Starting phenix.real_space_refine on Mon Jul 6 07:36:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ac4_15333/07_2026/8ac4_15333.cif" } resolution = 2.7 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 127 residue(s): 0.04s 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: 34 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" 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: "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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} 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: 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: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" 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: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'XP4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 34.637 46.742 24.508 1.00164.04 S ATOM 4207 SG CYS P 187 36.885 46.000 21.408 1.00157.45 S Time building chain proxies: 6.57, per 1000 atoms: 0.20 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.854, 129.735, 166.563, 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=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 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 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " 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: 197 helices and 21 sheets defined 61.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 3.748A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.516A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) 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: 6.851A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.777A 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: 3.777A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.817A 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: 4.112A 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: 3.631A 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 99 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 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 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.194A 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: 3.595A 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: 3.508A 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: 4.011A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.054A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 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 removed outlier: 3.526A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.995A 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: 3.658A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.546A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.374A 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: 3.634A 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: 3.612A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.606A 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: 3.525A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.805A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.814A 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: 3.711A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.599A 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 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 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 56 removed outlier: 4.321A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 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: 3.515A 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: 3.534A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.823A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.649A 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: 3.756A 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: 6.851A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.766A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.812A 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: 4.117A 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: 3.647A 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: 3.506A 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 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.186A 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: 3.594A 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: 4.009A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.060A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 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 removed outlier: 3.516A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.971A 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: 3.666A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.702A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.366A 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: 3.637A 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: 3.614A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.596A 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: 3.519A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.796A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.818A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (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: 3.853A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.600A 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 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 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.319A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.516A 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: 3.559A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.821A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.655A 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 removed outlier: 3.528A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.910A 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: 3.590A 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: 6.513A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.989A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.794A 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: 6.565A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.629A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.621A 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: 6.530A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.996A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.789A 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: 6.546A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.721A 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: 6.631A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.600A 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 1887 hydrogen bonds defined for protein. 5301 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: 5.51 Time building geometry restraints manager: 3.49 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: 13595 1.41 - 1.61: 19562 1.61 - 1.82: 172 1.82 - 2.03: 19 2.03 - 2.24: 19 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 U 101 " pdb=" O7 XP4 U 101 " ideal model delta sigma weight residual 1.328 1.467 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.465 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.572 -0.114 1.90e-02 2.77e+03 3.60e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.571 -0.113 1.90e-02 2.77e+03 3.53e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 42736 3.28 - 6.57: 2293 6.57 - 9.85: 254 9.85 - 13.13: 52 13.13 - 16.42: 17 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.24 12.09 1.14e+00 7.69e-01 1.12e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.36 11.97 1.20e+00 6.94e-01 9.95e+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 97.55 13.59 1.56e+00 4.11e-01 7.59e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.18 -9.52 1.14e+00 7.69e-01 6.98e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 99.09 12.18 1.47e+00 4.63e-01 6.87e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 18568 32.72 - 65.45: 864 65.45 - 98.17: 81 98.17 - 130.89: 1 130.89 - 163.62: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -105.65 -16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -105.96 -16.64 0 2.50e+00 1.60e-01 4.43e+01 dihedral pdb=" C ARG S 51 " pdb=" N ARG S 51 " pdb=" CA ARG S 51 " pdb=" CB ARG S 51 " ideal model delta harmonic sigma weight residual -122.60 -139.08 16.48 0 2.50e+00 1.60e-01 4.34e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 4546 0.192 - 0.384: 394 0.384 - 0.576: 16 0.576 - 0.768: 2 0.768 - 0.960: 4 Chirality restraints: 4962 Sorted by residual: 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 -1.61 -0.96 2.00e-01 2.50e+01 2.31e+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 -1.64 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CB4 CDL S 101 " pdb=" CB3 CDL S 101 " pdb=" CB6 CDL S 101 " pdb=" OB6 CDL S 101 " both_signs ideal model delta sigma weight residual False -2.57 -1.66 -0.91 2.00e-01 2.50e+01 2.09e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC O 401 " 0.008 2.00e-02 2.50e+03 2.80e-02 1.77e+01 pdb=" C2A HEC O 401 " 0.026 2.00e-02 2.50e+03 pdb=" C3A HEC O 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4A HEC O 401 " 0.043 2.00e-02 2.50e+03 pdb=" CAA HEC O 401 " -0.040 2.00e-02 2.50e+03 pdb=" CHA HEC O 401 " -0.007 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " -0.049 2.00e-02 2.50e+03 pdb=" CMA HEC O 401 " 0.003 2.00e-02 2.50e+03 pdb=" NA HEC O 401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " -0.005 2.00e-02 2.50e+03 2.67e-02 1.60e+01 pdb=" C1B HEC O 401 " -0.011 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.022 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.008 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " -0.012 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.047 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.013 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.039 2.00e-02 2.50e+03 3.20e-02 1.54e+01 pdb=" CG HIS N 96 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.036 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 10 2.33 - 2.97: 15441 2.97 - 3.61: 48714 3.61 - 4.26: 84300 4.26 - 4.90: 134141 Nonbonded interactions: 282606 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.683 3.460 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.039 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.047 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.092 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.125 3.080 ... (remaining 282601 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' and resid 26 through 3002) selection = chain 'L' } 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' } 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 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = (chain 'U' and resid 8 through 82) } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 31.000 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9488 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 0.206 33382 Z= 0.642 Angle : 1.733 18.241 45365 Z= 1.077 Chirality : 0.115 0.960 4962 Planarity : 0.007 0.049 5700 Dihedral : 17.655 163.616 12014 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 3.76 % Allowed : 7.43 % Favored : 88.81 % 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: -1.48 (0.12), residues: 3955 helix: -1.11 (0.09), residues: 2118 sheet: 0.08 (0.25), residues: 356 loop : -0.77 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG C 283 TYR 0.045 0.007 TYR D 237 PHE 0.049 0.006 PHE B 107 TRP 0.044 0.008 TRP P 120 HIS 0.024 0.004 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01059 / 0.64 (33367) covalent geometry : angle 1.72964 / 1.08 (45352) SS BOND : bond 0.02566 / 1.47 ( 5) SS BOND : angle 2.65149 / 1.35 ( 10) hydrogen bonds : bond 0.18708 / 12.43 ( 1887) hydrogen bonds : angle 6.95853 / 5.00 ( 5301) metal coordination : bond 0.07571 / 3.72 ( 4) metal coordination : angle 13.30502 / 7.24 ( 3) Misc. bond : bond 0.13607 / 6.88 ( 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 474 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 349 time to evaluate : 1.427 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: C 287 ASP cc_start: 0.8601 (t0) cc_final: 0.8341 (t0) REVERT: C 288 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8010 (ttpt) REVERT: P 182 PHE cc_start: 0.7450 (m-80) cc_final: 0.7024 (m-80) REVERT: P 186 PHE cc_start: 0.9131 (t80) cc_final: 0.8850 (t80) REVERT: P 202 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8862 (ttp-110) REVERT: P 213 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: G 12 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8980 (mm-30) REVERT: G 116 LYS cc_start: 0.8983 (tttm) cc_final: 0.8711 (ttmm) REVERT: F 114 TYR cc_start: 0.8798 (t80) cc_final: 0.8572 (t80) REVERT: B 251 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9077 (pm20) REVERT: B 377 ASN cc_start: 0.9561 (m-40) cc_final: 0.9348 (m-40) REVERT: H 35 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8787 (mtm-85) REVERT: H 78 GLU cc_start: 0.9327 (tt0) cc_final: 0.9040 (tm-30) REVERT: N 250 LYS cc_start: 0.9283 (ttmt) cc_final: 0.9079 (tptp) REVERT: N 369 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8819 (mtp) REVERT: E 55 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8672 (p0) REVERT: Q 84 GLU cc_start: 0.9232 (tt0) cc_final: 0.8927 (tp30) REVERT: Q 88 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8471 (mm-30) REVERT: Q 109 GLN cc_start: 0.9507 (mt0) cc_final: 0.9222 (mt0) REVERT: Q 122 ASP cc_start: 0.8734 (p0) cc_final: 0.8512 (p0) REVERT: L 87 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8437 (ptp90) REVERT: M 19 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9121 (mm-30) REVERT: M 31 GLN cc_start: 0.8783 (mt0) cc_final: 0.8577 (mm110) REVERT: M 236 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (mtp85) REVERT: M 341 TYR cc_start: 0.9340 (t80) cc_final: 0.8953 (t80) REVERT: S 78 GLU cc_start: 0.9276 (tt0) cc_final: 0.9033 (pp20) REVERT: U 80 ASN cc_start: 0.9322 (t0) cc_final: 0.8966 (t0) outliers start: 125 outliers final: 16 residues processed: 442 average time/residue: 0.7985 time to fit residues: 409.2782 Evaluate side-chains 300 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN G 54 ASN F 109 GLN F 132 HIS A 74 HIS A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 215 GLN B 316 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN Q 132 HIS L 135 GLN L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 197 ASN M 215 GLN ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.047105 restraints weight = 78521.843| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.22 r_work: 0.2517 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 33382 Z= 0.146 Angle : 0.614 15.533 45365 Z= 0.307 Chirality : 0.042 0.212 4962 Planarity : 0.004 0.041 5700 Dihedral : 11.917 136.526 4869 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.74 % Allowed : 11.13 % Favored : 87.13 % 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: 0.93 (0.13), residues: 3955 helix: 1.10 (0.11), residues: 2162 sheet: 0.52 (0.26), residues: 363 loop : 0.07 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 55 TYR 0.018 0.002 TYR O 237 PHE 0.019 0.002 PHE L 334 TRP 0.023 0.002 TRP C 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (33367) covalent geometry : angle 0.61254 / 0.31 (45352) SS BOND : bond 0.00217 / 0.13 ( 5) SS BOND : angle 0.68492 / 0.34 ( 10) hydrogen bonds : bond 0.05077 / 3.36 ( 1887) hydrogen bonds : angle 4.69886 / 3.38 ( 5301) metal coordination : bond 0.00983 / 0.49 ( 4) metal coordination : angle 5.14934 / 2.75 ( 3) Misc. bond : bond 0.29088 / 14.24 ( 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 344 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8012 (tttp) cc_final: 0.7754 (ttpt) REVERT: P 182 PHE cc_start: 0.7886 (m-80) cc_final: 0.7461 (m-80) REVERT: P 202 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8397 (ttp-110) REVERT: P 216 PHE cc_start: 0.7242 (m-80) cc_final: 0.7032 (m-80) REVERT: G 19 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8413 (tt) REVERT: G 97 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8731 (mt-10) REVERT: G 116 LYS cc_start: 0.8659 (tttm) cc_final: 0.8439 (ttmm) REVERT: F 110 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8533 (pt0) REVERT: F 114 TYR cc_start: 0.8846 (t80) cc_final: 0.8486 (t80) REVERT: F 126 GLU cc_start: 0.9148 (mp0) cc_final: 0.8780 (mp0) REVERT: H 35 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8630 (mtm-85) REVERT: H 78 GLU cc_start: 0.8963 (tt0) cc_final: 0.8585 (tm-30) REVERT: J 69 GLU cc_start: 0.7895 (pm20) cc_final: 0.7599 (pm20) REVERT: N 160 ASP cc_start: 0.8963 (m-30) cc_final: 0.8687 (m-30) REVERT: E 55 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8088 (p0) REVERT: E 96 ASP cc_start: 0.9198 (p0) cc_final: 0.8933 (p0) REVERT: Q 88 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8231 (mm-30) REVERT: Q 109 GLN cc_start: 0.9455 (mt0) cc_final: 0.9136 (mt0) REVERT: Q 122 ASP cc_start: 0.8522 (p0) cc_final: 0.8268 (p0) REVERT: S 78 GLU cc_start: 0.9020 (tt0) cc_final: 0.8769 (tm-30) REVERT: T 34 GLU cc_start: 0.8904 (tt0) cc_final: 0.8679 (tt0) REVERT: U 67 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8662 (pt) REVERT: U 73 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7210 (ptt-90) REVERT: U 80 ASN cc_start: 0.9177 (t0) cc_final: 0.8777 (t0) outliers start: 58 outliers final: 10 residues processed: 320 average time/residue: 0.8196 time to fit residues: 304.9757 Evaluate side-chains 275 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 377 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 292 optimal weight: 0.0980 chunk 384 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN A 50 GLN B 92 HIS B 121 GLN Q 135 ASN M 241 ASN M 408 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.047428 restraints weight = 78928.791| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.21 r_work: 0.2536 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9321 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.375 33382 Z= 0.127 Angle : 0.539 12.969 45365 Z= 0.265 Chirality : 0.040 0.144 4962 Planarity : 0.004 0.053 5700 Dihedral : 10.809 112.695 4827 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.50 % Allowed : 11.70 % Favored : 86.80 % 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: 1.76 (0.14), residues: 3955 helix: 1.77 (0.11), residues: 2154 sheet: 0.81 (0.27), residues: 369 loop : 0.48 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 104 TYR 0.015 0.001 TYR C 225 PHE 0.016 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33367) covalent geometry : angle 0.53866 / 0.26 (45352) SS BOND : bond 0.00251 / 0.16 ( 5) SS BOND : angle 0.77940 / 0.39 ( 10) hydrogen bonds : bond 0.04225 / 2.78 ( 1887) hydrogen bonds : angle 4.32790 / 3.12 ( 5301) metal coordination : bond 0.00387 / 0.19 ( 4) metal coordination : angle 3.08251 / 1.75 ( 3) Misc. bond : bond 0.26052 / 12.67 ( 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 328 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 1.152 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: C 287 ASP cc_start: 0.8279 (t0) cc_final: 0.8069 (t0) REVERT: C 288 LYS cc_start: 0.7963 (tttp) cc_final: 0.7640 (ttpt) REVERT: P 126 PHE cc_start: 0.8625 (m-10) cc_final: 0.8421 (m-10) REVERT: P 128 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8361 (tpt-90) REVERT: P 214 TYR cc_start: 0.7440 (p90) cc_final: 0.6881 (p90) REVERT: G 97 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8787 (mt-10) REVERT: G 115 GLU cc_start: 0.8971 (tt0) cc_final: 0.8722 (tt0) REVERT: G 116 LYS cc_start: 0.8655 (tttm) cc_final: 0.8439 (ttmm) REVERT: G 123 GLU cc_start: 0.8963 (tt0) cc_final: 0.8445 (pt0) REVERT: F 114 TYR cc_start: 0.8840 (t80) cc_final: 0.8468 (t80) REVERT: A 29 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8971 (tttm) REVERT: A 461 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8211 (p0) REVERT: H 35 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8625 (mtm-85) REVERT: H 78 GLU cc_start: 0.8971 (tt0) cc_final: 0.8616 (tm-30) REVERT: J 13 SER cc_start: 0.9038 (t) cc_final: 0.8746 (p) REVERT: J 69 GLU cc_start: 0.7957 (pm20) cc_final: 0.7557 (pm20) REVERT: E 55 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (p0) REVERT: E 96 ASP cc_start: 0.9232 (p0) cc_final: 0.8957 (p0) REVERT: Q 109 GLN cc_start: 0.9404 (mt0) cc_final: 0.9072 (mt0) REVERT: Q 122 ASP cc_start: 0.8569 (p0) cc_final: 0.8201 (p0) REVERT: S 78 GLU cc_start: 0.9002 (tt0) cc_final: 0.8732 (tm-30) REVERT: U 15 LYS cc_start: 0.9229 (pttt) cc_final: 0.8932 (pttt) REVERT: U 73 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7626 (ptt-90) REVERT: U 80 ASN cc_start: 0.9213 (t0) cc_final: 0.8828 (t0) outliers start: 50 outliers final: 10 residues processed: 308 average time/residue: 0.8035 time to fit residues: 288.5569 Evaluate side-chains 272 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 29 LYS 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 H residue 60 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 295 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 384 optimal weight: 0.5980 chunk 337 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN P 139 ASN P 157 GLN P 193 HIS G 84 HIS A 317 GLN B 377 ASN R 84 HIS L 317 GLN M 121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.047543 restraints weight = 78666.713| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.19 r_work: 0.2542 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9319 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.364 33382 Z= 0.121 Angle : 0.517 13.850 45365 Z= 0.252 Chirality : 0.040 0.142 4962 Planarity : 0.004 0.056 5700 Dihedral : 10.253 102.200 4825 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.53 % Allowed : 12.03 % Favored : 86.44 % 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: 2.06 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2155 sheet: 0.93 (0.27), residues: 369 loop : 0.61 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 144 TYR 0.015 0.001 TYR C 225 PHE 0.016 0.001 PHE A 334 TRP 0.012 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33367) covalent geometry : angle 0.51674 / 0.25 (45352) SS BOND : bond 0.00214 / 0.13 ( 5) SS BOND : angle 0.56816 / 0.29 ( 10) hydrogen bonds : bond 0.03948 / 2.59 ( 1887) hydrogen bonds : angle 4.19324 / 3.02 ( 5301) metal coordination : bond 0.00336 / 0.17 ( 4) metal coordination : angle 3.28362 / 1.83 ( 3) Misc. bond : bond 0.24501 / 12.07 ( 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 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: C 288 LYS cc_start: 0.7984 (tttp) cc_final: 0.7686 (ttpt) REVERT: P 126 PHE cc_start: 0.8658 (m-10) cc_final: 0.8446 (m-10) REVERT: P 128 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8500 (mmm160) REVERT: P 214 TYR cc_start: 0.7450 (p90) cc_final: 0.7062 (p90) REVERT: G 97 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8745 (mt-10) REVERT: G 115 GLU cc_start: 0.8993 (tt0) cc_final: 0.8670 (tt0) REVERT: G 116 LYS cc_start: 0.8642 (tttm) cc_final: 0.8439 (ttmm) REVERT: G 123 GLU cc_start: 0.8968 (tt0) cc_final: 0.8448 (pt0) REVERT: F 107 LYS cc_start: 0.9175 (tppp) cc_final: 0.8886 (tppp) REVERT: F 114 TYR cc_start: 0.8878 (t80) cc_final: 0.8628 (t80) REVERT: A 29 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8951 (tttm) REVERT: A 461 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8157 (p0) REVERT: B 392 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: H 35 ARG cc_start: 0.8962 (mtm-85) cc_final: 0.8627 (mtm-85) REVERT: H 78 GLU cc_start: 0.8976 (tt0) cc_final: 0.8623 (tm-30) REVERT: J 13 SER cc_start: 0.8998 (t) cc_final: 0.8761 (p) REVERT: J 69 GLU cc_start: 0.7889 (pm20) cc_final: 0.7402 (pm20) REVERT: N 160 ASP cc_start: 0.8977 (m-30) cc_final: 0.8551 (m-30) REVERT: E 55 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8139 (p0) REVERT: E 96 ASP cc_start: 0.9239 (p0) cc_final: 0.8959 (p0) REVERT: R 31 TYR cc_start: 0.9219 (t80) cc_final: 0.8932 (t80) REVERT: Q 100 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8067 (mp0) REVERT: Q 109 GLN cc_start: 0.9379 (mt0) cc_final: 0.9070 (mt0) REVERT: Q 122 ASP cc_start: 0.8485 (p0) cc_final: 0.8182 (p0) REVERT: S 57 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8449 (tp) REVERT: S 78 GLU cc_start: 0.9017 (tt0) cc_final: 0.8732 (tm-30) REVERT: U 80 ASN cc_start: 0.9214 (t0) cc_final: 0.8843 (t0) outliers start: 51 outliers final: 14 residues processed: 300 average time/residue: 0.8017 time to fit residues: 280.4424 Evaluate side-chains 276 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER 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 392 GLN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 369 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.045326 restraints weight = 79438.746| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.20 r_work: 0.2483 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.419 33382 Z= 0.210 Angle : 0.580 16.583 45365 Z= 0.280 Chirality : 0.042 0.146 4962 Planarity : 0.004 0.057 5700 Dihedral : 10.131 89.987 4825 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.68 % Allowed : 12.54 % 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: 2.02 (0.14), residues: 3955 helix: 1.99 (0.11), residues: 2155 sheet: 0.97 (0.27), residues: 365 loop : 0.55 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 144 TYR 0.020 0.001 TYR C 225 PHE 0.019 0.002 PHE C 240 TRP 0.016 0.001 TRP N 142 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (33367) covalent geometry : angle 0.57890 / 0.28 (45352) SS BOND : bond 0.00275 / 0.16 ( 5) SS BOND : angle 0.68685 / 0.34 ( 10) hydrogen bonds : bond 0.04527 / 2.98 ( 1887) hydrogen bonds : angle 4.27199 / 3.08 ( 5301) metal coordination : bond 0.00949 / 0.48 ( 4) metal coordination : angle 4.24833 / 2.36 ( 3) Misc. bond : bond 0.30891 / 15.55 ( 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 313 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8584 (mmm) REVERT: C 287 ASP cc_start: 0.8280 (t0) cc_final: 0.8035 (t0) REVERT: C 288 LYS cc_start: 0.8127 (tttp) cc_final: 0.7766 (ttpp) REVERT: P 128 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8506 (mmm160) REVERT: P 214 TYR cc_start: 0.7558 (p90) cc_final: 0.7200 (p90) REVERT: G 97 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8817 (mt-10) REVERT: G 112 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: G 115 GLU cc_start: 0.9005 (tt0) cc_final: 0.8683 (tt0) REVERT: G 116 LYS cc_start: 0.8689 (tttm) cc_final: 0.8454 (ttmm) REVERT: G 123 GLU cc_start: 0.8968 (tt0) cc_final: 0.8453 (pt0) REVERT: F 107 LYS cc_start: 0.9076 (tppp) cc_final: 0.8625 (mmmm) REVERT: F 114 TYR cc_start: 0.8868 (t80) cc_final: 0.8192 (t80) REVERT: F 115 ASP cc_start: 0.8986 (p0) cc_final: 0.8701 (p0) REVERT: A 29 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8974 (tttm) REVERT: A 461 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8197 (p0) REVERT: B 392 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: D 248 MET cc_start: 0.9504 (ttp) cc_final: 0.8599 (ttm) REVERT: H 78 GLU cc_start: 0.9003 (tt0) cc_final: 0.8641 (tm-30) REVERT: J 13 SER cc_start: 0.9063 (t) cc_final: 0.8813 (p) REVERT: J 69 GLU cc_start: 0.7905 (pm20) cc_final: 0.7420 (pm20) REVERT: N 287 ASP cc_start: 0.8255 (t0) cc_final: 0.8048 (t0) REVERT: E 96 ASP cc_start: 0.9241 (p0) cc_final: 0.8961 (p0) REVERT: R 33 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9181 (tmmm) REVERT: R 97 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8864 (mt-10) REVERT: Q 100 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8074 (mp0) REVERT: Q 109 GLN cc_start: 0.9353 (mt0) cc_final: 0.9020 (mt0) REVERT: Q 122 ASP cc_start: 0.8487 (p0) cc_final: 0.8226 (p0) REVERT: L 461 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7805 (p0) REVERT: M 339 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.9027 (ttm170) REVERT: O 248 MET cc_start: 0.9467 (ttp) cc_final: 0.8567 (ttm) REVERT: S 78 GLU cc_start: 0.9021 (tt0) cc_final: 0.8760 (tm-30) REVERT: T 34 GLU cc_start: 0.8858 (tt0) cc_final: 0.8357 (pt0) REVERT: U 73 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7251 (ptt-90) REVERT: U 80 ASN cc_start: 0.9225 (t0) cc_final: 0.8834 (t0) outliers start: 56 outliers final: 21 residues processed: 295 average time/residue: 0.7609 time to fit residues: 261.9540 Evaluate side-chains 283 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP 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 S residue 57 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 352 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 145 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN F 109 GLN I 39 ASN N 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.047190 restraints weight = 78920.212| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.20 r_work: 0.2537 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9328 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.357 33382 Z= 0.115 Angle : 0.511 13.268 45365 Z= 0.249 Chirality : 0.040 0.137 4962 Planarity : 0.004 0.056 5700 Dihedral : 9.637 88.212 4821 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.32 % Allowed : 13.20 % Favored : 85.47 % 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: 2.20 (0.14), residues: 3955 helix: 2.14 (0.11), residues: 2160 sheet: 0.92 (0.27), residues: 369 loop : 0.67 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 144 TYR 0.021 0.001 TYR Q 114 PHE 0.016 0.001 PHE A 334 TRP 0.014 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (33367) covalent geometry : angle 0.51077 / 0.25 (45352) SS BOND : bond 0.00226 / 0.14 ( 5) SS BOND : angle 0.64169 / 0.31 ( 10) hydrogen bonds : bond 0.03858 / 2.53 ( 1887) hydrogen bonds : angle 4.13180 / 2.98 ( 5301) metal coordination : bond 0.00420 / 0.21 ( 4) metal coordination : angle 3.18019 / 1.71 ( 3) Misc. bond : bond 0.24061 / 11.85 ( 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 310 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8600 (mmm) REVERT: C 287 ASP cc_start: 0.8254 (t0) cc_final: 0.7998 (t0) REVERT: C 288 LYS cc_start: 0.8058 (tttp) cc_final: 0.7713 (ttpp) REVERT: P 193 HIS cc_start: 0.8991 (m90) cc_final: 0.8360 (m-70) REVERT: P 214 TYR cc_start: 0.7565 (p90) cc_final: 0.7163 (p90) REVERT: G 97 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8782 (mt-10) REVERT: G 115 GLU cc_start: 0.8972 (tt0) cc_final: 0.8646 (tt0) REVERT: G 123 GLU cc_start: 0.8939 (tt0) cc_final: 0.8490 (pt0) REVERT: F 104 ARG cc_start: 0.9275 (ttp80) cc_final: 0.9050 (ttp80) REVERT: F 107 LYS cc_start: 0.9025 (tppp) cc_final: 0.8677 (mmmm) REVERT: F 110 GLU cc_start: 0.8480 (pp20) cc_final: 0.8211 (pp20) REVERT: F 114 TYR cc_start: 0.8834 (t80) cc_final: 0.8391 (t80) REVERT: F 115 ASP cc_start: 0.8925 (p0) cc_final: 0.8670 (p0) REVERT: A 29 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8954 (tttm) REVERT: A 461 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 392 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: H 78 GLU cc_start: 0.8995 (tt0) cc_final: 0.8634 (tm-30) REVERT: J 13 SER cc_start: 0.9045 (t) cc_final: 0.8750 (p) REVERT: J 15 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8535 (pttt) REVERT: J 69 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: N 160 ASP cc_start: 0.8939 (m-30) cc_final: 0.8580 (m-30) REVERT: N 287 ASP cc_start: 0.8219 (t0) cc_final: 0.8014 (t0) REVERT: E 96 ASP cc_start: 0.9242 (p0) cc_final: 0.8962 (p0) REVERT: R 33 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9124 (tmmm) REVERT: Q 100 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8015 (mp0) REVERT: Q 109 GLN cc_start: 0.9324 (mt0) cc_final: 0.8960 (mt0) REVERT: Q 122 ASP cc_start: 0.8487 (p0) cc_final: 0.7990 (p0) REVERT: L 461 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7716 (p0) REVERT: O 85 MET cc_start: 0.8716 (ptt) cc_final: 0.8421 (pmm) REVERT: S 57 LEU cc_start: 0.8956 (mm) cc_final: 0.8577 (tp) REVERT: S 78 GLU cc_start: 0.9022 (tt0) cc_final: 0.8737 (tm-30) REVERT: T 34 GLU cc_start: 0.8868 (tt0) cc_final: 0.8382 (pt0) REVERT: U 73 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7444 (ptt-90) REVERT: U 80 ASN cc_start: 0.9220 (t0) cc_final: 0.8850 (t0) outliers start: 44 outliers final: 16 residues processed: 296 average time/residue: 0.7451 time to fit residues: 257.1232 Evaluate side-chains 282 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.045237 restraints weight = 79772.064| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.19 r_work: 0.2482 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9372 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.412 33382 Z= 0.223 Angle : 0.587 15.949 45365 Z= 0.283 Chirality : 0.042 0.144 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.677 89.716 4821 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.44 % Allowed : 13.29 % Favored : 85.26 % 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: 2.09 (0.14), residues: 3955 helix: 2.05 (0.11), residues: 2158 sheet: 0.96 (0.26), residues: 365 loop : 0.60 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 236 TYR 0.020 0.002 TYR C 225 PHE 0.020 0.002 PHE C 240 TRP 0.016 0.001 TRP N 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (33367) covalent geometry : angle 0.58648 / 0.28 (45352) SS BOND : bond 0.00236 / 0.13 ( 5) SS BOND : angle 0.66499 / 0.32 ( 10) hydrogen bonds : bond 0.04456 / 2.93 ( 1887) hydrogen bonds : angle 4.23381 / 3.05 ( 5301) metal coordination : bond 0.00841 / 0.43 ( 4) metal coordination : angle 3.98792 / 2.18 ( 3) Misc. bond : bond 0.30202 / 15.18 ( 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 307 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8609 (mmm) REVERT: C 287 ASP cc_start: 0.8264 (t0) cc_final: 0.8011 (t0) REVERT: C 288 LYS cc_start: 0.8132 (tttp) cc_final: 0.7772 (ttpp) REVERT: P 128 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8596 (tpt-90) REVERT: P 193 HIS cc_start: 0.9003 (m90) cc_final: 0.8517 (m-70) REVERT: P 214 TYR cc_start: 0.7649 (p90) cc_final: 0.7272 (p90) REVERT: G 97 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8816 (mt-10) REVERT: G 112 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: G 115 GLU cc_start: 0.9002 (tt0) cc_final: 0.8689 (tt0) REVERT: G 123 GLU cc_start: 0.8971 (tt0) cc_final: 0.8498 (pt0) REVERT: F 104 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8966 (ttp80) REVERT: F 107 LYS cc_start: 0.9029 (tppp) cc_final: 0.8621 (mmmm) REVERT: F 110 GLU cc_start: 0.8512 (pp20) cc_final: 0.8233 (pp20) REVERT: F 114 TYR cc_start: 0.8776 (t80) cc_final: 0.8526 (t80) REVERT: F 115 ASP cc_start: 0.8950 (p0) cc_final: 0.8723 (p0) REVERT: A 29 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8966 (tttm) REVERT: A 461 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 392 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: D 193 GLN cc_start: 0.9329 (mp-120) cc_final: 0.8917 (mp10) REVERT: D 248 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.8751 (ttp) REVERT: H 78 GLU cc_start: 0.9014 (tt0) cc_final: 0.8589 (tm-30) REVERT: J 13 SER cc_start: 0.9105 (t) cc_final: 0.8783 (p) REVERT: J 15 LYS cc_start: 0.9145 (ptpp) cc_final: 0.8656 (pttp) REVERT: J 69 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: E 96 ASP cc_start: 0.9256 (p0) cc_final: 0.8973 (p0) REVERT: R 33 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9160 (tmmm) REVERT: R 116 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8541 (ttmm) REVERT: Q 109 GLN cc_start: 0.9339 (mt0) cc_final: 0.8967 (mt0) REVERT: Q 122 ASP cc_start: 0.8497 (p0) cc_final: 0.8216 (p0) REVERT: L 461 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7815 (p0) REVERT: M 339 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.9037 (ttm170) REVERT: S 57 LEU cc_start: 0.8993 (mm) cc_final: 0.8540 (tp) REVERT: S 78 GLU cc_start: 0.9039 (tt0) cc_final: 0.8776 (tm-30) REVERT: T 34 GLU cc_start: 0.8902 (tt0) cc_final: 0.8407 (pt0) REVERT: U 11 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8497 (tptp) REVERT: U 73 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7513 (ptt-90) REVERT: U 80 ASN cc_start: 0.9233 (t0) cc_final: 0.8853 (t0) outliers start: 48 outliers final: 19 residues processed: 293 average time/residue: 0.8199 time to fit residues: 279.5931 Evaluate side-chains 285 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP 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 U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 389 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.045166 restraints weight = 79888.648| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 2.19 r_work: 0.2481 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9365 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.417 33382 Z= 0.214 Angle : 0.578 15.763 45365 Z= 0.280 Chirality : 0.042 0.145 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.612 89.727 4821 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.26 % Allowed : 13.65 % Favored : 85.08 % 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: 2.06 (0.14), residues: 3955 helix: 2.02 (0.11), residues: 2158 sheet: 0.91 (0.26), residues: 365 loop : 0.60 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 236 TYR 0.019 0.001 TYR B 170 PHE 0.019 0.001 PHE L 334 TRP 0.018 0.001 TRP N 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (33367) covalent geometry : angle 0.57663 / 0.28 (45352) SS BOND : bond 0.00287 / 0.14 ( 5) SS BOND : angle 0.77883 / 0.37 ( 10) hydrogen bonds : bond 0.04445 / 2.92 ( 1887) hydrogen bonds : angle 4.25398 / 3.07 ( 5301) metal coordination : bond 0.00652 / 0.33 ( 4) metal coordination : angle 4.08907 / 2.19 ( 3) Misc. bond : bond 0.28930 / 14.88 ( 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 301 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8570 (mmm) REVERT: C 287 ASP cc_start: 0.8284 (t0) cc_final: 0.8015 (t0) REVERT: C 288 LYS cc_start: 0.8119 (tttp) cc_final: 0.7763 (ttpp) REVERT: P 116 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8988 (p) REVERT: P 128 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8616 (mmm160) REVERT: P 193 HIS cc_start: 0.9021 (m90) cc_final: 0.8402 (m-70) REVERT: P 214 TYR cc_start: 0.7677 (p90) cc_final: 0.7328 (p90) REVERT: G 97 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8811 (mt-10) REVERT: G 112 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: G 115 GLU cc_start: 0.8977 (tt0) cc_final: 0.8730 (tt0) REVERT: G 123 GLU cc_start: 0.8955 (tt0) cc_final: 0.8457 (pt0) REVERT: F 104 ARG cc_start: 0.9256 (ttp80) cc_final: 0.8978 (ttp80) REVERT: F 107 LYS cc_start: 0.9039 (tppp) cc_final: 0.8656 (mmmm) REVERT: F 110 GLU cc_start: 0.8517 (pp20) cc_final: 0.8271 (pp20) REVERT: F 114 TYR cc_start: 0.8805 (t80) cc_final: 0.8557 (t80) REVERT: F 115 ASP cc_start: 0.8926 (p0) cc_final: 0.8710 (p0) REVERT: A 29 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8957 (tttm) REVERT: A 461 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8133 (p0) REVERT: B 392 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: D 193 GLN cc_start: 0.9360 (mp-120) cc_final: 0.8939 (mp10) REVERT: D 248 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.8605 (ttm) REVERT: D 303 MET cc_start: 0.9214 (mtm) cc_final: 0.8980 (mtt) REVERT: H 78 GLU cc_start: 0.9018 (tt0) cc_final: 0.8647 (tm-30) REVERT: J 13 SER cc_start: 0.9125 (t) cc_final: 0.8649 (p) REVERT: J 15 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8668 (pttp) REVERT: J 69 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: N 160 ASP cc_start: 0.9001 (m-30) cc_final: 0.8671 (m-30) REVERT: N 287 ASP cc_start: 0.8296 (t0) cc_final: 0.8096 (t0) REVERT: E 96 ASP cc_start: 0.9250 (p0) cc_final: 0.8968 (p0) REVERT: R 33 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9147 (tmmm) REVERT: R 116 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8517 (ttmm) REVERT: Q 100 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8140 (mp0) REVERT: Q 109 GLN cc_start: 0.9332 (mt0) cc_final: 0.8938 (mt0) REVERT: Q 122 ASP cc_start: 0.8528 (p0) cc_final: 0.8046 (p0) REVERT: L 461 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7802 (p0) REVERT: M 339 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8988 (ttm170) REVERT: S 57 LEU cc_start: 0.8985 (mm) cc_final: 0.8513 (tp) REVERT: S 78 GLU cc_start: 0.9035 (tt0) cc_final: 0.8755 (tm-30) REVERT: T 31 MET cc_start: 0.8596 (mmm) cc_final: 0.7718 (mmm) REVERT: T 34 GLU cc_start: 0.8875 (tt0) cc_final: 0.8357 (pt0) REVERT: U 73 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: U 80 ASN cc_start: 0.9250 (t0) cc_final: 0.8857 (t0) outliers start: 42 outliers final: 20 residues processed: 288 average time/residue: 0.7715 time to fit residues: 259.1712 Evaluate side-chains 283 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 294 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.046070 restraints weight = 79109.766| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.20 r_work: 0.2505 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9351 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 33382 Z= 0.150 Angle : 0.557 14.669 45365 Z= 0.270 Chirality : 0.041 0.141 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.389 88.589 4821 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.23 % Allowed : 13.98 % Favored : 84.78 % 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: 2.17 (0.14), residues: 3955 helix: 2.11 (0.11), residues: 2159 sheet: 0.95 (0.26), residues: 365 loop : 0.65 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 236 TYR 0.025 0.001 TYR B 170 PHE 0.018 0.001 PHE A 334 TRP 0.015 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (33367) covalent geometry : angle 0.55597 / 0.27 (45352) SS BOND : bond 0.00200 / 0.10 ( 5) SS BOND : angle 0.67520 / 0.32 ( 10) hydrogen bonds : bond 0.04141 / 2.72 ( 1887) hydrogen bonds : angle 4.18689 / 3.02 ( 5301) metal coordination : bond 0.00561 / 0.28 ( 4) metal coordination : angle 3.83084 / 2.04 ( 3) Misc. bond : bond 0.26349 / 13.36 ( 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 299 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8565 (mmm) REVERT: C 287 ASP cc_start: 0.8254 (t0) cc_final: 0.7987 (t0) REVERT: C 288 LYS cc_start: 0.8090 (tttp) cc_final: 0.7737 (ttpp) REVERT: P 116 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9007 (p) REVERT: P 128 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8623 (tpt-90) REVERT: P 193 HIS cc_start: 0.9097 (m90) cc_final: 0.8432 (m-70) REVERT: P 214 TYR cc_start: 0.7726 (p90) cc_final: 0.7383 (p90) REVERT: G 97 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8798 (mt-10) REVERT: G 112 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: G 115 GLU cc_start: 0.8978 (tt0) cc_final: 0.8676 (tt0) REVERT: G 123 GLU cc_start: 0.8964 (tt0) cc_final: 0.8499 (pt0) REVERT: F 104 ARG cc_start: 0.9273 (ttp80) cc_final: 0.9012 (ttp80) REVERT: F 107 LYS cc_start: 0.9056 (tppp) cc_final: 0.8653 (mmmm) REVERT: F 110 GLU cc_start: 0.8534 (pp20) cc_final: 0.8280 (pp20) REVERT: F 114 TYR cc_start: 0.8778 (t80) cc_final: 0.8532 (t80) REVERT: F 115 ASP cc_start: 0.8931 (p0) cc_final: 0.8723 (p0) REVERT: A 29 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8963 (tttm) REVERT: A 461 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 392 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: D 193 GLN cc_start: 0.9367 (mp-120) cc_final: 0.8944 (mp10) REVERT: H 78 GLU cc_start: 0.9025 (tt0) cc_final: 0.8641 (tm-30) REVERT: J 13 SER cc_start: 0.9118 (t) cc_final: 0.8637 (p) REVERT: J 15 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8679 (pttt) REVERT: J 69 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: E 96 ASP cc_start: 0.9250 (p0) cc_final: 0.8965 (p0) REVERT: R 116 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8397 (ttmm) REVERT: Q 100 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8128 (mt-10) REVERT: Q 109 GLN cc_start: 0.9320 (mt0) cc_final: 0.8913 (mt0) REVERT: Q 122 ASP cc_start: 0.8532 (p0) cc_final: 0.8242 (p0) REVERT: L 461 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7788 (p0) REVERT: S 57 LEU cc_start: 0.8980 (mm) cc_final: 0.8514 (tp) REVERT: S 78 GLU cc_start: 0.9028 (tt0) cc_final: 0.8749 (tm-30) REVERT: T 34 GLU cc_start: 0.8883 (tt0) cc_final: 0.8403 (pt0) REVERT: U 11 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8505 (tptp) REVERT: U 73 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7614 (ptt-90) REVERT: U 80 ASN cc_start: 0.9246 (t0) cc_final: 0.8860 (t0) outliers start: 41 outliers final: 21 residues processed: 285 average time/residue: 0.7311 time to fit residues: 242.3245 Evaluate side-chains 286 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 130 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 265 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.045972 restraints weight = 79762.885| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 2.21 r_work: 0.2504 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9351 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.385 33382 Z= 0.160 Angle : 0.559 14.890 45365 Z= 0.271 Chirality : 0.041 0.140 4962 Planarity : 0.004 0.057 5700 Dihedral : 9.275 88.536 4821 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.99 % Allowed : 14.02 % Favored : 84.99 % 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: 2.20 (0.14), residues: 3955 helix: 2.13 (0.11), residues: 2159 sheet: 0.99 (0.27), residues: 365 loop : 0.66 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 236 TYR 0.028 0.001 TYR B 170 PHE 0.018 0.001 PHE A 334 TRP 0.014 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (33367) covalent geometry : angle 0.55778 / 0.27 (45352) SS BOND : bond 0.00195 / 0.10 ( 5) SS BOND : angle 0.69871 / 0.32 ( 10) hydrogen bonds : bond 0.04148 / 2.73 ( 1887) hydrogen bonds : angle 4.17272 / 3.01 ( 5301) metal coordination : bond 0.00583 / 0.29 ( 4) metal coordination : angle 3.72691 / 1.98 ( 3) Misc. bond : bond 0.26509 / 13.44 ( 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 290 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: C 287 ASP cc_start: 0.8250 (t0) cc_final: 0.7982 (t0) REVERT: C 288 LYS cc_start: 0.8114 (tttp) cc_final: 0.7734 (ttpt) REVERT: P 116 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.9025 (p) REVERT: P 128 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8607 (tpt-90) REVERT: P 193 HIS cc_start: 0.9085 (m90) cc_final: 0.8371 (m-70) REVERT: P 202 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7788 (mmt180) REVERT: P 214 TYR cc_start: 0.7752 (p90) cc_final: 0.7387 (p90) REVERT: G 97 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8805 (mt-10) REVERT: G 112 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: G 115 GLU cc_start: 0.8972 (tt0) cc_final: 0.8757 (tt0) REVERT: G 123 GLU cc_start: 0.8949 (tt0) cc_final: 0.8463 (pt0) REVERT: F 104 ARG cc_start: 0.9297 (ttp80) cc_final: 0.9044 (ttp80) REVERT: F 107 LYS cc_start: 0.9057 (tppp) cc_final: 0.8648 (mmmm) REVERT: F 110 GLU cc_start: 0.8532 (pp20) cc_final: 0.8281 (pp20) REVERT: F 114 TYR cc_start: 0.8754 (t80) cc_final: 0.8501 (t80) REVERT: F 115 ASP cc_start: 0.8912 (p0) cc_final: 0.8697 (p0) REVERT: A 29 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8957 (tttm) REVERT: A 461 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8128 (p0) REVERT: B 392 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: D 193 GLN cc_start: 0.9377 (mp-120) cc_final: 0.8965 (mp10) REVERT: D 248 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8633 (ttm) REVERT: H 78 GLU cc_start: 0.9039 (tt0) cc_final: 0.8659 (tm-30) REVERT: J 13 SER cc_start: 0.9133 (t) cc_final: 0.8649 (p) REVERT: J 15 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8712 (pttt) REVERT: J 69 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: N 160 ASP cc_start: 0.8975 (m-30) cc_final: 0.8593 (m-30) REVERT: E 96 ASP cc_start: 0.9258 (p0) cc_final: 0.8971 (p0) REVERT: R 116 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8396 (ttmm) REVERT: Q 122 ASP cc_start: 0.8522 (p0) cc_final: 0.8042 (p0) REVERT: L 461 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7790 (p0) REVERT: M 339 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.9011 (ttm170) REVERT: O 248 MET cc_start: 0.9196 (ttp) cc_final: 0.8468 (ttm) REVERT: S 57 LEU cc_start: 0.8980 (mm) cc_final: 0.8510 (tp) REVERT: S 78 GLU cc_start: 0.9010 (tt0) cc_final: 0.8741 (tm-30) REVERT: T 31 MET cc_start: 0.8558 (mmm) cc_final: 0.7711 (mmm) REVERT: T 34 GLU cc_start: 0.8888 (tt0) cc_final: 0.8387 (pt0) REVERT: U 11 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8518 (tptp) REVERT: U 73 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7624 (ptt-90) REVERT: U 80 ASN cc_start: 0.9262 (t0) cc_final: 0.8878 (t0) outliers start: 33 outliers final: 19 residues processed: 279 average time/residue: 0.7529 time to fit residues: 245.4304 Evaluate side-chains 283 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 130 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP 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 U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 chunk 377 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.047286 restraints weight = 79371.739| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.21 r_work: 0.2541 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.344 33382 Z= 0.116 Angle : 0.533 12.821 45365 Z= 0.260 Chirality : 0.040 0.140 4962 Planarity : 0.004 0.056 5700 Dihedral : 8.989 86.580 4819 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.99 % Allowed : 14.23 % Favored : 84.78 % 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: 2.28 (0.14), residues: 3955 helix: 2.18 (0.11), residues: 2166 sheet: 1.04 (0.27), residues: 365 loop : 0.73 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 144 TYR 0.014 0.001 TYR G 31 PHE 0.016 0.001 PHE A 334 TRP 0.011 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (33367) covalent geometry : angle 0.53194 / 0.26 (45352) SS BOND : bond 0.00193 / 0.10 ( 5) SS BOND : angle 0.70823 / 0.36 ( 10) hydrogen bonds : bond 0.03793 / 2.49 ( 1887) hydrogen bonds : angle 4.09319 / 2.95 ( 5301) metal coordination : bond 0.00495 / 0.25 ( 4) metal coordination : angle 3.17426 / 1.67 ( 3) Misc. bond : bond 0.22955 / 11.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10921.57 seconds wall clock time: 186 minutes 49.01 seconds (11209.01 seconds total)