVERT: C 121 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.6548 (mpt) REVERT: C 206 THR cc_start: 0.7757 (p) cc_final: 0.7467 (t) REVERT: C 209 ARG cc_start: 0.6969 (tpt170) cc_final: 0.5512 (tmm160) REVERT: C 234 TYR cc_start: 0.8194 (t80) cc_final: 0.7867 (t80) REVERT: D 402 LYS cc_start: 0.7745 (tttm) cc_final: 0.7228 (ttpp) REVERT: E 13 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7647 (mtt-85) REVERT: E 151 ASP cc_start: 0.8339 (m-30) cc_final: 0.7965 (m-30) REVERT: E 249 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7732 (mp0) REVERT: F 209 ARG cc_start: 0.7096 (tpt170) cc_final: 0.6665 (tpt170) REVERT: F 234 TYR cc_start: 0.8220 (t80) cc_final: 0.7850 (t80) REVERT: G 167 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.4811 (m-80) REVERT: G 338 GLU cc_start: 0.6678 (mt-10) cc_final: 0.5575 (mm-30) REVERT: G 402 LYS cc_start: 0.7642 (tttm) cc_final: 0.7173 (ttmt) REVERT: G 450 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: G 504 GLN cc_start: 0.7716 (mt0) cc_final: 0.7495 (mt0) REVERT: G 515 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7624 (mmmt) REVERT: G 523 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7859 (ttp-110) REVERT: G 543 ARG cc_start: 0.7286 (mtt-85) cc_final: 0.7011 (mtm-85) REVERT: G 565 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: H 249 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: I 33 MET cc_start: 0.8636 (tmm) cc_final: 0.8271 (tmm) REVERT: I 44 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: I 114 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8235 (t) REVERT: I 209 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6781 (tpt170) outliers start: 65 outliers final: 34 residues processed: 367 average time/residue: 0.8689 time to fit residues: 362.6556 Evaluate side-chains 370 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 450 ASP Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106532 restraints weight = 26863.159| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.13 r_work: 0.3002 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 28183 Z= 0.211 Angle : 1.334 81.057 38269 Z= 0.400 Chirality : 0.061 1.634 4071 Planarity : 0.004 0.035 4860 Dihedral : 11.970 175.551 4656 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.12 % Allowed : 20.86 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3363 helix: 1.14 (0.12), residues: 1644 sheet: 0.78 (0.32), residues: 237 loop : -0.29 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 93 TYR 0.019 0.002 TYR D 254 PHE 0.014 0.002 PHE G 117 TRP 0.014 0.002 TRP H 102 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00490 (28144) covalent geometry : angle 1.00555 (38188) hydrogen bonds : bond 0.04830 ( 1344) hydrogen bonds : angle 4.74585 ( 3753) metal coordination : bond 0.01185 ( 33) metal coordination : angle 19.08553 ( 81) Misc. bond : bond 0.15173 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6726 Ramachandran restraints generated. 3363 Oldfield, 0 Emsley, 3363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 325 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 317 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7616 (mmmt) REVERT: A 339 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: A 350 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7887 (tmm160) REVERT: A 402 LYS cc_start: 0.7551 (tttm) cc_final: 0.7043 (ttpt) REVERT: A 565 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 569 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 9 ARG cc_start: 0.7375 (mtt90) cc_final: 0.6712 (mtp180) REVERT: C 63 HIS cc_start: 0.7747 (m170) cc_final: 0.7430 (t-90) REVERT: C 121 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.6576 (mpt) REVERT: C 209 ARG cc_start: 0.6987 (tpt170) cc_final: 0.5536 (tmm160) REVERT: C 234 TYR cc_start: 0.8206 (t80) cc_final: 0.7888 (t80) REVERT: D 349 PRO cc_start: 0.6886 (Cg_exo) cc_final: 0.6621 (Cg_endo) REVERT: D 402 LYS cc_start: 0.7719 (tttm) cc_final: 0.7200 (ttpp) REVERT: E 13 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: E 151 ASP cc_start: 0.8340 (m-30) cc_final: 0.7924 (m-30) REVERT: E 249 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7796 (mp0) REVERT: F 209 ARG cc_start: 0.7162 (tpt170) cc_final: 0.5609 (tmm160) REVERT: F 234 TYR cc_start: 0.8215 (t80) cc_final: 0.7926 (t80) REVERT: G 125 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8279 (t0) REVERT: G 167 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: G 338 GLU cc_start: 0.6654 (mt-10) cc_final: 0.5554 (mm-30) REVERT: G 402 LYS cc_start: 0.7638 (tttm) cc_final: 0.7184 (ttmt) REVERT: G 515 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7658 (mmmt) REVERT: G 523 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7833 (ttp-110) REVERT: G 543 ARG cc_start: 0.7282 (mtt-85) cc_final: 0.7014 (mtm-85) REVERT: G 544 GLU cc_start: 0.7420 (tt0) cc_final: 0.7069 (pt0) REVERT: G 565 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: H 13 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: I 33 MET cc_start: 0.8655 (tmm) cc_final: 0.8268 (tmm) REVERT: I 44 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: I 209 ARG cc_start: 0.7176 (tpt170) cc_final: 0.6799 (tpt170) outliers start: 58 outliers final: 36 residues processed: 366 average time/residue: 0.8839 time to fit residues: 367.1447 Evaluate side-chains 365 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 595 HIS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 167 PHE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 515 LYS Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain G residue 565 GLU Chi-restraints excluded: chain G residue 595 HIS Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 44 GLU Chi-restraints excluded: chain I residue 114 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 12 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN C 150 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** G 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN G 559 ASN H 79 ASN I 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109044 restraints weight = 26717.819| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.12 r_work: 0.3044 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 28183 Z= 0.159 Angle : 1.300 81.240 38269 Z= 0.383 Chirality : 0.059 1.591 4071 Planarity : 0.003 0.036 4860 Dihedral : 11.680 179.393 4656 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.76 % Allowed : 21.15 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3363 helix: 1.25 (0.12), residues: 1662 sheet: 0.71 (0.31), residues: 237 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.021 0.001 TYR D 254 PHE 0.012 0.001 PHE G 117 TRP 0.012 0.001 TRP H 102 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00356 (28144) covalent geometry : angle 0.97663 (38188) hydrogen bonds : bond 0.04461 ( 1344) hydrogen bonds : angle 4.59561 ( 3753) metal coordination : bond 0.00800 ( 33) metal coordination : angle 18.69087 ( 81) Misc. bond : bond 0.12954 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10420.75 seconds wall clock time: 178 minutes 26.33 seconds (10706.33 seconds total)