Starting phenix.real_space_refine on Mon Jul 6 07:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aba_15316/07_2026/8aba_15316.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 31 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'FES': 1, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.901 46.532 27.632 1.00284.47 S ATOM 4207 SG CYS P 187 32.231 44.484 25.278 1.00237.01 S Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 128.805, 165.369, 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 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 21 sheets defined 61.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.709A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.769A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.807A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.807A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.043A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.611A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.541A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.188A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.579A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.519A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.996A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.559A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.985A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.583A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.564A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.664A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.590A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.568A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.786A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.815A pdb=" N VAL B 283 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.686A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.590A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.923A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 321 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.417A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.534A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.535A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.764A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.692A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.712A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.779A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.817A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.815A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.044A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.608A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.544A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.194A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.586A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.989A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.555A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.978A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.582A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.624A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.659A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.583A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.560A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 removed outlier: 3.512A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.792A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.894A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.572A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 3.910A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 321 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.419A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.528A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.593A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.763A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.687A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.873A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 176 through 177 removed outlier: 3.613A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.498A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.930A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.051A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.588A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.482A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 306 through 308 removed outlier: 3.911A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.559A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.595A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1888 hydrogen bonds defined for protein. 5343 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: 5.73 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13593 1.41 - 1.61: 19561 1.61 - 1.82: 174 1.82 - 2.03: 19 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.638 -0.180 1.90e-02 2.77e+03 9.00e+01 bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.637 -0.179 1.90e-02 2.77e+03 8.86e+01 bond pdb=" C31 CDL A3001 " pdb=" CA7 CDL A3001 " ideal model delta sigma weight residual 1.500 1.615 -0.115 1.50e-02 4.44e+03 5.89e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.600 -0.142 1.90e-02 2.77e+03 5.60e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.475 -0.147 2.00e-02 2.50e+03 5.40e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 44211 4.46 - 8.91: 1047 8.91 - 13.37: 83 13.37 - 17.83: 9 17.83 - 22.29: 2 Bond angle restraints: 45352 Sorted by residual: angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 89.71 22.29 2.20e+00 2.07e-01 1.03e+02 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 91.29 20.71 2.20e+00 2.07e-01 8.86e+01 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.98 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 97.13 14.01 1.56e+00 4.11e-01 8.07e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.70 10.63 1.20e+00 6.94e-01 7.85e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.84: 18407 30.84 - 61.68: 1000 61.68 - 92.52: 106 92.52 - 123.36: 1 123.36 - 154.20: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.74 -17.86 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.75 63.75 2 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -2.96 62.96 2 1.00e+01 1.00e-02 3.81e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4605 0.199 - 0.398: 341 0.398 - 0.596: 12 0.596 - 0.795: 0 0.795 - 0.994: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.58 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.62 -0.96 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.65 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.015 2.00e-02 2.50e+03 3.21e-02 2.32e+01 pdb=" C2A HEC D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.031 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.032 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.051 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.011 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.060 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.010 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.027 2.00e-02 2.50e+03 2.96e-02 1.98e+01 pdb=" C2C HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.001 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.047 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.058 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " 0.057 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 474 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " 0.021 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 312 2.63 - 3.20: 29149 3.20 - 3.77: 53647 3.77 - 4.33: 79408 4.33 - 4.90: 122150 Nonbonded interactions: 284666 Sorted by model distance: nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.090 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.131 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.162 3.120 nonbonded pdb=" SD MET O 248 " pdb="FE HEC O 401 " model vdw 2.171 3.360 ... (remaining 284661 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 'L' and resid 26 through 3002) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = chain 'D' selection = (chain 'O' and resid 85 through 401) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 4 through 57) selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 32.190 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9417 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 : 0.011 0.221 33382 Z= 0.664 Angle : 1.767 22.287 45365 Z= 1.105 Chirality : 0.112 0.994 4962 Planarity : 0.007 0.081 5700 Dihedral : 17.809 154.198 12014 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.58 % Allowed : 8.24 % Favored : 88.18 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.12), residues: 3955 helix: -1.23 (0.09), residues: 2141 sheet: 0.01 (0.25), residues: 357 loop : -0.70 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG C 283 TYR 0.041 0.007 TYR O 120 PHE 0.046 0.006 PHE B 107 TRP 0.057 0.007 TRP A 474 HIS 0.027 0.004 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.66 (33367) covalent geometry : angle 1.76355 / 1.11 (45352) SS BOND : bond 0.03022 / 1.76 ( 5) SS BOND : angle 2.76565 / 1.47 ( 10) hydrogen bonds : bond 0.18567 / 12.28 ( 1888) hydrogen bonds : angle 7.13130 / 5.12 ( 5343) metal coordination : bond 0.07059 / 3.42 ( 4) metal coordination : angle 13.91860 / 7.24 ( 3) Misc. bond : bond 0.14020 / 7.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 486 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (ttm) REVERT: P 92 SER cc_start: 0.9643 (t) cc_final: 0.9262 (p) REVERT: P 114 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8661 (mmmm) REVERT: P 158 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8269 (ttmm) REVERT: P 164 MET cc_start: 0.9097 (mtm) cc_final: 0.8782 (mtm) REVERT: P 213 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: F 91 CYS cc_start: 0.8785 (m) cc_final: 0.8585 (m) REVERT: F 116 HIS cc_start: 0.8910 (m-70) cc_final: 0.8520 (m90) REVERT: A 141 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: A 275 MET cc_start: 0.9391 (mtp) cc_final: 0.9186 (mtp) REVERT: B 364 MET cc_start: 0.9204 (tpp) cc_final: 0.8984 (mmm) REVERT: D 224 GLU cc_start: 0.9344 (tt0) cc_final: 0.9101 (pm20) REVERT: D 248 MET cc_start: 0.9306 (ttp) cc_final: 0.8576 (ttp) REVERT: H 57 LEU cc_start: 0.8989 (mt) cc_final: 0.8665 (tp) REVERT: H 76 LYS cc_start: 0.9087 (tptm) cc_final: 0.8817 (tppt) REVERT: I 30 ASP cc_start: 0.9438 (t70) cc_final: 0.9169 (t0) REVERT: I 43 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8658 (ttp80) REVERT: J 13 SER cc_start: 0.9256 (t) cc_final: 0.8970 (p) REVERT: J 58 GLN cc_start: 0.9333 (tp40) cc_final: 0.8662 (tm-30) REVERT: J 63 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8725 (mptt) REVERT: J 80 ASN cc_start: 0.9340 (t0) cc_final: 0.9035 (t0) REVERT: N 186 MET cc_start: 0.9544 (tpp) cc_final: 0.9290 (mmt) REVERT: N 287 ASP cc_start: 0.8786 (t0) cc_final: 0.8346 (t70) REVERT: E 55 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8435 (p0) REVERT: R 44 MET cc_start: 0.9540 (tmm) cc_final: 0.9320 (tmm) REVERT: R 50 GLU cc_start: 0.9084 (pt0) cc_final: 0.8799 (pm20) REVERT: Q 95 LYS cc_start: 0.9415 (tptt) cc_final: 0.9209 (tptp) REVERT: Q 122 ASP cc_start: 0.8692 (p0) cc_final: 0.8412 (p0) REVERT: Q 126 GLU cc_start: 0.9293 (mp0) cc_final: 0.8578 (mp0) REVERT: L 29 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8996 (ptmm) REVERT: L 48 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8899 (tt) REVERT: L 159 ASN cc_start: 0.7654 (p0) cc_final: 0.7411 (p0) REVERT: L 405 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9037 (tm-30) REVERT: M 341 TYR cc_start: 0.9210 (t80) cc_final: 0.8794 (t80) REVERT: M 345 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9218 (ttmm) REVERT: S 22 LYS cc_start: 0.9409 (tttt) cc_final: 0.9206 (tttm) REVERT: U 10 LYS cc_start: 0.9506 (tttm) cc_final: 0.9288 (tptm) REVERT: U 13 SER cc_start: 0.9290 (t) cc_final: 0.9088 (p) REVERT: U 58 GLN cc_start: 0.9378 (tp40) cc_final: 0.9169 (tt0) REVERT: U 74 GLU cc_start: 0.8966 (mp0) cc_final: 0.8522 (pp20) outliers start: 119 outliers final: 13 residues processed: 563 average time/residue: 0.2321 time to fit residues: 200.4699 Evaluate side-chains 354 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 345 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 14 ASN C 173 ASN C 202 HIS C 332 ASN P 85 GLN P 90 ASN G 54 ASN A 192 GLN A 222 HIS A 317 GLN A 371 ASN B 87 HIS B 197 ASN I 49 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 197 ASN M 316 GLN M 377 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.068848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.052970 restraints weight = 73494.462| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.16 r_work: 0.2524 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.510 33382 Z= 0.145 Angle : 0.635 17.690 45365 Z= 0.314 Chirality : 0.042 0.193 4962 Planarity : 0.004 0.040 5700 Dihedral : 12.155 127.277 4875 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.47 % Allowed : 10.95 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.68 (0.13), residues: 3955 helix: 0.91 (0.11), residues: 2156 sheet: 0.35 (0.26), residues: 368 loop : -0.05 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 104 TYR 0.025 0.002 TYR F 114 PHE 0.020 0.002 PHE L 334 TRP 0.028 0.002 TRP N 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (33367) covalent geometry : angle 0.62862 / 0.31 (45352) SS BOND : bond 0.00272 / 0.14 ( 5) SS BOND : angle 1.22418 / 0.70 ( 10) hydrogen bonds : bond 0.04831 / 3.21 ( 1888) hydrogen bonds : angle 4.91097 / 3.52 ( 5343) metal coordination : bond 0.01779 / 0.89 ( 4) metal coordination : angle 10.66334 / 5.64 ( 3) Misc. bond : bond 0.34697 / 20.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9177 (m-30) cc_final: 0.8857 (m-30) REVERT: P 150 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: P 164 MET cc_start: 0.8749 (mtm) cc_final: 0.8439 (mtm) REVERT: P 202 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.6945 (mtp-110) REVERT: P 213 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7390 (mp0) REVERT: G 97 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 77 ASP cc_start: 0.8648 (t0) cc_final: 0.8407 (t0) REVERT: F 107 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8820 (tptp) REVERT: F 114 TYR cc_start: 0.8495 (t80) cc_final: 0.7996 (t80) REVERT: F 120 LYS cc_start: 0.9313 (mttp) cc_final: 0.8595 (mmtp) REVERT: F 125 GLU cc_start: 0.8695 (tt0) cc_final: 0.8406 (mt-10) REVERT: B 60 PHE cc_start: 0.9565 (OUTLIER) cc_final: 0.9304 (t80) REVERT: B 168 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: D 248 MET cc_start: 0.9016 (ttp) cc_final: 0.8089 (ttp) REVERT: H 57 LEU cc_start: 0.8974 (mt) cc_final: 0.8704 (tp) REVERT: H 76 LYS cc_start: 0.8942 (tptm) cc_final: 0.8488 (tppt) REVERT: I 43 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8376 (ttp80) REVERT: J 13 SER cc_start: 0.9210 (t) cc_final: 0.8929 (p) REVERT: J 63 LYS cc_start: 0.9122 (mmtp) cc_final: 0.8912 (mmtm) REVERT: J 80 ASN cc_start: 0.9211 (t0) cc_final: 0.8786 (t0) REVERT: N 287 ASP cc_start: 0.8396 (t0) cc_final: 0.7876 (t70) REVERT: N 288 LYS cc_start: 0.8912 (tttt) cc_final: 0.8704 (tttp) REVERT: N 353 GLN cc_start: 0.8994 (mt0) cc_final: 0.8769 (mt0) REVERT: E 55 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7717 (p0) REVERT: R 31 TYR cc_start: 0.8994 (t80) cc_final: 0.8652 (t80) REVERT: R 51 GLU cc_start: 0.9283 (mp0) cc_final: 0.8720 (mp0) REVERT: Q 77 ASP cc_start: 0.8625 (t0) cc_final: 0.8421 (t0) REVERT: Q 126 GLU cc_start: 0.9159 (mp0) cc_final: 0.8752 (mp0) REVERT: L 48 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8735 (tt) REVERT: L 87 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8400 (ptp90) REVERT: M 60 PHE cc_start: 0.9597 (OUTLIER) cc_final: 0.9233 (t80) REVERT: O 90 HIS cc_start: 0.9002 (m-70) cc_final: 0.8736 (m-70) REVERT: S 22 LYS cc_start: 0.9277 (tttt) cc_final: 0.8845 (tttm) REVERT: S 83 LYS cc_start: 0.8508 (mttt) cc_final: 0.8298 (mttt) REVERT: U 55 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8419 (ttm-80) outliers start: 49 outliers final: 15 residues processed: 418 average time/residue: 0.2207 time to fit residues: 144.3735 Evaluate side-chains 344 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 150 GLN Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 292 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN D 93 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.050749 restraints weight = 74775.709| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 2.05 r_work: 0.2483 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2345 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9303 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.486 33382 Z= 0.235 Angle : 0.624 17.471 45365 Z= 0.301 Chirality : 0.043 0.168 4962 Planarity : 0.004 0.048 5700 Dihedral : 11.035 103.622 4832 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.35 % Allowed : 11.28 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.13), residues: 3955 helix: 1.55 (0.11), residues: 2156 sheet: 0.53 (0.27), residues: 368 loop : 0.25 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 155 TYR 0.018 0.002 TYR C 16 PHE 0.018 0.002 PHE B 107 TRP 0.020 0.001 TRP C 142 HIS 0.012 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (33367) covalent geometry : angle 0.61783 / 0.30 (45352) SS BOND : bond 0.00190 / 0.11 ( 5) SS BOND : angle 0.83774 / 0.43 ( 10) hydrogen bonds : bond 0.04593 / 3.05 ( 1888) hydrogen bonds : angle 4.63920 / 3.33 ( 5343) metal coordination : bond 0.01832 / 0.92 ( 4) metal coordination : angle 10.81861 / 5.64 ( 3) Misc. bond : bond 0.35737 / 20.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9206 (m-30) cc_final: 0.8880 (m-30) REVERT: P 92 SER cc_start: 0.9497 (t) cc_final: 0.9080 (p) REVERT: P 150 GLN cc_start: 0.8658 (tt0) cc_final: 0.8352 (tt0) REVERT: P 199 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8615 (ptp90) REVERT: P 213 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: G 97 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8501 (mt-10) REVERT: F 95 LYS cc_start: 0.8961 (tptt) cc_final: 0.8678 (ttmm) REVERT: F 107 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8846 (tptp) REVERT: F 125 GLU cc_start: 0.8617 (tt0) cc_final: 0.8416 (mt-10) REVERT: F 126 GLU cc_start: 0.9026 (mp0) cc_final: 0.8803 (mp0) REVERT: A 461 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8306 (p0) REVERT: B 60 PHE cc_start: 0.9616 (OUTLIER) cc_final: 0.9364 (t80) REVERT: B 168 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: H 57 LEU cc_start: 0.9022 (mt) cc_final: 0.8769 (tp) REVERT: H 76 LYS cc_start: 0.9061 (tptm) cc_final: 0.8621 (tppt) REVERT: I 43 ARG cc_start: 0.8623 (mtm110) cc_final: 0.8417 (ttp80) REVERT: J 13 SER cc_start: 0.9205 (t) cc_final: 0.8994 (p) REVERT: J 63 LYS cc_start: 0.9120 (mmtp) cc_final: 0.8678 (mptt) REVERT: J 80 ASN cc_start: 0.9194 (t0) cc_final: 0.8744 (t0) REVERT: N 186 MET cc_start: 0.9527 (tpp) cc_final: 0.9129 (mmt) REVERT: N 287 ASP cc_start: 0.8472 (t0) cc_final: 0.8010 (t70) REVERT: E 55 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7968 (p0) REVERT: R 50 GLU cc_start: 0.8399 (pm20) cc_final: 0.8019 (pm20) REVERT: R 51 GLU cc_start: 0.9231 (mp0) cc_final: 0.8363 (mp0) REVERT: Q 77 ASP cc_start: 0.8628 (t0) cc_final: 0.8414 (t0) REVERT: M 60 PHE cc_start: 0.9631 (OUTLIER) cc_final: 0.9260 (t80) REVERT: S 22 LYS cc_start: 0.9387 (tttt) cc_final: 0.8953 (tttm) REVERT: U 74 GLU cc_start: 0.8719 (pm20) cc_final: 0.8434 (pp20) outliers start: 45 outliers final: 25 residues processed: 361 average time/residue: 0.2092 time to fit residues: 121.1573 Evaluate side-chains 340 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain U residue 13 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 384 optimal weight: 0.0070 chunk 337 optimal weight: 7.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 316 GLN D 93 HIS L 50 GLN L 317 GLN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.052690 restraints weight = 73807.972| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.14 r_work: 0.2526 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9240 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.440 33382 Z= 0.122 Angle : 0.536 15.987 45365 Z= 0.257 Chirality : 0.040 0.201 4962 Planarity : 0.004 0.049 5700 Dihedral : 10.454 93.107 4825 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.32 % Allowed : 11.82 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2159 sheet: 0.59 (0.27), residues: 368 loop : 0.39 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 202 TYR 0.016 0.001 TYR D 117 PHE 0.015 0.001 PHE U 20 TRP 0.014 0.001 TRP C 142 HIS 0.008 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (33367) covalent geometry : angle 0.52873 / 0.26 (45352) SS BOND : bond 0.00189 / 0.11 ( 5) SS BOND : angle 0.58345 / 0.30 ( 10) hydrogen bonds : bond 0.03916 / 2.59 ( 1888) hydrogen bonds : angle 4.44438 / 3.19 ( 5343) metal coordination : bond 0.01335 / 0.67 ( 4) metal coordination : angle 10.82666 / 5.61 ( 3) Misc. bond : bond 0.31611 / 17.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 335 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9212 (m-30) cc_final: 0.8840 (m-30) REVERT: P 92 SER cc_start: 0.9442 (t) cc_final: 0.8992 (p) REVERT: P 150 GLN cc_start: 0.8727 (tt0) cc_final: 0.8330 (tt0) REVERT: P 199 ARG cc_start: 0.8916 (ptp90) cc_final: 0.8633 (ptp90) REVERT: P 213 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: G 97 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8492 (mt-10) REVERT: F 95 LYS cc_start: 0.8885 (tptt) cc_final: 0.8656 (ttmm) REVERT: F 103 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8263 (mp0) REVERT: F 107 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8969 (mtmm) REVERT: F 114 TYR cc_start: 0.8056 (t80) cc_final: 0.6928 (t80) REVERT: F 120 LYS cc_start: 0.9274 (mttp) cc_final: 0.8464 (mmtp) REVERT: F 125 GLU cc_start: 0.8642 (tt0) cc_final: 0.8373 (mt-10) REVERT: F 126 GLU cc_start: 0.8946 (mp0) cc_final: 0.8575 (mp0) REVERT: B 60 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.9286 (t80) REVERT: B 83 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9003 (mtmm) REVERT: B 168 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: D 193 GLN cc_start: 0.9215 (mp10) cc_final: 0.8934 (mp10) REVERT: D 248 MET cc_start: 0.8896 (ttp) cc_final: 0.8166 (ttp) REVERT: H 57 LEU cc_start: 0.8953 (mt) cc_final: 0.8691 (tp) REVERT: H 76 LYS cc_start: 0.8927 (tptm) cc_final: 0.8492 (tppt) REVERT: I 43 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8351 (ttp80) REVERT: J 13 SER cc_start: 0.9190 (t) cc_final: 0.8941 (p) REVERT: J 63 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8581 (mptt) REVERT: J 69 GLU cc_start: 0.7698 (pp20) cc_final: 0.7330 (pp20) REVERT: J 80 ASN cc_start: 0.9173 (t0) cc_final: 0.8766 (t0) REVERT: N 186 MET cc_start: 0.9508 (tpp) cc_final: 0.9280 (mmp) REVERT: N 287 ASP cc_start: 0.8389 (t0) cc_final: 0.7916 (t0) REVERT: E 55 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7915 (p0) REVERT: R 50 GLU cc_start: 0.8460 (pm20) cc_final: 0.8252 (pm20) REVERT: R 51 GLU cc_start: 0.9247 (mp0) cc_final: 0.8879 (mp0) REVERT: Q 77 ASP cc_start: 0.8574 (t0) cc_final: 0.8297 (t0) REVERT: Q 126 GLU cc_start: 0.9034 (mp0) cc_final: 0.8776 (mp0) REVERT: L 87 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7765 (ptp90) REVERT: M 60 PHE cc_start: 0.9582 (OUTLIER) cc_final: 0.9187 (t80) REVERT: O 90 HIS cc_start: 0.8751 (m90) cc_final: 0.8450 (m170) REVERT: S 22 LYS cc_start: 0.9373 (tttt) cc_final: 0.8879 (tttm) REVERT: T 42 ASP cc_start: 0.8891 (m-30) cc_final: 0.8645 (m-30) REVERT: T 51 LYS cc_start: 0.9576 (ptpp) cc_final: 0.9370 (ptpp) REVERT: U 10 LYS cc_start: 0.9147 (tppt) cc_final: 0.8913 (tptt) REVERT: U 74 GLU cc_start: 0.8794 (pm20) cc_final: 0.8456 (pp20) outliers start: 44 outliers final: 21 residues processed: 367 average time/residue: 0.1905 time to fit residues: 113.1804 Evaluate side-chains 342 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 369 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS N 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.051525 restraints weight = 75155.190| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.39 r_work: 0.2502 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.403 33382 Z= 0.124 Angle : 0.521 14.595 45365 Z= 0.249 Chirality : 0.040 0.179 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.972 88.526 4825 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.59 % Allowed : 12.21 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.03 (0.14), residues: 3955 helix: 2.07 (0.11), residues: 2157 sheet: 0.68 (0.27), residues: 360 loop : 0.52 (0.18), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 202 TYR 0.017 0.001 TYR Q 114 PHE 0.015 0.001 PHE U 20 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (33367) covalent geometry : angle 0.51397 / 0.25 (45352) SS BOND : bond 0.00179 / 0.13 ( 5) SS BOND : angle 0.59295 / 0.31 ( 10) hydrogen bonds : bond 0.03765 / 2.49 ( 1888) hydrogen bonds : angle 4.32480 / 3.10 ( 5343) metal coordination : bond 0.00833 / 0.42 ( 4) metal coordination : angle 10.27027 / 5.37 ( 3) Misc. bond : bond 0.28116 / 16.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9218 (m-30) cc_final: 0.8811 (m-30) REVERT: C 322 SER cc_start: 0.9420 (OUTLIER) cc_final: 0.9014 (m) REVERT: P 92 SER cc_start: 0.9399 (t) cc_final: 0.8949 (p) REVERT: P 150 GLN cc_start: 0.8739 (tt0) cc_final: 0.8356 (tt0) REVERT: P 194 TYR cc_start: 0.8390 (m-80) cc_final: 0.7566 (m-10) REVERT: P 196 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7954 (tp) REVERT: P 201 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7944 (mmm-85) REVERT: P 213 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: G 50 GLU cc_start: 0.8948 (pm20) cc_final: 0.8604 (pm20) REVERT: G 97 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8480 (mt-10) REVERT: F 107 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8748 (mtmm) REVERT: F 110 GLU cc_start: 0.8748 (pt0) cc_final: 0.8465 (pp20) REVERT: F 114 TYR cc_start: 0.8121 (t80) cc_final: 0.7023 (t80) REVERT: F 120 LYS cc_start: 0.9279 (mttp) cc_final: 0.8279 (mmtp) REVERT: F 125 GLU cc_start: 0.8670 (tt0) cc_final: 0.8367 (mt-10) REVERT: F 126 GLU cc_start: 0.8941 (mp0) cc_final: 0.8579 (mp0) REVERT: A 461 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8037 (p0) REVERT: B 60 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9217 (t80) REVERT: B 83 LYS cc_start: 0.9274 (mmtm) cc_final: 0.8895 (mtmm) REVERT: B 168 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: H 57 LEU cc_start: 0.8901 (mt) cc_final: 0.8645 (tp) REVERT: H 76 LYS cc_start: 0.8865 (tptm) cc_final: 0.8440 (tppt) REVERT: I 43 ARG cc_start: 0.8525 (mtm110) cc_final: 0.8246 (ttp80) REVERT: J 11 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8598 (tmtt) REVERT: J 13 SER cc_start: 0.9166 (t) cc_final: 0.8935 (p) REVERT: J 63 LYS cc_start: 0.9002 (mmtp) cc_final: 0.8555 (mptt) REVERT: J 69 GLU cc_start: 0.7762 (pp20) cc_final: 0.7405 (pp20) REVERT: J 80 ASN cc_start: 0.9188 (t0) cc_final: 0.8791 (t0) REVERT: N 287 ASP cc_start: 0.8348 (t0) cc_final: 0.7923 (t70) REVERT: N 374 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8537 (mt-10) REVERT: E 55 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8009 (p0) REVERT: R 50 GLU cc_start: 0.8589 (pm20) cc_final: 0.8315 (pm20) REVERT: R 51 GLU cc_start: 0.9265 (mp0) cc_final: 0.8759 (mp0) REVERT: Q 113 ASP cc_start: 0.8757 (p0) cc_final: 0.8486 (p0) REVERT: L 87 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7503 (ptp90) REVERT: L 461 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (p0) REVERT: M 60 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.9110 (t80) REVERT: M 124 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8505 (mt-10) REVERT: M 339 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8609 (ttp-110) REVERT: O 90 HIS cc_start: 0.8751 (m90) cc_final: 0.8420 (m170) REVERT: S 22 LYS cc_start: 0.9407 (tttt) cc_final: 0.8873 (tttm) REVERT: T 42 ASP cc_start: 0.8912 (m-30) cc_final: 0.8631 (m-30) REVERT: T 51 LYS cc_start: 0.9575 (ptpp) cc_final: 0.9364 (pttt) REVERT: U 10 LYS cc_start: 0.9111 (tppt) cc_final: 0.8815 (tptt) REVERT: U 74 GLU cc_start: 0.8866 (pm20) cc_final: 0.8520 (pp20) outliers start: 53 outliers final: 24 residues processed: 364 average time/residue: 0.2049 time to fit residues: 119.9611 Evaluate side-chains 344 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 309 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 301 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 352 optimal weight: 0.0050 chunk 153 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.050977 restraints weight = 75375.559| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.42 r_work: 0.2475 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2331 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.422 33382 Z= 0.162 Angle : 0.539 15.777 45365 Z= 0.256 Chirality : 0.041 0.208 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.764 88.195 4825 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.44 % Allowed : 12.39 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.10 (0.14), residues: 3955 helix: 2.11 (0.11), residues: 2155 sheet: 0.73 (0.27), residues: 370 loop : 0.59 (0.18), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 202 TYR 0.019 0.001 TYR P 214 PHE 0.019 0.001 PHE E 64 TRP 0.015 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (33367) covalent geometry : angle 0.53340 / 0.26 (45352) SS BOND : bond 0.00217 / 0.14 ( 5) SS BOND : angle 0.59640 / 0.31 ( 10) hydrogen bonds : bond 0.03861 / 2.56 ( 1888) hydrogen bonds : angle 4.31901 / 3.10 ( 5343) metal coordination : bond 0.00923 / 0.46 ( 4) metal coordination : angle 9.81359 / 5.17 ( 3) Misc. bond : bond 0.27509 / 16.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9223 (m-30) cc_final: 0.8810 (m-30) REVERT: C 322 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9004 (m) REVERT: C 345 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8472 (mp0) REVERT: P 92 SER cc_start: 0.9358 (t) cc_final: 0.8885 (p) REVERT: P 150 GLN cc_start: 0.8740 (tt0) cc_final: 0.8378 (tt0) REVERT: P 201 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7952 (mmm-85) REVERT: P 213 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: G 50 GLU cc_start: 0.8954 (pm20) cc_final: 0.8628 (pm20) REVERT: G 97 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8462 (mt-10) REVERT: G 117 ASP cc_start: 0.8569 (t0) cc_final: 0.8354 (t0) REVERT: F 107 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8710 (mtmm) REVERT: F 110 GLU cc_start: 0.8780 (pt0) cc_final: 0.8511 (pp20) REVERT: F 114 TYR cc_start: 0.8133 (t80) cc_final: 0.6939 (t80) REVERT: F 120 LYS cc_start: 0.9269 (mttp) cc_final: 0.8446 (mmtp) REVERT: F 125 GLU cc_start: 0.8684 (tt0) cc_final: 0.8372 (mt-10) REVERT: F 126 GLU cc_start: 0.8974 (mp0) cc_final: 0.8591 (mp0) REVERT: A 461 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8079 (p0) REVERT: B 60 PHE cc_start: 0.9508 (OUTLIER) cc_final: 0.9260 (t80) REVERT: B 83 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8871 (mtmm) REVERT: D 85 MET cc_start: 0.8692 (mtm) cc_final: 0.8469 (mtm) REVERT: H 57 LEU cc_start: 0.8886 (mt) cc_final: 0.8618 (tp) REVERT: H 76 LYS cc_start: 0.8863 (tptm) cc_final: 0.8439 (tppt) REVERT: I 43 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8209 (ttp80) REVERT: J 11 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8631 (tmtt) REVERT: J 13 SER cc_start: 0.9171 (t) cc_final: 0.8961 (p) REVERT: J 58 GLN cc_start: 0.9049 (tp40) cc_final: 0.8562 (tt0) REVERT: J 63 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8515 (mptt) REVERT: J 69 GLU cc_start: 0.7759 (pp20) cc_final: 0.7404 (pp20) REVERT: J 80 ASN cc_start: 0.9176 (t0) cc_final: 0.8753 (t0) REVERT: N 287 ASP cc_start: 0.8333 (t0) cc_final: 0.7843 (t0) REVERT: E 55 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8124 (p0) REVERT: E 68 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8662 (mpp) REVERT: R 50 GLU cc_start: 0.8641 (pm20) cc_final: 0.8347 (pm20) REVERT: R 51 GLU cc_start: 0.9282 (mp0) cc_final: 0.8732 (mp0) REVERT: Q 99 ASP cc_start: 0.9133 (m-30) cc_final: 0.8744 (p0) REVERT: L 48 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8682 (tt) REVERT: L 87 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: L 461 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8139 (p0) REVERT: M 60 PHE cc_start: 0.9542 (OUTLIER) cc_final: 0.9155 (t80) REVERT: M 339 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8611 (ttp-110) REVERT: O 90 HIS cc_start: 0.8732 (m90) cc_final: 0.8391 (m170) REVERT: S 22 LYS cc_start: 0.9434 (tttt) cc_final: 0.8891 (tttm) REVERT: T 42 ASP cc_start: 0.8929 (m-30) cc_final: 0.8512 (m-30) REVERT: T 51 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9313 (pttt) REVERT: U 10 LYS cc_start: 0.9105 (tppt) cc_final: 0.8779 (tptt) outliers start: 48 outliers final: 29 residues processed: 352 average time/residue: 0.2097 time to fit residues: 118.8677 Evaluate side-chains 349 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 301 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 10.0000 chunk 183 optimal weight: 0.0020 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 304 optimal weight: 0.3980 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.051547 restraints weight = 75456.934| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.39 r_work: 0.2502 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.401 33382 Z= 0.128 Angle : 0.519 14.384 45365 Z= 0.247 Chirality : 0.040 0.171 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.537 89.218 4823 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.41 % Allowed : 12.48 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.21 (0.14), residues: 3955 helix: 2.18 (0.11), residues: 2155 sheet: 0.79 (0.27), residues: 365 loop : 0.66 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 202 TYR 0.023 0.001 TYR P 214 PHE 0.014 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (33367) covalent geometry : angle 0.51341 / 0.25 (45352) SS BOND : bond 0.00214 / 0.14 ( 5) SS BOND : angle 0.59462 / 0.31 ( 10) hydrogen bonds : bond 0.03688 / 2.45 ( 1888) hydrogen bonds : angle 4.26375 / 3.06 ( 5343) metal coordination : bond 0.00761 / 0.37 ( 4) metal coordination : angle 9.43344 / 4.98 ( 3) Misc. bond : bond 0.25785 / 15.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9225 (m-30) cc_final: 0.8806 (m-30) REVERT: C 322 SER cc_start: 0.9427 (OUTLIER) cc_final: 0.9034 (m) REVERT: C 345 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8529 (mp0) REVERT: P 92 SER cc_start: 0.9382 (t) cc_final: 0.8912 (p) REVERT: P 150 GLN cc_start: 0.8739 (tt0) cc_final: 0.8328 (tt0) REVERT: P 196 ILE cc_start: 0.8542 (mm) cc_final: 0.8117 (tp) REVERT: P 201 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8002 (mmm-85) REVERT: P 213 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: G 50 GLU cc_start: 0.8923 (pm20) cc_final: 0.8604 (pm20) REVERT: G 66 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8574 (mm-30) REVERT: G 97 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8471 (mt-10) REVERT: G 117 ASP cc_start: 0.8581 (t0) cc_final: 0.8367 (t0) REVERT: F 107 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8730 (mtmm) REVERT: F 110 GLU cc_start: 0.8791 (pt0) cc_final: 0.8472 (pp20) REVERT: F 114 TYR cc_start: 0.8158 (t80) cc_final: 0.7012 (t80) REVERT: F 120 LYS cc_start: 0.9267 (mttp) cc_final: 0.8436 (mmtp) REVERT: F 125 GLU cc_start: 0.8677 (tt0) cc_final: 0.8339 (mt-10) REVERT: F 126 GLU cc_start: 0.8973 (mp0) cc_final: 0.8590 (mp0) REVERT: A 461 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (p0) REVERT: B 60 PHE cc_start: 0.9512 (OUTLIER) cc_final: 0.9260 (t80) REVERT: B 83 LYS cc_start: 0.9264 (mmtm) cc_final: 0.8871 (mtmm) REVERT: B 168 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (mm-40) REVERT: D 85 MET cc_start: 0.8728 (mtm) cc_final: 0.8505 (mtm) REVERT: H 57 LEU cc_start: 0.8898 (mt) cc_final: 0.8644 (tp) REVERT: H 76 LYS cc_start: 0.8880 (tptm) cc_final: 0.8449 (tppt) REVERT: I 43 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8204 (ttp80) REVERT: I 52 ASP cc_start: 0.9248 (m-30) cc_final: 0.9010 (m-30) REVERT: J 11 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8711 (ttpp) REVERT: J 58 GLN cc_start: 0.9058 (tp40) cc_final: 0.8720 (tt0) REVERT: J 63 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8541 (mptt) REVERT: J 69 GLU cc_start: 0.7828 (pp20) cc_final: 0.7440 (pp20) REVERT: J 80 ASN cc_start: 0.9196 (t0) cc_final: 0.8776 (t0) REVERT: N 287 ASP cc_start: 0.8343 (t0) cc_final: 0.7876 (t0) REVERT: E 55 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8134 (p0) REVERT: R 50 GLU cc_start: 0.8632 (pm20) cc_final: 0.8354 (pm20) REVERT: R 51 GLU cc_start: 0.9229 (mp0) cc_final: 0.8653 (mp0) REVERT: L 87 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7482 (ptp90) REVERT: M 60 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.9148 (t80) REVERT: M 339 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8646 (ttp-110) REVERT: O 90 HIS cc_start: 0.8697 (m90) cc_final: 0.8285 (m170) REVERT: S 22 LYS cc_start: 0.9427 (tttt) cc_final: 0.8884 (tttm) REVERT: T 42 ASP cc_start: 0.8917 (m-30) cc_final: 0.8696 (m-30) REVERT: T 51 LYS cc_start: 0.9573 (ptpp) cc_final: 0.9359 (pttm) REVERT: U 10 LYS cc_start: 0.9098 (tppt) cc_final: 0.8772 (tptt) outliers start: 47 outliers final: 30 residues processed: 359 average time/residue: 0.2083 time to fit residues: 120.7887 Evaluate side-chains 348 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 301 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 389 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 341 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.066366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.050156 restraints weight = 75894.682| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.42 r_work: 0.2464 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9233 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.442 33382 Z= 0.205 Angle : 0.566 17.112 45365 Z= 0.268 Chirality : 0.042 0.174 4962 Planarity : 0.004 0.055 5700 Dihedral : 9.555 87.896 4823 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.38 % Allowed : 12.84 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.18 (0.14), residues: 3955 helix: 2.17 (0.11), residues: 2148 sheet: 0.71 (0.26), residues: 370 loop : 0.65 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 202 TYR 0.022 0.001 TYR P 214 PHE 0.020 0.001 PHE P 186 TRP 0.019 0.001 TRP P 185 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (33367) covalent geometry : angle 0.56138 / 0.27 (45352) SS BOND : bond 0.00259 / 0.17 ( 5) SS BOND : angle 0.67847 / 0.36 ( 10) hydrogen bonds : bond 0.03978 / 2.64 ( 1888) hydrogen bonds : angle 4.30407 / 3.09 ( 5343) metal coordination : bond 0.01046 / 0.52 ( 4) metal coordination : angle 8.82691 / 4.63 ( 3) Misc. bond : bond 0.29479 / 17.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9228 (m-30) cc_final: 0.8798 (m-30) REVERT: C 322 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.8981 (m) REVERT: P 92 SER cc_start: 0.9383 (t) cc_final: 0.8965 (p) REVERT: P 150 GLN cc_start: 0.8739 (tt0) cc_final: 0.8331 (tt0) REVERT: P 196 ILE cc_start: 0.8638 (mm) cc_final: 0.8234 (tp) REVERT: P 201 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: P 213 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: G 50 GLU cc_start: 0.8967 (pm20) cc_final: 0.8640 (pm20) REVERT: G 97 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8468 (mt-10) REVERT: G 117 ASP cc_start: 0.8578 (t0) cc_final: 0.8344 (t0) REVERT: G 123 GLU cc_start: 0.8942 (tt0) cc_final: 0.8658 (tt0) REVERT: F 103 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8340 (mp0) REVERT: F 107 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8726 (mtmm) REVERT: F 110 GLU cc_start: 0.8828 (pt0) cc_final: 0.8511 (pp20) REVERT: F 114 TYR cc_start: 0.8208 (t80) cc_final: 0.7078 (t80) REVERT: F 120 LYS cc_start: 0.9240 (mttp) cc_final: 0.8214 (mmtp) REVERT: F 125 GLU cc_start: 0.8652 (tt0) cc_final: 0.8341 (mt-10) REVERT: F 126 GLU cc_start: 0.8897 (mp0) cc_final: 0.8491 (mp0) REVERT: A 461 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (p0) REVERT: B 60 PHE cc_start: 0.9514 (OUTLIER) cc_final: 0.9251 (t80) REVERT: B 83 LYS cc_start: 0.9258 (mmtm) cc_final: 0.8907 (mtmm) REVERT: H 57 LEU cc_start: 0.8867 (mt) cc_final: 0.8630 (tp) REVERT: H 76 LYS cc_start: 0.8875 (tptm) cc_final: 0.8445 (tppt) REVERT: H 88 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8753 (mp0) REVERT: I 7 PHE cc_start: 0.8577 (t80) cc_final: 0.8267 (t80) REVERT: I 43 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8171 (ttp80) REVERT: J 11 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8721 (ttpp) REVERT: J 58 GLN cc_start: 0.9059 (tp40) cc_final: 0.8724 (tt0) REVERT: J 63 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8507 (mptt) REVERT: J 69 GLU cc_start: 0.7846 (pp20) cc_final: 0.7469 (pp20) REVERT: J 80 ASN cc_start: 0.9190 (t0) cc_final: 0.8761 (t0) REVERT: N 287 ASP cc_start: 0.8344 (t0) cc_final: 0.7851 (t0) REVERT: E 55 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8241 (p0) REVERT: E 68 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8759 (mpp) REVERT: R 50 GLU cc_start: 0.8696 (pm20) cc_final: 0.8298 (pm20) REVERT: R 51 GLU cc_start: 0.9253 (mp0) cc_final: 0.8620 (mp0) REVERT: L 87 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7478 (ptp90) REVERT: L 461 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8136 (p0) REVERT: M 60 PHE cc_start: 0.9548 (OUTLIER) cc_final: 0.9195 (t80) REVERT: M 339 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8611 (ttp-110) REVERT: O 90 HIS cc_start: 0.8725 (m90) cc_final: 0.8300 (m170) REVERT: U 10 LYS cc_start: 0.9080 (tppt) cc_final: 0.8729 (tptt) REVERT: U 11 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8895 (mtmm) outliers start: 46 outliers final: 28 residues processed: 346 average time/residue: 0.2143 time to fit residues: 118.4158 Evaluate side-chains 344 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain O residue 301 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.066367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.050089 restraints weight = 75442.829| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 2.42 r_work: 0.2463 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2322 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.452 33382 Z= 0.197 Angle : 0.560 16.678 45365 Z= 0.266 Chirality : 0.042 0.176 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.525 87.404 4823 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.41 % Allowed : 12.63 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.15 (0.14), residues: 3955 helix: 2.14 (0.11), residues: 2154 sheet: 0.70 (0.26), residues: 370 loop : 0.65 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 54 TYR 0.022 0.001 TYR P 214 PHE 0.021 0.001 PHE P 186 TRP 0.017 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (33367) covalent geometry : angle 0.55528 / 0.27 (45352) SS BOND : bond 0.00184 / 0.11 ( 5) SS BOND : angle 1.09156 / 0.58 ( 10) hydrogen bonds : bond 0.03970 / 2.64 ( 1888) hydrogen bonds : angle 4.31042 / 3.10 ( 5343) metal coordination : bond 0.00768 / 0.38 ( 4) metal coordination : angle 9.02630 / 4.68 ( 3) Misc. bond : bond 0.31306 / 18.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9231 (m-30) cc_final: 0.8797 (m-30) REVERT: C 322 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.8974 (m) REVERT: P 150 GLN cc_start: 0.8747 (tt0) cc_final: 0.8334 (tt0) REVERT: P 196 ILE cc_start: 0.8677 (mm) cc_final: 0.8294 (tp) REVERT: P 201 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: P 213 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: G 50 GLU cc_start: 0.8966 (pm20) cc_final: 0.8646 (pm20) REVERT: G 97 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8470 (mt-10) REVERT: G 117 ASP cc_start: 0.8604 (t0) cc_final: 0.8317 (t0) REVERT: G 123 GLU cc_start: 0.8946 (tt0) cc_final: 0.8659 (tt0) REVERT: F 103 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8353 (mp0) REVERT: F 107 LYS cc_start: 0.9254 (ttmt) cc_final: 0.8746 (mtmm) REVERT: F 110 GLU cc_start: 0.8849 (pt0) cc_final: 0.8522 (pp20) REVERT: F 114 TYR cc_start: 0.8117 (t80) cc_final: 0.6970 (t80) REVERT: F 120 LYS cc_start: 0.9209 (mttp) cc_final: 0.8169 (mmtp) REVERT: F 125 GLU cc_start: 0.8642 (tt0) cc_final: 0.8310 (mt-10) REVERT: F 126 GLU cc_start: 0.8890 (mp0) cc_final: 0.8477 (mp0) REVERT: F 131 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8961 (mm110) REVERT: A 461 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8178 (p0) REVERT: B 60 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.9248 (t80) REVERT: B 83 LYS cc_start: 0.9256 (mmtm) cc_final: 0.8898 (mtmm) REVERT: B 168 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: D 248 MET cc_start: 0.9157 (ttp) cc_final: 0.8338 (ttp) REVERT: H 57 LEU cc_start: 0.8883 (mt) cc_final: 0.8632 (tp) REVERT: H 76 LYS cc_start: 0.8871 (tptm) cc_final: 0.8440 (tppt) REVERT: H 88 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8762 (mp0) REVERT: J 11 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8696 (ttpp) REVERT: J 58 GLN cc_start: 0.9064 (tp40) cc_final: 0.8728 (tt0) REVERT: J 63 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8519 (mptt) REVERT: J 80 ASN cc_start: 0.9191 (t0) cc_final: 0.8754 (t0) REVERT: N 287 ASP cc_start: 0.8355 (t0) cc_final: 0.7879 (t0) REVERT: N 374 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8572 (mt-10) REVERT: E 55 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8260 (p0) REVERT: R 31 TYR cc_start: 0.8888 (t80) cc_final: 0.8541 (t80) REVERT: R 50 GLU cc_start: 0.8681 (pm20) cc_final: 0.8312 (pm20) REVERT: R 51 GLU cc_start: 0.9259 (mp0) cc_final: 0.8623 (mp0) REVERT: L 87 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7463 (ptp90) REVERT: L 461 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8130 (p0) REVERT: M 60 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.9193 (t80) REVERT: M 339 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8621 (ttp-110) REVERT: O 90 HIS cc_start: 0.8729 (m90) cc_final: 0.8311 (m170) REVERT: O 248 MET cc_start: 0.8833 (tpp) cc_final: 0.8545 (tpp) REVERT: S 22 LYS cc_start: 0.9445 (tttt) cc_final: 0.8944 (tttm) REVERT: U 10 LYS cc_start: 0.9096 (tppt) cc_final: 0.8742 (tptt) REVERT: U 11 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8908 (mtmm) outliers start: 47 outliers final: 33 residues processed: 344 average time/residue: 0.2022 time to fit residues: 111.6528 Evaluate side-chains 345 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 186 PHE Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.068251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.052178 restraints weight = 75354.055| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 2.42 r_work: 0.2512 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2369 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.386 33382 Z= 0.112 Angle : 0.514 13.420 45365 Z= 0.247 Chirality : 0.040 0.167 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.227 89.700 4823 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.14 % Allowed : 12.93 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.27 (0.14), residues: 3955 helix: 2.23 (0.11), residues: 2151 sheet: 0.73 (0.26), residues: 370 loop : 0.72 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 202 TYR 0.022 0.001 TYR P 214 PHE 0.025 0.001 PHE E 64 TRP 0.013 0.001 TRP T 50 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (33367) covalent geometry : angle 0.50873 / 0.25 (45352) SS BOND : bond 0.00488 / 0.36 ( 5) SS BOND : angle 1.40260 / 0.72 ( 10) hydrogen bonds : bond 0.03590 / 2.39 ( 1888) hydrogen bonds : angle 4.20450 / 3.02 ( 5343) metal coordination : bond 0.00829 / 0.41 ( 4) metal coordination : angle 9.14667 / 4.82 ( 3) Misc. bond : bond 0.25783 / 15.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9204 (m-30) cc_final: 0.8787 (m-30) REVERT: C 322 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9019 (m) REVERT: C 345 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8550 (mp0) REVERT: P 92 SER cc_start: 0.9359 (t) cc_final: 0.8896 (p) REVERT: P 150 GLN cc_start: 0.8767 (tt0) cc_final: 0.8381 (tt0) REVERT: P 196 ILE cc_start: 0.8700 (mm) cc_final: 0.8312 (tp) REVERT: P 201 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: G 50 GLU cc_start: 0.8932 (pm20) cc_final: 0.8625 (pm20) REVERT: G 117 ASP cc_start: 0.8545 (t0) cc_final: 0.8315 (t0) REVERT: G 123 GLU cc_start: 0.8947 (tt0) cc_final: 0.8676 (tt0) REVERT: F 103 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8324 (mp0) REVERT: F 107 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8768 (mtmm) REVERT: F 110 GLU cc_start: 0.8876 (pt0) cc_final: 0.8516 (pp20) REVERT: F 114 TYR cc_start: 0.8062 (t80) cc_final: 0.6874 (t80) REVERT: F 120 LYS cc_start: 0.9204 (mttp) cc_final: 0.8173 (mmtp) REVERT: F 125 GLU cc_start: 0.8649 (tt0) cc_final: 0.8327 (mt-10) REVERT: F 126 GLU cc_start: 0.8909 (mp0) cc_final: 0.8504 (mp0) REVERT: F 131 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8946 (mm110) REVERT: A 461 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 60 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9268 (t80) REVERT: B 83 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8877 (mtmm) REVERT: B 168 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8513 (mm-40) REVERT: D 248 MET cc_start: 0.9034 (ttp) cc_final: 0.8138 (ttp) REVERT: H 57 LEU cc_start: 0.8871 (mt) cc_final: 0.8630 (tp) REVERT: H 76 LYS cc_start: 0.8844 (tptm) cc_final: 0.8412 (tppt) REVERT: H 88 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8728 (mp0) REVERT: J 11 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8633 (ttpp) REVERT: J 58 GLN cc_start: 0.9051 (tp40) cc_final: 0.8724 (tt0) REVERT: J 63 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8525 (mptt) REVERT: J 80 ASN cc_start: 0.9184 (t0) cc_final: 0.8738 (t0) REVERT: N 287 ASP cc_start: 0.8298 (t0) cc_final: 0.7835 (t0) REVERT: E 55 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8113 (p0) REVERT: R 22 LYS cc_start: 0.8895 (tttm) cc_final: 0.8647 (ptmm) REVERT: R 50 GLU cc_start: 0.8662 (pm20) cc_final: 0.8227 (pm20) REVERT: R 51 GLU cc_start: 0.9228 (mp0) cc_final: 0.8389 (mp0) REVERT: Q 99 ASP cc_start: 0.9112 (m-30) cc_final: 0.8896 (m-30) REVERT: L 87 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7302 (ptp90) REVERT: L 461 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8064 (p0) REVERT: M 60 PHE cc_start: 0.9523 (OUTLIER) cc_final: 0.9158 (t80) REVERT: O 90 HIS cc_start: 0.8672 (m90) cc_final: 0.8274 (m170) REVERT: O 248 MET cc_start: 0.8796 (tpp) cc_final: 0.8457 (tpp) REVERT: S 22 LYS cc_start: 0.9378 (tttt) cc_final: 0.8826 (tttm) REVERT: U 10 LYS cc_start: 0.9093 (tppt) cc_final: 0.8745 (tptt) REVERT: U 11 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8921 (mtmm) outliers start: 38 outliers final: 25 residues processed: 352 average time/residue: 0.1965 time to fit residues: 110.9466 Evaluate side-chains 342 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 186 PHE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 377 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051963 restraints weight = 75289.859| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 2.42 r_work: 0.2511 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2369 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.390 33382 Z= 0.119 Angle : 0.521 14.234 45365 Z= 0.247 Chirality : 0.040 0.164 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.106 89.912 4823 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.57 % Favored : 98.41 % Rotamer: Outliers : 1.08 % Allowed : 13.14 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.30 (0.14), residues: 3955 helix: 2.26 (0.11), residues: 2154 sheet: 0.73 (0.27), residues: 371 loop : 0.73 (0.18), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 144 TYR 0.021 0.001 TYR P 214 PHE 0.029 0.001 PHE E 64 TRP 0.012 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (33367) covalent geometry : angle 0.51553 / 0.25 (45352) SS BOND : bond 0.00158 / 0.08 ( 5) SS BOND : angle 1.42000 / 0.73 ( 10) hydrogen bonds : bond 0.03587 / 2.39 ( 1888) hydrogen bonds : angle 4.18579 / 3.01 ( 5343) metal coordination : bond 0.00755 / 0.37 ( 4) metal coordination : angle 9.13349 / 4.80 ( 3) Misc. bond : bond 0.26158 / 15.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7499.54 seconds wall clock time: 129 minutes 35.13 seconds (7775.13 seconds total)