Starting phenix.real_space_refine on Mon Jul 6 08:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.map" model { file = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abk_15324/07_2026/8abk_15324.cif" } resolution = 2.5 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= 0.003 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 21060 2.51 5 N 5294 2.21 5 O 6079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32573 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: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 452 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} 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: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 271 Unusual residues: {'CDL': 1, 'DCQ': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'FES': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 321 Unusual residues: {'CDL': 2, 'DCQ': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.103 49.821 34.598 1.00185.10 S ATOM 4207 SG CYS P 187 32.683 47.068 33.637 1.00174.07 S Time building chain proxies: 6.69, per 1000 atoms: 0.21 Number of scatterers: 32573 At special positions: 0 Unit cell: (118.854, 128.898, 164.889, 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 6079 8.00 N 5294 7.00 C 21060 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=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.05 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 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=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.5 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 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7482 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 21 sheets defined 61.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 3.761A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.524A 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: 6.875A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.809A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.815A 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: 4.081A 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: 3.620A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.580A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.303A 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: 3.590A 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: 3.521A 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: 4.019A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.551A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.524A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.023A 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: 3.668A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.566A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.353A 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: 3.624A 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: 3.570A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.875A 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: 3.595A 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 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.843A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.757A 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: 3.685A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.545A 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 219 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 81 removed outlier: 4.323A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.520A 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: 3.502A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.776A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.655A 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: 3.765A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.545A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) 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: 6.875A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.802A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.825A 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: 4.091A 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: 3.636A 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 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.588A 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: 4.243A 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: 3.591A 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 78 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: 4.015A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.553A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.519A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.001A 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: 3.663A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.675A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.619A 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: 3.562A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.590A 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 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.845A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.760A 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: 3.913A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.526A 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 219 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: 4.321A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.515A 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: 3.609A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.783A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.650A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.901A 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: 3.501A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.636A 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: 6.537A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.283A 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: 3.911A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.153A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.614A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.628A 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: 6.548A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.308A 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: 3.936A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.859A 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: 4.137A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.598A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.620A 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 1891 hydrogen bonds defined for protein. 5313 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: 6.96 Time building geometry restraints manager: 4.79 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: 13592 1.41 - 1.61: 19606 1.61 - 1.82: 160 1.82 - 2.03: 22 2.03 - 2.24: 20 Bond restraints: 33400 Sorted by residual: bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.464 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.461 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.460 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 33395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 43752 3.81 - 7.62: 1444 7.62 - 11.44: 162 11.44 - 15.25: 27 15.25 - 19.06: 7 Bond angle restraints: 45392 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 94.80 16.47 1.47e+00 4.63e-01 1.26e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.28 15.99 1.47e+00 4.63e-01 1.18e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.28 12.05 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 92.23 12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 92.56 17.08 1.77e+00 3.19e-01 9.31e+01 ... (remaining 45387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 18578 32.30 - 64.60: 860 64.60 - 96.90: 87 96.90 - 129.20: 1 129.20 - 161.50: 1 Dihedral angle restraints: 19527 sinusoidal: 7914 harmonic: 11613 Sorted by residual: 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 -101.73 -20.87 0 2.50e+00 1.60e-01 6.97e+01 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 -101.98 -20.62 0 2.50e+00 1.60e-01 6.80e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -103.64 -18.96 0 2.50e+00 1.60e-01 5.75e+01 ... (remaining 19524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 4194 0.152 - 0.303: 703 0.303 - 0.455: 50 0.455 - 0.607: 6 0.607 - 0.759: 6 Chirality restraints: 4959 Sorted by residual: 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 -1.82 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.82 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA ARG H 51 " pdb=" N ARG H 51 " pdb=" C ARG H 51 " pdb=" CB ARG H 51 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 4956 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 506 " -0.044 2.00e-02 2.50e+03 1.31e-01 5.15e+02 pdb=" C1M DCQ C 506 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DCQ C 506 " -0.054 2.00e-02 2.50e+03 pdb=" C3 DCQ C 506 " -0.072 2.00e-02 2.50e+03 pdb=" C4 DCQ C 506 " -0.115 2.00e-02 2.50e+03 pdb=" C5 DCQ C 506 " -0.165 2.00e-02 2.50e+03 pdb=" C6 DCQ C 506 " -0.058 2.00e-02 2.50e+03 pdb=" C7 DCQ C 506 " 0.247 2.00e-02 2.50e+03 pdb=" O2 DCQ C 506 " -0.020 2.00e-02 2.50e+03 pdb=" O3 DCQ C 506 " 0.098 2.00e-02 2.50e+03 pdb=" O4 DCQ C 506 " 0.255 2.00e-02 2.50e+03 pdb=" O5 DCQ C 506 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ N 507 " 0.040 2.00e-02 2.50e+03 1.25e-01 4.66e+02 pdb=" C1M DCQ N 507 " -0.045 2.00e-02 2.50e+03 pdb=" C2 DCQ N 507 " 0.080 2.00e-02 2.50e+03 pdb=" C3 DCQ N 507 " 0.047 2.00e-02 2.50e+03 pdb=" C4 DCQ N 507 " 0.101 2.00e-02 2.50e+03 pdb=" C5 DCQ N 507 " 0.137 2.00e-02 2.50e+03 pdb=" C6 DCQ N 507 " 0.024 2.00e-02 2.50e+03 pdb=" C7 DCQ N 507 " -0.236 2.00e-02 2.50e+03 pdb=" O2 DCQ N 507 " 0.067 2.00e-02 2.50e+03 pdb=" O3 DCQ N 507 " -0.199 2.00e-02 2.50e+03 pdb=" O4 DCQ N 507 " -0.157 2.00e-02 2.50e+03 pdb=" O5 DCQ N 507 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 401 " 0.030 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" C2C HEC D 401 " 0.030 2.00e-02 2.50e+03 pdb=" C3C HEC D 401 " -0.015 2.00e-02 2.50e+03 pdb=" C4C HEC D 401 " 0.016 2.00e-02 2.50e+03 pdb=" CAC HEC D 401 " -0.047 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " -0.060 2.00e-02 2.50e+03 pdb=" CHD HEC D 401 " 0.014 2.00e-02 2.50e+03 pdb=" CMC HEC D 401 " 0.028 2.00e-02 2.50e+03 pdb=" NC HEC D 401 " 0.004 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 327 2.64 - 3.20: 29113 3.20 - 3.77: 54068 3.77 - 4.33: 79094 4.33 - 4.90: 122117 Nonbonded interactions: 284719 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.069 3.120 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.072 3.080 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.090 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.175 3.080 nonbonded pdb=" OB3 CDL H 701 " pdb=" O1 CDL H 702 " model vdw 2.223 3.040 ... (remaining 284714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } 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' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.320 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9418 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 0.635 33417 Z= 0.756 Angle : 1.709 19.428 45405 Z= 1.055 Chirality : 0.112 0.759 4959 Planarity : 0.008 0.131 5700 Dihedral : 17.525 161.497 12030 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.10 % Allowed : 6.83 % Favored : 90.07 % Cbeta Deviations : 0.83 % 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: -1.30 (0.12), residues: 3953 helix: -0.97 (0.09), residues: 2119 sheet: 0.09 (0.26), residues: 351 loop : -0.66 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG G 76 TYR 0.055 0.008 TYR O 120 PHE 0.052 0.007 PHE B 107 TRP 0.038 0.008 TRP C 142 HIS 0.025 0.004 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01014 / 0.62 (33400) covalent geometry : angle 1.70451 / 1.06 (45392) SS BOND : bond 0.02442 / 1.48 ( 5) SS BOND : angle 2.07903 / 1.09 ( 10) hydrogen bonds : bond 0.18360 / 12.39 ( 1891) hydrogen bonds : angle 6.94854 / 4.98 ( 5313) metal coordination : bond 0.06663 / 3.31 ( 4) metal coordination : angle 14.34724 / 7.73 ( 3) Misc. bond : bond 0.29959 / 14.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 565 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 116 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7303 (p) REVERT: P 131 THR cc_start: 0.3964 (OUTLIER) cc_final: 0.3747 (t) REVERT: P 137 GLU cc_start: 0.7878 (tt0) cc_final: 0.7385 (mm-30) REVERT: P 159 PRO cc_start: 0.8274 (Cg_exo) cc_final: 0.7929 (Cg_endo) REVERT: P 196 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7196 (mm) REVERT: A 87 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8465 (mtt90) REVERT: A 146 ARG cc_start: 0.8814 (ttp-110) cc_final: 0.8505 (ttp-170) REVERT: B 170 TYR cc_start: 0.7815 (p90) cc_final: 0.7543 (p90) REVERT: B 364 MET cc_start: 0.8635 (tpp) cc_final: 0.8312 (mmm) REVERT: D 160 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8478 (mm-30) REVERT: I 43 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8473 (mtt90) REVERT: J 13 SER cc_start: 0.8901 (t) cc_final: 0.8580 (p) REVERT: J 15 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9176 (pttt) REVERT: J 69 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8854 (mp0) REVERT: E 40 LYS cc_start: 0.7968 (tttt) cc_final: 0.7460 (ttpt) REVERT: E 55 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7749 (p0) REVERT: E 74 MET cc_start: 0.9040 (ttp) cc_final: 0.8831 (tmm) REVERT: L 153 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8443 (ttt180) REVERT: L 193 THR cc_start: 0.9012 (p) cc_final: 0.8810 (t) REVERT: L 390 LYS cc_start: 0.8869 (tptt) cc_final: 0.8529 (ttmt) REVERT: M 31 GLN cc_start: 0.8473 (mt0) cc_final: 0.8244 (tp40) REVERT: M 239 THR cc_start: 0.9039 (p) cc_final: 0.8736 (t) REVERT: M 334 GLU cc_start: 0.8423 (tp30) cc_final: 0.8096 (tp30) REVERT: M 356 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8216 (t0) REVERT: O 235 MET cc_start: 0.9113 (mmt) cc_final: 0.8828 (mmt) REVERT: S 88 GLU cc_start: 0.8545 (mp0) cc_final: 0.8250 (mp0) REVERT: T 54 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8479 (ttp80) REVERT: U 10 LYS cc_start: 0.9191 (tttm) cc_final: 0.8935 (ttmm) outliers start: 103 outliers final: 9 residues processed: 622 average time/residue: 0.8664 time to fit residues: 620.9525 Evaluate side-chains 400 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 383 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 356 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0040 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 202 HIS C 332 ASN P 90 ASN P 115 ASN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN B 241 ASN B 295 ASN B 316 GLN D 93 HIS I 39 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN L 50 GLN L 159 ASN L 192 GLN L 196 ASN L 332 ASN L 371 ASN M 87 HIS M 316 GLN O 93 HIS T 49 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.063186 restraints weight = 53577.766| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 1.70 r_work: 0.2635 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9263 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.438 33417 Z= 0.137 Angle : 0.634 17.772 45405 Z= 0.313 Chirality : 0.042 0.163 4959 Planarity : 0.004 0.054 5700 Dihedral : 11.983 138.420 4871 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.84 % Allowed : 11.79 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.13), residues: 3953 helix: 1.08 (0.11), residues: 2149 sheet: 0.59 (0.27), residues: 368 loop : 0.08 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 202 TYR 0.020 0.002 TYR D 237 PHE 0.022 0.002 PHE B 107 TRP 0.029 0.002 TRP N 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (33400) covalent geometry : angle 0.63300 / 0.31 (45392) SS BOND : bond 0.00597 / 0.30 ( 5) SS BOND : angle 0.84077 / 0.40 ( 10) hydrogen bonds : bond 0.05116 / 3.40 ( 1891) hydrogen bonds : angle 4.77029 / 3.39 ( 5313) metal coordination : bond 0.01318 / 0.65 ( 4) metal coordination : angle 5.00494 / 2.79 ( 3) Misc. bond : bond 0.26697 / 12.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 417 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 55 ASP cc_start: 0.8383 (p0) cc_final: 0.8169 (p0) REVERT: P 74 MET cc_start: 0.8795 (ttp) cc_final: 0.8394 (tmm) REVERT: P 116 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7761 (m) REVERT: P 161 TRP cc_start: 0.6755 (m100) cc_final: 0.6125 (m100) REVERT: P 220 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6494 (tp30) REVERT: G 6 SER cc_start: 0.9198 (m) cc_final: 0.8845 (p) REVERT: G 19 LEU cc_start: 0.8184 (tp) cc_final: 0.7677 (tm) REVERT: G 21 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8838 (t) REVERT: G 85 LYS cc_start: 0.8980 (mttp) cc_final: 0.8743 (mtmt) REVERT: F 96 HIS cc_start: 0.8819 (t-90) cc_final: 0.8574 (t-90) REVERT: F 126 GLU cc_start: 0.8947 (mp0) cc_final: 0.8661 (mp0) REVERT: A 87 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8494 (ptm160) REVERT: A 146 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8184 (ttp-170) REVERT: A 153 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7867 (ttt-90) REVERT: A 424 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 60 PHE cc_start: 0.9604 (OUTLIER) cc_final: 0.9111 (t80) REVERT: B 251 GLU cc_start: 0.7645 (pm20) cc_final: 0.7430 (pm20) REVERT: D 160 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8202 (mm-30) REVERT: J 13 SER cc_start: 0.8761 (t) cc_final: 0.8497 (p) REVERT: N 6 LYS cc_start: 0.8880 (tttp) cc_final: 0.8559 (ttmt) REVERT: E 40 LYS cc_start: 0.7876 (tttt) cc_final: 0.7295 (ttpt) REVERT: E 74 MET cc_start: 0.9014 (ttp) cc_final: 0.8777 (tmm) REVERT: R 6 SER cc_start: 0.9183 (m) cc_final: 0.8900 (p) REVERT: R 66 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: Q 84 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8478 (mt-10) REVERT: Q 137 ASN cc_start: 0.8822 (m-40) cc_final: 0.8543 (m110) REVERT: L 153 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8355 (ttt90) REVERT: L 390 LYS cc_start: 0.8824 (tptt) cc_final: 0.8549 (ttmt) REVERT: M 31 GLN cc_start: 0.8476 (mt0) cc_final: 0.8211 (tp40) REVERT: M 202 ASP cc_start: 0.8758 (m-30) cc_final: 0.8557 (m-30) REVERT: M 334 GLU cc_start: 0.8013 (tp30) cc_final: 0.7703 (tp30) REVERT: M 356 ASP cc_start: 0.7917 (t70) cc_final: 0.7524 (t0) REVERT: O 235 MET cc_start: 0.9038 (mmt) cc_final: 0.8730 (mmt) REVERT: S 88 GLU cc_start: 0.8114 (mp0) cc_final: 0.7821 (mp0) REVERT: T 43 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8448 (mtm180) outliers start: 61 outliers final: 16 residues processed: 453 average time/residue: 0.8259 time to fit residues: 434.5057 Evaluate side-chains 377 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 354 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 220 GLU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain T residue 43 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 310 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN P 115 ASN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 392 GLN I 39 ASN L 102 HIS L 332 ASN M 196 ASN O 93 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.060665 restraints weight = 54063.736| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.69 r_work: 0.2587 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.387 33417 Z= 0.216 Angle : 0.643 16.622 45405 Z= 0.310 Chirality : 0.044 0.173 4959 Planarity : 0.004 0.042 5700 Dihedral : 11.222 117.860 4840 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.87 % Allowed : 12.76 % Favored : 85.38 % 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: 1.45 (0.13), residues: 3953 helix: 1.50 (0.11), residues: 2157 sheet: 0.68 (0.27), residues: 368 loop : 0.35 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 62 TYR 0.021 0.002 TYR N 225 PHE 0.021 0.002 PHE C 240 TRP 0.019 0.002 TRP C 142 HIS 0.012 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (33400) covalent geometry : angle 0.64165 / 0.31 (45392) SS BOND : bond 0.00259 / 0.16 ( 5) SS BOND : angle 0.44361 / 0.23 ( 10) hydrogen bonds : bond 0.05146 / 3.42 ( 1891) hydrogen bonds : angle 4.59868 / 3.27 ( 5313) metal coordination : bond 0.01964 / 0.97 ( 4) metal coordination : angle 5.45006 / 3.02 ( 3) Misc. bond : bond 0.26477 / 12.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 357 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 116 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7738 (m) REVERT: P 161 TRP cc_start: 0.7163 (m100) cc_final: 0.6243 (m100) REVERT: P 178 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6337 (mt-10) REVERT: G 6 SER cc_start: 0.9197 (m) cc_final: 0.8845 (p) REVERT: G 21 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8894 (t) REVERT: G 66 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: F 101 CYS cc_start: 0.7097 (t) cc_final: 0.6793 (t) REVERT: F 120 LYS cc_start: 0.8563 (mttm) cc_final: 0.8125 (mmtm) REVERT: A 146 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8142 (ttp-170) REVERT: A 153 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.7870 (ttt-90) REVERT: A 405 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8573 (mt-10) REVERT: A 424 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 139 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8627 (ttmt) REVERT: B 168 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: D 160 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8200 (mm-30) REVERT: I 54 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8473 (ttp80) REVERT: J 13 SER cc_start: 0.8834 (t) cc_final: 0.8562 (p) REVERT: J 15 LYS cc_start: 0.9179 (pttp) cc_final: 0.8922 (pttt) REVERT: N 6 LYS cc_start: 0.8827 (tttp) cc_final: 0.8471 (ttmt) REVERT: E 40 LYS cc_start: 0.7880 (tttt) cc_final: 0.7316 (ttpt) REVERT: R 6 SER cc_start: 0.9175 (m) cc_final: 0.8957 (p) REVERT: R 66 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: Q 137 ASN cc_start: 0.8753 (m-40) cc_final: 0.8422 (m110) REVERT: L 153 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8364 (ttt90) REVERT: L 390 LYS cc_start: 0.8883 (tptt) cc_final: 0.8563 (ttmt) REVERT: M 31 GLN cc_start: 0.8487 (mt0) cc_final: 0.8263 (tp40) REVERT: M 249 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8909 (mt) REVERT: M 334 GLU cc_start: 0.8000 (tp30) cc_final: 0.7674 (tp30) REVERT: M 356 ASP cc_start: 0.7943 (t70) cc_final: 0.7544 (t0) REVERT: S 88 GLU cc_start: 0.8119 (mp0) cc_final: 0.7763 (mp0) REVERT: U 73 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.7983 (ptp-170) outliers start: 62 outliers final: 22 residues processed: 401 average time/residue: 0.8097 time to fit residues: 377.1113 Evaluate side-chains 374 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 344 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 44 MET Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 179 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 379 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 134 optimal weight: 0.0770 chunk 378 optimal weight: 3.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 121 GLN D 93 HIS I 39 ASN L 50 GLN L 317 GLN M 197 ASN O 93 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.063724 restraints weight = 53839.876| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.69 r_work: 0.2656 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9256 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.381 33417 Z= 0.116 Angle : 0.537 13.540 45405 Z= 0.260 Chirality : 0.040 0.157 4959 Planarity : 0.004 0.056 5700 Dihedral : 10.566 107.817 4836 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.59 % Allowed : 13.06 % Favored : 85.35 % 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: 1.87 (0.14), residues: 3953 helix: 1.87 (0.11), residues: 2153 sheet: 0.86 (0.27), residues: 368 loop : 0.53 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.014 0.001 TYR O 237 PHE 0.019 0.001 PHE A 334 TRP 0.017 0.001 TRP P 185 HIS 0.009 0.001 HIS P 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (33400) covalent geometry : angle 0.53587 / 0.26 (45392) SS BOND : bond 0.00147 / 0.09 ( 5) SS BOND : angle 0.38625 / 0.20 ( 10) hydrogen bonds : bond 0.04120 / 2.73 ( 1891) hydrogen bonds : angle 4.35078 / 3.09 ( 5313) metal coordination : bond 0.01763 / 0.86 ( 4) metal coordination : angle 3.36371 / 1.87 ( 3) Misc. bond : bond 0.23958 / 10.66 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 366 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: P 74 MET cc_start: 0.9005 (ttp) cc_final: 0.8401 (tmm) REVERT: P 116 VAL cc_start: 0.8031 (t) cc_final: 0.7797 (m) REVERT: P 134 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6895 (mt-10) REVERT: P 161 TRP cc_start: 0.7212 (m100) cc_final: 0.6325 (m100) REVERT: G 21 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (t) REVERT: F 120 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8100 (mmtm) REVERT: F 126 GLU cc_start: 0.9025 (mp0) cc_final: 0.8791 (mp0) REVERT: A 146 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.8115 (ttp-170) REVERT: A 153 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.7817 (ttt-90) REVERT: A 390 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8769 (ttmt) REVERT: A 405 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8535 (mt-10) REVERT: A 424 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 16 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8078 (t) REVERT: B 109 ASP cc_start: 0.8497 (m-30) cc_final: 0.8099 (m-30) REVERT: D 160 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8211 (mm-30) REVERT: I 39 ASN cc_start: 0.8776 (m-40) cc_final: 0.8565 (m110) REVERT: J 10 LYS cc_start: 0.8839 (tptt) cc_final: 0.8452 (tptm) REVERT: J 13 SER cc_start: 0.8843 (t) cc_final: 0.8572 (p) REVERT: N 6 LYS cc_start: 0.8770 (tttp) cc_final: 0.8440 (ttmt) REVERT: E 40 LYS cc_start: 0.7859 (tttt) cc_final: 0.7285 (ttpt) REVERT: Q 95 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8496 (tmtt) REVERT: Q 99 ASP cc_start: 0.8701 (m-30) cc_final: 0.8101 (m-30) REVERT: Q 137 ASN cc_start: 0.8706 (m-40) cc_final: 0.8329 (m110) REVERT: L 87 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8510 (ptp90) REVERT: L 153 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8252 (ttt90) REVERT: L 390 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8539 (ttmt) REVERT: M 31 GLN cc_start: 0.8518 (mt0) cc_final: 0.8288 (tp40) REVERT: M 334 GLU cc_start: 0.7930 (tp30) cc_final: 0.7598 (tp30) REVERT: M 356 ASP cc_start: 0.7833 (t70) cc_final: 0.7438 (t0) REVERT: O 154 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7688 (mp0) REVERT: S 88 GLU cc_start: 0.8124 (mp0) cc_final: 0.7758 (mp0) outliers start: 53 outliers final: 15 residues processed: 402 average time/residue: 0.8067 time to fit residues: 377.2596 Evaluate side-chains 367 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 345 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 368 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS L 50 GLN M 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.063561 restraints weight = 53871.776| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.70 r_work: 0.2650 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.353 33417 Z= 0.118 Angle : 0.531 15.149 45405 Z= 0.255 Chirality : 0.040 0.154 4959 Planarity : 0.004 0.056 5700 Dihedral : 10.222 94.595 4835 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.71 % Allowed : 13.33 % Favored : 84.96 % 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: 2.07 (0.14), residues: 3953 helix: 2.02 (0.11), residues: 2156 sheet: 0.91 (0.27), residues: 368 loop : 0.62 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.017 0.001 TYR M 170 PHE 0.019 0.001 PHE A 334 TRP 0.014 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33400) covalent geometry : angle 0.52961 / 0.25 (45392) SS BOND : bond 0.00212 / 0.12 ( 5) SS BOND : angle 0.89231 / 0.41 ( 10) hydrogen bonds : bond 0.04084 / 2.71 ( 1891) hydrogen bonds : angle 4.24883 / 3.02 ( 5313) metal coordination : bond 0.00894 / 0.45 ( 4) metal coordination : angle 4.56967 / 2.58 ( 3) Misc. bond : bond 0.20431 / 8.98 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 74 MET cc_start: 0.8990 (ttp) cc_final: 0.8391 (tmm) REVERT: P 161 TRP cc_start: 0.7108 (m100) cc_final: 0.5812 (m100) REVERT: P 222 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7696 (tt) REVERT: G 21 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8837 (t) REVERT: F 120 LYS cc_start: 0.8530 (mttm) cc_final: 0.8053 (mmtm) REVERT: F 126 GLU cc_start: 0.9108 (mp0) cc_final: 0.8874 (mp0) REVERT: A 146 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8138 (ttp-170) REVERT: A 153 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.7801 (ttt-90) REVERT: A 390 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8769 (ttmt) REVERT: A 405 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 424 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 16 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8149 (t) REVERT: B 109 ASP cc_start: 0.8566 (m-30) cc_final: 0.8172 (m-30) REVERT: B 139 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8884 (ttpp) REVERT: D 160 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8222 (mm-30) REVERT: I 39 ASN cc_start: 0.8739 (m-40) cc_final: 0.8523 (m110) REVERT: J 10 LYS cc_start: 0.8866 (tptt) cc_final: 0.8495 (tptm) REVERT: J 13 SER cc_start: 0.8812 (t) cc_final: 0.8533 (p) REVERT: J 15 LYS cc_start: 0.9176 (pttp) cc_final: 0.8940 (pttt) REVERT: N 6 LYS cc_start: 0.8768 (tttp) cc_final: 0.8452 (ttmt) REVERT: E 40 LYS cc_start: 0.7791 (tttt) cc_final: 0.7215 (ttpt) REVERT: R 9 LYS cc_start: 0.8866 (mttt) cc_final: 0.8661 (mmtp) REVERT: Q 95 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8473 (tmtt) REVERT: Q 96 HIS cc_start: 0.8941 (t70) cc_final: 0.8713 (t-90) REVERT: Q 99 ASP cc_start: 0.8688 (m-30) cc_final: 0.8096 (m-30) REVERT: Q 137 ASN cc_start: 0.8716 (m-40) cc_final: 0.8316 (m110) REVERT: L 153 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8229 (ttt90) REVERT: L 390 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8552 (ttmt) REVERT: M 31 GLN cc_start: 0.8542 (mt0) cc_final: 0.8312 (tp40) REVERT: M 334 GLU cc_start: 0.7884 (tp30) cc_final: 0.7583 (tp30) REVERT: M 356 ASP cc_start: 0.7834 (t70) cc_final: 0.7425 (t0) REVERT: O 154 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7685 (mp0) REVERT: S 88 GLU cc_start: 0.8158 (mp0) cc_final: 0.7769 (mp0) outliers start: 57 outliers final: 26 residues processed: 394 average time/residue: 0.7517 time to fit residues: 344.9433 Evaluate side-chains 376 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 343 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 287 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 190 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 305 optimal weight: 0.6980 chunk 291 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 chunk 272 optimal weight: 0.0370 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN A 102 HIS A 317 GLN B 168 GLN B 392 GLN D 93 HIS L 50 GLN M 184 GLN O 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065802 restraints weight = 53607.908| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.71 r_work: 0.2694 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 33417 Z= 0.099 Angle : 0.506 13.095 45405 Z= 0.244 Chirality : 0.039 0.151 4959 Planarity : 0.004 0.058 5700 Dihedral : 9.803 89.554 4835 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.47 % Allowed : 13.96 % Favored : 84.57 % 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: 2.22 (0.14), residues: 3953 helix: 2.11 (0.11), residues: 2166 sheet: 0.98 (0.27), residues: 368 loop : 0.76 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.015 0.001 TYR L 106 PHE 0.017 0.001 PHE A 334 TRP 0.012 0.001 TRP C 142 HIS 0.004 0.001 HIS Q 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (33400) covalent geometry : angle 0.50558 / 0.24 (45392) SS BOND : bond 0.00619 / 0.31 ( 5) SS BOND : angle 0.87273 / 0.40 ( 10) hydrogen bonds : bond 0.03714 / 2.46 ( 1891) hydrogen bonds : angle 4.14731 / 2.95 ( 5313) metal coordination : bond 0.01125 / 0.54 ( 4) metal coordination : angle 2.92925 / 1.69 ( 3) Misc. bond : bond 0.20054 / 8.74 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 74 MET cc_start: 0.8984 (ttp) cc_final: 0.8391 (tmm) REVERT: P 161 TRP cc_start: 0.7163 (m100) cc_final: 0.5691 (m100) REVERT: G 21 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8773 (t) REVERT: F 120 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8011 (mmtm) REVERT: F 126 GLU cc_start: 0.9034 (mp0) cc_final: 0.8755 (mp0) REVERT: A 146 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.8139 (ttp-170) REVERT: A 153 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7816 (ttt-90) REVERT: A 390 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8764 (ttmt) REVERT: A 405 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8500 (mt-10) REVERT: A 424 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 109 ASP cc_start: 0.8523 (m-30) cc_final: 0.8080 (m-30) REVERT: D 160 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 248 MET cc_start: 0.8866 (ttm) cc_final: 0.8334 (ttm) REVERT: I 39 ASN cc_start: 0.8739 (m-40) cc_final: 0.8532 (m110) REVERT: J 10 LYS cc_start: 0.8883 (tptt) cc_final: 0.8518 (tptm) REVERT: J 13 SER cc_start: 0.8859 (t) cc_final: 0.8461 (p) REVERT: J 58 GLN cc_start: 0.8750 (tt0) cc_final: 0.8529 (mt0) REVERT: N 6 LYS cc_start: 0.8748 (tttp) cc_final: 0.8449 (ttmt) REVERT: E 40 LYS cc_start: 0.7800 (tttt) cc_final: 0.7228 (ttpt) REVERT: R 66 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: R 85 LYS cc_start: 0.9037 (mttt) cc_final: 0.8816 (mttp) REVERT: Q 96 HIS cc_start: 0.8889 (t70) cc_final: 0.8687 (t-90) REVERT: Q 137 ASN cc_start: 0.8693 (m-40) cc_final: 0.8307 (m110) REVERT: L 87 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8223 (ptp90) REVERT: L 153 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8262 (ttt90) REVERT: L 390 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8561 (ttmt) REVERT: M 31 GLN cc_start: 0.8528 (mt0) cc_final: 0.8313 (tp40) REVERT: M 334 GLU cc_start: 0.7839 (tp30) cc_final: 0.7523 (tp30) REVERT: M 356 ASP cc_start: 0.7775 (t70) cc_final: 0.7386 (t0) REVERT: M 364 MET cc_start: 0.8847 (tpp) cc_final: 0.8642 (mmm) REVERT: O 85 MET cc_start: 0.7903 (mtm) cc_final: 0.7619 (mtt) REVERT: O 154 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7627 (mp0) REVERT: S 88 GLU cc_start: 0.8111 (mp0) cc_final: 0.7737 (mp0) outliers start: 49 outliers final: 18 residues processed: 396 average time/residue: 0.7913 time to fit residues: 364.2083 Evaluate side-chains 370 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 346 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 353 GLU Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 373 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 209 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 325 optimal weight: 9.9990 chunk 311 optimal weight: 0.0870 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN D 93 HIS E 90 ASN L 50 GLN L 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.064294 restraints weight = 54161.598| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.70 r_work: 0.2667 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9250 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.330 33417 Z= 0.117 Angle : 0.522 14.866 45405 Z= 0.250 Chirality : 0.040 0.152 4959 Planarity : 0.004 0.056 5700 Dihedral : 9.732 89.354 4835 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.38 % Allowed : 14.23 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.14), residues: 3953 helix: 2.15 (0.11), residues: 2166 sheet: 1.03 (0.27), residues: 368 loop : 0.77 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 54 TYR 0.021 0.001 TYR M 170 PHE 0.019 0.001 PHE A 334 TRP 0.021 0.001 TRP P 185 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (33400) covalent geometry : angle 0.52148 / 0.25 (45392) SS BOND : bond 0.00548 / 0.28 ( 5) SS BOND : angle 1.17499 / 0.54 ( 10) hydrogen bonds : bond 0.03940 / 2.61 ( 1891) hydrogen bonds : angle 4.14629 / 2.95 ( 5313) metal coordination : bond 0.00297 / 0.14 ( 4) metal coordination : angle 3.29328 / 1.90 ( 3) Misc. bond : bond 0.18711 / 8.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 74 MET cc_start: 0.9020 (ttp) cc_final: 0.8415 (tmm) REVERT: P 161 TRP cc_start: 0.7137 (m100) cc_final: 0.5581 (m100) REVERT: P 220 GLU cc_start: 0.6370 (tp30) cc_final: 0.5759 (tm-30) REVERT: G 112 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: F 120 LYS cc_start: 0.8471 (mttm) cc_final: 0.7955 (mmtm) REVERT: F 126 GLU cc_start: 0.9036 (mp0) cc_final: 0.8630 (mp0) REVERT: A 146 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8181 (ttp-170) REVERT: A 153 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7814 (ttt-90) REVERT: A 390 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8764 (ttmt) REVERT: A 405 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8487 (mt-10) REVERT: A 424 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 109 ASP cc_start: 0.8541 (m-30) cc_final: 0.8114 (m-30) REVERT: B 392 GLN cc_start: 0.8274 (mp10) cc_final: 0.8024 (mp10) REVERT: D 160 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8205 (mm-30) REVERT: J 10 LYS cc_start: 0.8910 (tptt) cc_final: 0.8546 (tptm) REVERT: J 13 SER cc_start: 0.8854 (t) cc_final: 0.8460 (p) REVERT: J 15 LYS cc_start: 0.9197 (pttp) cc_final: 0.8939 (pttt) REVERT: J 58 GLN cc_start: 0.8734 (tt0) cc_final: 0.8522 (mt0) REVERT: N 6 LYS cc_start: 0.8758 (tttp) cc_final: 0.8457 (ttmt) REVERT: E 40 LYS cc_start: 0.7801 (tttt) cc_final: 0.7235 (ttpt) REVERT: R 85 LYS cc_start: 0.9038 (mttt) cc_final: 0.8815 (mttp) REVERT: Q 96 HIS cc_start: 0.8891 (t70) cc_final: 0.8224 (t-90) REVERT: Q 137 ASN cc_start: 0.8721 (m-40) cc_final: 0.8324 (m110) REVERT: L 87 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8289 (ptp90) REVERT: L 153 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8273 (ttt90) REVERT: L 390 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8566 (ttmt) REVERT: M 31 GLN cc_start: 0.8521 (mt0) cc_final: 0.8314 (tp40) REVERT: M 334 GLU cc_start: 0.7862 (tp30) cc_final: 0.7549 (tp30) REVERT: M 356 ASP cc_start: 0.7800 (t70) cc_final: 0.7417 (t0) REVERT: O 85 MET cc_start: 0.7925 (mtm) cc_final: 0.7662 (mtt) REVERT: O 154 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7628 (mp0) REVERT: S 88 GLU cc_start: 0.8129 (mp0) cc_final: 0.7749 (mp0) REVERT: U 73 ARG cc_start: 0.8609 (ptp90) cc_final: 0.7881 (ptp90) outliers start: 46 outliers final: 23 residues processed: 387 average time/residue: 0.8154 time to fit residues: 366.4115 Evaluate side-chains 372 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 345 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 14 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 373 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 380 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN D 93 HIS N 11 ASN L 50 GLN U 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062126 restraints weight = 53898.422| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.69 r_work: 0.2622 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9281 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.340 33417 Z= 0.162 Angle : 0.566 16.110 45405 Z= 0.272 Chirality : 0.042 0.159 4959 Planarity : 0.004 0.061 5700 Dihedral : 9.886 89.770 4835 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.32 % Allowed : 14.53 % Favored : 84.15 % 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: 3953 helix: 2.04 (0.11), residues: 2165 sheet: 0.98 (0.27), residues: 368 loop : 0.78 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 54 TYR 0.021 0.002 TYR N 225 PHE 0.022 0.002 PHE C 240 TRP 0.016 0.001 TRP P 185 HIS 0.013 0.001 HIS Q 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (33400) covalent geometry : angle 0.56564 / 0.27 (45392) SS BOND : bond 0.00129 / 0.08 ( 5) SS BOND : angle 1.14578 / 0.53 ( 10) hydrogen bonds : bond 0.04434 / 2.94 ( 1891) hydrogen bonds : angle 4.26199 / 3.04 ( 5313) metal coordination : bond 0.00576 / 0.29 ( 4) metal coordination : angle 3.37662 / 1.96 ( 3) Misc. bond : bond 0.19985 / 8.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 74 MET cc_start: 0.9081 (ttp) cc_final: 0.8610 (tmm) REVERT: P 161 TRP cc_start: 0.7133 (m100) cc_final: 0.5601 (m100) REVERT: P 220 GLU cc_start: 0.6367 (tp30) cc_final: 0.5819 (tm-30) REVERT: G 112 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: F 120 LYS cc_start: 0.8464 (mttm) cc_final: 0.7893 (mmtm) REVERT: F 126 GLU cc_start: 0.8958 (mp0) cc_final: 0.8494 (mp0) REVERT: A 146 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.8173 (ttp-170) REVERT: A 153 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.7793 (ttt-90) REVERT: A 390 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8760 (ttmt) REVERT: A 405 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 424 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 109 ASP cc_start: 0.8554 (m-30) cc_final: 0.8312 (m-30) REVERT: D 160 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8219 (mm-30) REVERT: J 13 SER cc_start: 0.8831 (t) cc_final: 0.8528 (p) REVERT: J 15 LYS cc_start: 0.9166 (pttp) cc_final: 0.8907 (pttt) REVERT: J 58 GLN cc_start: 0.8791 (tt0) cc_final: 0.8569 (mt0) REVERT: N 6 LYS cc_start: 0.8803 (tttp) cc_final: 0.8471 (ttmt) REVERT: E 40 LYS cc_start: 0.7829 (tttt) cc_final: 0.7246 (ttpt) REVERT: Q 96 HIS cc_start: 0.8852 (t70) cc_final: 0.8550 (t-90) REVERT: Q 137 ASN cc_start: 0.8742 (m-40) cc_final: 0.8366 (m110) REVERT: L 87 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8396 (ptp90) REVERT: L 153 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8283 (ttt90) REVERT: L 390 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8577 (ttmt) REVERT: M 31 GLN cc_start: 0.8506 (mt0) cc_final: 0.8274 (tp40) REVERT: M 334 GLU cc_start: 0.7885 (tp30) cc_final: 0.7571 (tp30) REVERT: M 356 ASP cc_start: 0.7860 (t70) cc_final: 0.7467 (t0) REVERT: M 364 MET cc_start: 0.8927 (tpp) cc_final: 0.8720 (mmm) REVERT: O 85 MET cc_start: 0.8152 (mtm) cc_final: 0.7505 (mmt) REVERT: O 154 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7649 (mp0) REVERT: S 88 GLU cc_start: 0.8136 (mp0) cc_final: 0.7754 (mp0) REVERT: U 73 ARG cc_start: 0.8657 (ptp90) cc_final: 0.7900 (ptp90) outliers start: 44 outliers final: 25 residues processed: 372 average time/residue: 0.8068 time to fit residues: 347.3095 Evaluate side-chains 367 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 57 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062974 restraints weight = 53744.739| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.68 r_work: 0.2640 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9269 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.350 33417 Z= 0.135 Angle : 0.547 15.141 45405 Z= 0.263 Chirality : 0.041 0.149 4959 Planarity : 0.004 0.063 5700 Dihedral : 9.711 89.092 4835 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.99 % Allowed : 14.98 % Favored : 84.03 % 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: 3953 helix: 2.07 (0.11), residues: 2165 sheet: 0.99 (0.27), residues: 368 loop : 0.79 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.019 0.001 TYR M 170 PHE 0.020 0.001 PHE A 334 TRP 0.015 0.001 TRP C 142 HIS 0.015 0.001 HIS Q 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (33400) covalent geometry : angle 0.54601 / 0.26 (45392) SS BOND : bond 0.00170 / 0.10 ( 5) SS BOND : angle 0.82070 / 0.38 ( 10) hydrogen bonds : bond 0.04193 / 2.78 ( 1891) hydrogen bonds : angle 4.22166 / 3.01 ( 5313) metal coordination : bond 0.00317 / 0.16 ( 4) metal coordination : angle 3.19236 / 1.85 ( 3) Misc. bond : bond 0.20178 / 8.87 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 343 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 74 MET cc_start: 0.9062 (ttp) cc_final: 0.8582 (tmm) REVERT: P 161 TRP cc_start: 0.7150 (m100) cc_final: 0.5520 (m100) REVERT: P 220 GLU cc_start: 0.6386 (tp30) cc_final: 0.5841 (tm-30) REVERT: G 112 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: F 96 HIS cc_start: 0.8961 (t-90) cc_final: 0.8671 (t-90) REVERT: F 120 LYS cc_start: 0.8456 (mttm) cc_final: 0.7943 (mmtm) REVERT: F 126 GLU cc_start: 0.8977 (mp0) cc_final: 0.8517 (mp0) REVERT: A 146 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.8163 (ttp-170) REVERT: A 153 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7790 (ttt-90) REVERT: A 390 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8749 (ttmt) REVERT: A 405 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8511 (mt-10) REVERT: A 424 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 109 ASP cc_start: 0.8586 (m-30) cc_final: 0.8340 (m-30) REVERT: D 160 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8204 (mm-30) REVERT: D 248 MET cc_start: 0.9055 (ttm) cc_final: 0.8534 (ttm) REVERT: J 13 SER cc_start: 0.8839 (t) cc_final: 0.8540 (p) REVERT: J 15 LYS cc_start: 0.9174 (pttp) cc_final: 0.8904 (pttt) REVERT: N 6 LYS cc_start: 0.8793 (tttp) cc_final: 0.8461 (ttmt) REVERT: E 40 LYS cc_start: 0.7824 (tttt) cc_final: 0.7236 (ttpt) REVERT: Q 96 HIS cc_start: 0.8829 (t70) cc_final: 0.8556 (t-90) REVERT: Q 137 ASN cc_start: 0.8740 (m-40) cc_final: 0.8351 (m110) REVERT: L 87 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8288 (ptp90) REVERT: L 153 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8283 (ttt90) REVERT: L 390 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8570 (ttmt) REVERT: M 31 GLN cc_start: 0.8497 (mt0) cc_final: 0.8274 (tp40) REVERT: M 334 GLU cc_start: 0.7861 (tp30) cc_final: 0.7551 (tp30) REVERT: M 356 ASP cc_start: 0.7861 (t70) cc_final: 0.7487 (t0) REVERT: O 85 MET cc_start: 0.8144 (mtm) cc_final: 0.7473 (mmt) REVERT: O 154 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7623 (mp0) REVERT: S 88 GLU cc_start: 0.8132 (mp0) cc_final: 0.7750 (mp0) REVERT: U 73 ARG cc_start: 0.8672 (ptp90) cc_final: 0.7910 (ptp90) outliers start: 33 outliers final: 24 residues processed: 365 average time/residue: 0.8450 time to fit residues: 357.4154 Evaluate side-chains 366 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 338 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 311 optimal weight: 0.0970 chunk 241 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 286 optimal weight: 0.0770 chunk 76 optimal weight: 7.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN L 50 GLN U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065460 restraints weight = 54229.401| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.71 r_work: 0.2696 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9231 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.336 33417 Z= 0.102 Angle : 0.517 13.475 45405 Z= 0.248 Chirality : 0.039 0.148 4959 Planarity : 0.004 0.062 5700 Dihedral : 9.313 89.842 4835 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.96 % Allowed : 15.07 % Favored : 83.97 % 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: 2.34 (0.14), residues: 3953 helix: 2.16 (0.11), residues: 2173 sheet: 1.07 (0.27), residues: 368 loop : 0.87 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 54 TYR 0.017 0.001 TYR M 170 PHE 0.017 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.014 0.001 HIS Q 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (33400) covalent geometry : angle 0.51619 / 0.25 (45392) SS BOND : bond 0.00102 / 0.07 ( 5) SS BOND : angle 0.80116 / 0.37 ( 10) hydrogen bonds : bond 0.03690 / 2.44 ( 1891) hydrogen bonds : angle 4.09858 / 2.92 ( 5313) metal coordination : bond 0.00353 / 0.18 ( 4) metal coordination : angle 2.51529 / 1.48 ( 3) Misc. bond : bond 0.19287 / 8.43 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 361 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7934 (pm20) cc_final: 0.7578 (pm20) REVERT: P 74 MET cc_start: 0.9023 (ttp) cc_final: 0.8416 (tmm) REVERT: P 137 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6985 (tm-30) REVERT: P 161 TRP cc_start: 0.7205 (m100) cc_final: 0.6364 (m100) REVERT: P 210 GLU cc_start: 0.8373 (tt0) cc_final: 0.7919 (tm-30) REVERT: P 220 GLU cc_start: 0.6235 (tp30) cc_final: 0.5722 (tm-30) REVERT: G 112 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: F 96 HIS cc_start: 0.8963 (t-90) cc_final: 0.8683 (t-90) REVERT: F 120 LYS cc_start: 0.8526 (mttm) cc_final: 0.8034 (mmtm) REVERT: A 146 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8145 (ttp-110) REVERT: A 153 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.7830 (ttt-90) REVERT: A 390 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8725 (ttmt) REVERT: A 405 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 424 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 109 ASP cc_start: 0.8650 (m-30) cc_final: 0.8448 (m-30) REVERT: B 183 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8220 (ptp-110) REVERT: D 160 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 248 MET cc_start: 0.8923 (ttm) cc_final: 0.8429 (ttm) REVERT: J 13 SER cc_start: 0.8897 (t) cc_final: 0.8523 (p) REVERT: J 15 LYS cc_start: 0.9165 (pttp) cc_final: 0.8895 (pttt) REVERT: N 6 LYS cc_start: 0.8753 (tttp) cc_final: 0.8445 (ttmt) REVERT: N 288 LYS cc_start: 0.8721 (tttp) cc_final: 0.8455 (tttm) REVERT: E 40 LYS cc_start: 0.7815 (tttt) cc_final: 0.7229 (ttpt) REVERT: Q 96 HIS cc_start: 0.8834 (t70) cc_final: 0.8567 (t-90) REVERT: Q 137 ASN cc_start: 0.8713 (m-40) cc_final: 0.8332 (m110) REVERT: L 36 LYS cc_start: 0.9066 (tppp) cc_final: 0.8745 (mtpp) REVERT: L 87 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8097 (ptp90) REVERT: L 153 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8302 (ttt90) REVERT: L 390 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8594 (ttmt) REVERT: M 31 GLN cc_start: 0.8508 (mt0) cc_final: 0.8307 (tp40) REVERT: M 334 GLU cc_start: 0.7799 (tp30) cc_final: 0.7494 (tp30) REVERT: M 356 ASP cc_start: 0.7815 (t70) cc_final: 0.7412 (t0) REVERT: O 85 MET cc_start: 0.8044 (mtm) cc_final: 0.7410 (mmt) REVERT: S 88 GLU cc_start: 0.8123 (mp0) cc_final: 0.7742 (mp0) REVERT: U 55 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.7947 (ttm110) REVERT: U 73 ARG cc_start: 0.8692 (ptp90) cc_final: 0.7951 (ptp90) outliers start: 32 outliers final: 19 residues processed: 381 average time/residue: 0.8371 time to fit residues: 369.1097 Evaluate side-chains 367 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 344 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 344 optimal weight: 0.9990 chunk 339 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.064106 restraints weight = 53869.993| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.71 r_work: 0.2660 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.323 33417 Z= 0.126 Angle : 0.546 14.953 45405 Z= 0.261 Chirality : 0.040 0.147 4959 Planarity : 0.004 0.075 5700 Dihedral : 9.392 89.679 4835 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.84 % Allowed : 15.49 % Favored : 83.66 % 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: 2.35 (0.14), residues: 3953 helix: 2.19 (0.11), residues: 2167 sheet: 1.04 (0.27), residues: 369 loop : 0.85 (0.18), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 202 TYR 0.032 0.001 TYR M 170 PHE 0.019 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.016 0.001 HIS Q 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (33400) covalent geometry : angle 0.54591 / 0.26 (45392) SS BOND : bond 0.00149 / 0.10 ( 5) SS BOND : angle 0.68970 / 0.32 ( 10) hydrogen bonds : bond 0.03992 / 2.64 ( 1891) hydrogen bonds : angle 4.12486 / 2.94 ( 5313) metal coordination : bond 0.00246 / 0.12 ( 4) metal coordination : angle 2.96008 / 1.74 ( 3) Misc. bond : bond 0.18645 / 8.18 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12778.94 seconds wall clock time: 218 minutes 23.44 seconds (13103.44 seconds total)