Starting phenix.real_space_refine on Mon Jul 6 07:51:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ab8_15314/07_2026/8ab8_15314.cif" } resolution = 2.6 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 21041 2.51 5 N 5294 2.21 5 O 6075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 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: 32550 Number of models: 1 Model: "" Number of chains: 33 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "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: 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: "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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.131 51.898 36.540 1.00 94.04 S ATOM 4207 SG CYS P 187 32.524 48.942 36.024 1.00 92.14 S Time building chain proxies: 6.54, per 1000 atoms: 0.20 Number of scatterers: 32550 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 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 6075 8.00 N 5294 7.00 C 21041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.05 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=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 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, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 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: 3.751A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.564A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 149 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: 3.739A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.800A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.870A 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: 4.120A 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: 3.649A 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 removed outlier: 3.654A pdb=" N MET P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) 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: 3.536A 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: 4.283A 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: 3.599A 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: 3.542A 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: 4.021A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.558A 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: 3.510A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.047A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.658A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.563A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.689A 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: 3.592A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.592A 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: 3.835A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.766A 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: 3.725A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.563A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.985A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.408A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.510A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) 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: 3.512A 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: 3.517A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.784A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.669A 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: 3.754A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.565A 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: 6.873A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.793A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.859A 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: 4.120A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.647A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.527A 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: 4.294A 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: 3.605A 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 removed outlier: 3.522A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) 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: 4.019A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.039A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.510A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.046A 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: 3.662A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.689A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.683A 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: 3.578A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.587A 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: 3.835A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.766A 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: 3.912A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.547A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 3.985A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.408A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.068A 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 removed outlier: 3.513A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) 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: 3.509A 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: 3.598A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.782A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.676A 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: 3.925A 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: 3.508A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.616A 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: 6.529A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.320A 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: 3.957A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.841A 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: 6.601A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.630A 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: 6.539A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.335A 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: 3.991A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.887A 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: 4.155A 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: 6.586A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.611A 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 1882 hydrogen bonds defined for protein. 5304 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: 6.27 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 13344 1.39 - 1.60: 19799 1.60 - 1.82: 187 1.82 - 2.03: 27 2.03 - 2.24: 20 Bond restraints: 33377 Sorted by residual: bond pdb=" C4M DCQ C 507 " pdb=" O4 DCQ C 507 " ideal model delta sigma weight residual 1.427 1.694 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.466 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.458 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.463 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.09e+01 ... (remaining 33372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 44018 3.86 - 7.71: 1210 7.71 - 11.57: 114 11.57 - 15.42: 15 15.42 - 19.28: 6 Bond angle restraints: 45363 Sorted by residual: angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.98 15.29 1.47e+00 4.63e-01 1.08e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 96.76 14.51 1.47e+00 4.63e-01 9.74e+01 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.36 10.97 1.14e+00 7.69e-01 9.26e+01 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 92.66 16.98 1.77e+00 3.19e-01 9.21e+01 angle pdb=" C GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta sigma weight residual 109.64 92.76 16.88 1.77e+00 3.19e-01 9.10e+01 ... (remaining 45358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 18473 30.86 - 61.73: 934 61.73 - 92.59: 108 92.59 - 123.45: 0 123.45 - 154.32: 2 Dihedral angle restraints: 19517 sinusoidal: 7904 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 -101.51 -21.09 0 2.50e+00 1.60e-01 7.12e+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 -101.78 -20.82 0 2.50e+00 1.60e-01 6.94e+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 -104.65 -17.95 0 2.50e+00 1.60e-01 5.16e+01 ... (remaining 19514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4246 0.155 - 0.310: 665 0.310 - 0.465: 40 0.465 - 0.620: 3 0.620 - 0.776: 5 Chirality restraints: 4959 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.80 -0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.81 -0.77 2.00e-01 2.50e+01 1.46e+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 -1.87 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 4956 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 507 " 0.102 2.00e-02 2.50e+03 1.75e-01 9.19e+02 pdb=" C1M DCQ C 507 " 0.207 2.00e-02 2.50e+03 pdb=" C2 DCQ C 507 " 0.038 2.00e-02 2.50e+03 pdb=" C3 DCQ C 507 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DCQ C 507 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DCQ C 507 " 0.031 2.00e-02 2.50e+03 pdb=" C6 DCQ C 507 " -0.018 2.00e-02 2.50e+03 pdb=" C7 DCQ C 507 " -0.371 2.00e-02 2.50e+03 pdb=" O2 DCQ C 507 " 0.058 2.00e-02 2.50e+03 pdb=" O3 DCQ C 507 " -0.355 2.00e-02 2.50e+03 pdb=" O4 DCQ C 507 " 0.200 2.00e-02 2.50e+03 pdb=" O5 DCQ C 507 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 279 " 0.047 2.00e-02 2.50e+03 3.39e-02 2.30e+01 pdb=" CG TYR C 279 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 279 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 279 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 279 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 279 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 279 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR C 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.018 2.00e-02 2.50e+03 2.79e-02 1.76e+01 pdb=" C2C HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.022 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.044 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.054 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.028 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.011 2.00e-02 2.50e+03 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 272 2.63 - 3.20: 28697 3.20 - 3.77: 54006 3.77 - 4.33: 78534 4.33 - 4.90: 121468 Nonbonded interactions: 282977 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 N 82 " pdb="FE HEM N 501 " model vdw 2.077 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.101 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.181 3.080 nonbonded pdb=" OB3 CDL S 701 " pdb=" O1 CDL S 702 " model vdw 2.224 3.040 ... (remaining 282972 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 506) selection = chain 'N' } 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' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.810 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9457 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 : 0.010 0.267 33392 Z= 0.590 Angle : 1.621 21.125 45376 Z= 1.007 Chirality : 0.111 0.776 4959 Planarity : 0.007 0.175 5699 Dihedral : 17.490 154.318 12020 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 3.28 % Allowed : 6.65 % Favored : 90.07 % Cbeta Deviations : 0.91 % 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: -1.23 (0.12), residues: 3953 helix: -0.92 (0.09), residues: 2124 sheet: 0.14 (0.26), residues: 351 loop : -0.62 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 283 TYR 0.063 0.006 TYR C 279 PHE 0.050 0.006 PHE B 107 TRP 0.044 0.006 TRP C 142 HIS 0.026 0.004 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00979 / 0.59 (33377) covalent geometry : angle 1.61640 / 1.01 (45363) SS BOND : bond 0.02462 / 1.47 ( 5) SS BOND : angle 2.18005 / 1.15 ( 10) hydrogen bonds : bond 0.18516 / 12.55 ( 1882) hydrogen bonds : angle 6.87795 / 5.03 ( 5304) metal coordination : bond 0.07174 / 3.57 ( 4) metal coordination : angle 14.66318 / 7.62 ( 3) Misc. bond : bond 0.13370 / 6.72 ( 6) *********************** 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 568 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 459 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9163 (tttt) cc_final: 0.8940 (ttmt) REVERT: C 52 MET cc_start: 0.9436 (mtt) cc_final: 0.9215 (mtt) REVERT: P 105 VAL cc_start: 0.8554 (t) cc_final: 0.8287 (p) REVERT: P 143 VAL cc_start: 0.5239 (OUTLIER) cc_final: 0.4918 (t) REVERT: P 214 TYR cc_start: 0.7813 (p90) cc_final: 0.7606 (p90) REVERT: G 9 LYS cc_start: 0.9194 (mttp) cc_final: 0.8779 (tttm) REVERT: G 66 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8859 (mt-10) REVERT: F 126 GLU cc_start: 0.9001 (mp0) cc_final: 0.8554 (mp0) REVERT: A 87 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: A 390 LYS cc_start: 0.8939 (tptt) cc_final: 0.8652 (mttt) REVERT: A 433 HIS cc_start: 0.8630 (t70) cc_final: 0.8320 (m-70) REVERT: B 134 GLU cc_start: 0.8969 (tt0) cc_final: 0.8768 (tt0) REVERT: B 139 LYS cc_start: 0.9162 (tttt) cc_final: 0.8917 (tppt) REVERT: B 170 TYR cc_start: 0.8084 (p90) cc_final: 0.7789 (p90) REVERT: B 388 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 78 GLU cc_start: 0.9029 (tt0) cc_final: 0.8675 (mt-10) REVERT: J 13 SER cc_start: 0.8788 (t) cc_final: 0.8583 (p) REVERT: J 75 ILE cc_start: 0.9208 (mm) cc_final: 0.9006 (tp) REVERT: R 9 LYS cc_start: 0.9098 (mttp) cc_final: 0.8843 (ttpt) REVERT: R 85 LYS cc_start: 0.9176 (mttm) cc_final: 0.8968 (mmtt) REVERT: Q 138 THR cc_start: 0.9258 (m) cc_final: 0.9049 (p) REVERT: L 87 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7266 (mtp85) REVERT: L 240 GLN cc_start: 0.8820 (mp10) cc_final: 0.8387 (mm110) REVERT: M 16 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8941 (p) REVERT: M 19 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8946 (tp30) REVERT: M 205 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8743 (tm130) REVERT: M 370 VAL cc_start: 0.7671 (t) cc_final: 0.7285 (m) REVERT: M 388 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8112 (tm-30) REVERT: U 10 LYS cc_start: 0.9146 (tttm) cc_final: 0.8923 (tptm) REVERT: U 11 LYS cc_start: 0.8844 (tttt) cc_final: 0.8445 (ptpp) outliers start: 109 outliers final: 8 residues processed: 525 average time/residue: 0.7399 time to fit residues: 449.9905 Evaluate side-chains 330 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 317 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 143 VAL 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 B residue 79 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 90 ASN P 115 ASN A 50 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 377 ASN D 93 HIS J 80 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN Q 131 GLN L 332 ASN L 371 ASN M 87 HIS M 241 ASN M 354 ASN U 80 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.057128 restraints weight = 60142.056| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 1.81 r_work: 0.2577 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.387 33392 Z= 0.132 Angle : 0.612 14.957 45376 Z= 0.304 Chirality : 0.042 0.157 4959 Planarity : 0.004 0.045 5699 Dihedral : 11.810 125.833 4852 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % Rotamer: Outliers : 1.74 % Allowed : 10.26 % Favored : 88.00 % 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: 1.05 (0.13), residues: 3953 helix: 1.18 (0.11), residues: 2140 sheet: 0.65 (0.26), residues: 359 loop : 0.15 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 153 TYR 0.018 0.001 TYR D 237 PHE 0.021 0.002 PHE L 334 TRP 0.024 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (33377) covalent geometry : angle 0.61000 / 0.30 (45363) SS BOND : bond 0.00606 / 0.32 ( 5) SS BOND : angle 1.93557 / 1.04 ( 10) hydrogen bonds : bond 0.04891 / 3.29 ( 1882) hydrogen bonds : angle 4.69712 / 3.43 ( 5304) metal coordination : bond 0.01324 / 0.66 ( 4) metal coordination : angle 4.67128 / 2.57 ( 3) Misc. bond : bond 0.28566 / 16.23 ( 6) *********************** 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 406 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8886 (tttt) cc_final: 0.8604 (ttmt) REVERT: P 106 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7636 (mmtm) REVERT: P 129 HIS cc_start: 0.6136 (t70) cc_final: 0.5754 (t70) REVERT: G 9 LYS cc_start: 0.8985 (mttp) cc_final: 0.8534 (tttm) REVERT: G 66 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8592 (mt-10) REVERT: A 87 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7848 (mtp85) REVERT: A 120 LYS cc_start: 0.8864 (tttt) cc_final: 0.8619 (ptmt) REVERT: A 230 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8288 (tp30) REVERT: A 390 LYS cc_start: 0.8934 (tptt) cc_final: 0.8732 (mttm) REVERT: B 134 GLU cc_start: 0.8815 (tt0) cc_final: 0.8553 (tt0) REVERT: B 139 LYS cc_start: 0.9112 (tttt) cc_final: 0.8842 (tppt) REVERT: B 388 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 163 ASP cc_start: 0.8914 (m-30) cc_final: 0.8496 (p0) REVERT: H 78 GLU cc_start: 0.8919 (tt0) cc_final: 0.8465 (mt-10) REVERT: I 54 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8769 (ttp80) REVERT: N 6 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8658 (ttpt) REVERT: R 85 LYS cc_start: 0.9061 (mttm) cc_final: 0.8785 (mmtt) REVERT: L 240 GLN cc_start: 0.8588 (mp10) cc_final: 0.8298 (mm110) REVERT: M 19 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (tp30) REVERT: M 307 LYS cc_start: 0.9060 (pttt) cc_final: 0.8857 (ptmt) REVERT: M 350 GLU cc_start: 0.8434 (pt0) cc_final: 0.8225 (tt0) REVERT: M 370 VAL cc_start: 0.7811 (t) cc_final: 0.7422 (m) REVERT: M 388 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7969 (tm-30) REVERT: M 392 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: O 193 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8928 (mt0) REVERT: S 76 LYS cc_start: 0.9056 (tptt) cc_final: 0.8728 (tptm) outliers start: 58 outliers final: 13 residues processed: 382 average time/residue: 0.7342 time to fit residues: 326.2732 Evaluate side-chains 318 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 299 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 392 GLN Chi-restraints excluded: chain O residue 193 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 384 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 38 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 149 ASN P 129 HIS B 197 ASN B 316 GLN B 354 ASN B 377 ASN D 93 HIS L 102 HIS L 317 GLN M 316 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.056327 restraints weight = 60106.108| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 1.83 r_work: 0.2562 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9315 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.405 33392 Z= 0.140 Angle : 0.565 14.419 45376 Z= 0.276 Chirality : 0.041 0.175 4959 Planarity : 0.004 0.050 5699 Dihedral : 10.996 107.283 4834 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.56 % Allowed : 11.22 % Favored : 87.21 % 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: 1.68 (0.14), residues: 3953 helix: 1.73 (0.11), residues: 2136 sheet: 0.69 (0.26), residues: 368 loop : 0.44 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 155 TYR 0.027 0.001 TYR P 214 PHE 0.020 0.001 PHE A 334 TRP 0.021 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (33377) covalent geometry : angle 0.56338 / 0.28 (45363) SS BOND : bond 0.00394 / 0.21 ( 5) SS BOND : angle 1.79620 / 0.96 ( 10) hydrogen bonds : bond 0.04636 / 3.11 ( 1882) hydrogen bonds : angle 4.42659 / 3.24 ( 5304) metal coordination : bond 0.00980 / 0.49 ( 4) metal coordination : angle 5.13121 / 2.75 ( 3) Misc. bond : bond 0.27874 / 14.56 ( 6) *********************** 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 363 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 1.122 Fit side-chains REVERT: C 6 LYS cc_start: 0.8900 (tttt) cc_final: 0.8629 (ttmt) REVERT: P 106 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7804 (mmtm) REVERT: P 129 HIS cc_start: 0.6330 (t-170) cc_final: 0.5866 (t-90) REVERT: P 147 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5676 (ttm-80) REVERT: P 196 ILE cc_start: 0.7077 (mm) cc_final: 0.6269 (tp) REVERT: G 9 LYS cc_start: 0.9011 (mttp) cc_final: 0.8539 (tttm) REVERT: G 66 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8576 (mt-10) REVERT: A 120 LYS cc_start: 0.8830 (tttt) cc_final: 0.8581 (ptmt) REVERT: A 230 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8359 (tp30) REVERT: A 390 LYS cc_start: 0.8927 (tptt) cc_final: 0.8724 (mttm) REVERT: B 134 GLU cc_start: 0.8808 (tt0) cc_final: 0.8562 (tt0) REVERT: B 139 LYS cc_start: 0.9110 (tttt) cc_final: 0.8867 (tppt) REVERT: B 168 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: B 388 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7900 (tm-30) REVERT: D 163 ASP cc_start: 0.8924 (m-30) cc_final: 0.8472 (p0) REVERT: D 248 MET cc_start: 0.9234 (ttp) cc_final: 0.8941 (ttm) REVERT: H 78 GLU cc_start: 0.8922 (tt0) cc_final: 0.8425 (mt-10) REVERT: I 54 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (ttp80) REVERT: N 6 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8643 (ttpt) REVERT: R 85 LYS cc_start: 0.9078 (mttm) cc_final: 0.8772 (mmtt) REVERT: L 240 GLN cc_start: 0.8613 (mp10) cc_final: 0.8330 (mm110) REVERT: M 19 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8744 (tp30) REVERT: M 307 LYS cc_start: 0.9078 (pttt) cc_final: 0.8865 (ptmt) REVERT: M 370 VAL cc_start: 0.7959 (t) cc_final: 0.7617 (m) REVERT: M 388 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7898 (tm-30) REVERT: M 392 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: U 15 LYS cc_start: 0.9224 (pttt) cc_final: 0.8984 (pttm) outliers start: 52 outliers final: 17 residues processed: 343 average time/residue: 0.7267 time to fit residues: 289.0880 Evaluate side-chains 316 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 392 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 170 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 273 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN B 377 ASN D 93 HIS R 84 HIS L 332 ASN M 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.054654 restraints weight = 60411.642| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 1.81 r_work: 0.2527 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9345 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.346 33392 Z= 0.198 Angle : 0.592 15.800 45376 Z= 0.288 Chirality : 0.043 0.233 4959 Planarity : 0.004 0.056 5699 Dihedral : 10.881 89.453 4830 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.05 % Allowed : 10.83 % Favored : 87.12 % 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: 1.82 (0.14), residues: 3953 helix: 1.85 (0.11), residues: 2140 sheet: 0.68 (0.26), residues: 369 loop : 0.51 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 62 TYR 0.029 0.002 TYR P 214 PHE 0.021 0.002 PHE A 334 TRP 0.024 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (33377) covalent geometry : angle 0.58949 / 0.29 (45363) SS BOND : bond 0.00383 / 0.21 ( 5) SS BOND : angle 1.58952 / 0.85 ( 10) hydrogen bonds : bond 0.04912 / 3.30 ( 1882) hydrogen bonds : angle 4.38826 / 3.21 ( 5304) metal coordination : bond 0.01580 / 0.79 ( 4) metal coordination : angle 5.80600 / 3.09 ( 3) Misc. bond : bond 0.27290 / 15.20 ( 6) *********************** 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 369 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 1.157 Fit side-chains REVERT: C 6 LYS cc_start: 0.8913 (tttt) cc_final: 0.8678 (ttmt) REVERT: P 106 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7853 (mmtm) REVERT: P 115 ASN cc_start: 0.4140 (OUTLIER) cc_final: 0.3693 (p0) REVERT: P 129 HIS cc_start: 0.6368 (t-170) cc_final: 0.5820 (t-90) REVERT: P 147 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5558 (ttm-80) REVERT: P 196 ILE cc_start: 0.7028 (mm) cc_final: 0.6343 (tp) REVERT: G 9 LYS cc_start: 0.8995 (mttp) cc_final: 0.8549 (tttm) REVERT: G 66 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8610 (mt-10) REVERT: F 120 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8613 (mmtm) REVERT: A 120 LYS cc_start: 0.8831 (tttt) cc_final: 0.8575 (ptmt) REVERT: A 141 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: A 230 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8401 (tp30) REVERT: A 390 LYS cc_start: 0.8943 (tptt) cc_final: 0.8705 (mttt) REVERT: B 134 GLU cc_start: 0.8822 (tt0) cc_final: 0.8562 (tt0) REVERT: B 139 LYS cc_start: 0.9106 (tttt) cc_final: 0.8868 (tppt) REVERT: B 170 TYR cc_start: 0.8322 (p90) cc_final: 0.7997 (p90) REVERT: B 388 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 85 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8470 (ttp) REVERT: D 163 ASP cc_start: 0.8932 (m-30) cc_final: 0.8485 (p0) REVERT: H 78 GLU cc_start: 0.8938 (tt0) cc_final: 0.8445 (mt-10) REVERT: I 54 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8780 (ttp80) REVERT: N 6 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8701 (ttpt) REVERT: R 85 LYS cc_start: 0.9099 (mttm) cc_final: 0.8782 (mmtt) REVERT: R 117 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8670 (t0) REVERT: Q 103 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: Q 107 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8533 (mmtm) REVERT: L 240 GLN cc_start: 0.8640 (mp10) cc_final: 0.8335 (mm110) REVERT: M 19 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8718 (tp30) REVERT: M 236 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8051 (ttp-170) REVERT: M 370 VAL cc_start: 0.8179 (t) cc_final: 0.7889 (m) REVERT: M 388 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7932 (tm-30) REVERT: M 392 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: O 193 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8858 (mt0) REVERT: O 248 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8354 (ttm) outliers start: 68 outliers final: 21 residues processed: 343 average time/residue: 0.7286 time to fit residues: 290.1472 Evaluate side-chains 321 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 392 GLN Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 226 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 284 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 286 optimal weight: 0.0970 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN L 161 GLN M 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.055776 restraints weight = 60234.435| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 1.81 r_work: 0.2547 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.333 33392 Z= 0.142 Angle : 0.547 14.710 45376 Z= 0.266 Chirality : 0.041 0.215 4959 Planarity : 0.004 0.056 5699 Dihedral : 10.619 86.832 4830 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.74 % Allowed : 11.70 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.14), residues: 3953 helix: 2.03 (0.11), residues: 2126 sheet: 0.73 (0.26), residues: 369 loop : 0.60 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 55 TYR 0.026 0.001 TYR P 214 PHE 0.022 0.001 PHE U 20 TRP 0.019 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (33377) covalent geometry : angle 0.54482 / 0.27 (45363) SS BOND : bond 0.00333 / 0.19 ( 5) SS BOND : angle 1.48025 / 0.79 ( 10) hydrogen bonds : bond 0.04469 / 2.99 ( 1882) hydrogen bonds : angle 4.32235 / 3.16 ( 5304) metal coordination : bond 0.01018 / 0.51 ( 4) metal coordination : angle 5.64122 / 3.04 ( 3) Misc. bond : bond 0.24777 / 14.01 ( 6) *********************** 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 352 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.923 Fit side-chains REVERT: C 6 LYS cc_start: 0.8913 (tttt) cc_final: 0.8686 (ttmt) REVERT: P 106 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7878 (mmtm) REVERT: P 129 HIS cc_start: 0.6366 (t-170) cc_final: 0.5744 (t-90) REVERT: P 147 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5618 (ttm-80) REVERT: P 196 ILE cc_start: 0.7009 (mm) cc_final: 0.6337 (tp) REVERT: G 9 LYS cc_start: 0.8989 (mttp) cc_final: 0.8546 (tttm) REVERT: G 66 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8616 (mt-10) REVERT: A 120 LYS cc_start: 0.8842 (tttt) cc_final: 0.8581 (ptmt) REVERT: A 141 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: A 230 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8385 (tp30) REVERT: A 390 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8672 (mttt) REVERT: B 134 GLU cc_start: 0.8809 (tt0) cc_final: 0.8543 (tt0) REVERT: B 139 LYS cc_start: 0.9108 (tttt) cc_final: 0.8868 (tppt) REVERT: B 388 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 163 ASP cc_start: 0.8928 (m-30) cc_final: 0.8484 (p0) REVERT: D 248 MET cc_start: 0.9266 (ttp) cc_final: 0.8869 (ttm) REVERT: H 78 GLU cc_start: 0.8966 (tt0) cc_final: 0.8470 (mt-10) REVERT: I 54 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8773 (ttp80) REVERT: J 11 LYS cc_start: 0.8840 (mtpm) cc_final: 0.8633 (pttp) REVERT: N 6 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8706 (ttpt) REVERT: R 85 LYS cc_start: 0.9086 (mttm) cc_final: 0.8782 (mmtt) REVERT: R 117 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8651 (t0) REVERT: L 240 GLN cc_start: 0.8645 (mp10) cc_final: 0.8308 (mm110) REVERT: M 19 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8739 (tp30) REVERT: M 236 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7877 (ttp-170) REVERT: M 388 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7988 (tm-30) REVERT: M 392 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: O 193 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8865 (mt0) outliers start: 58 outliers final: 19 residues processed: 333 average time/residue: 0.7381 time to fit residues: 284.9777 Evaluate side-chains 315 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 392 GLN Chi-restraints excluded: chain O residue 193 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 108 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 254 optimal weight: 0.0370 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.057187 restraints weight = 59920.460| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.81 r_work: 0.2585 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9306 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.303 33392 Z= 0.111 Angle : 0.519 15.295 45376 Z= 0.251 Chirality : 0.040 0.276 4959 Planarity : 0.004 0.058 5699 Dihedral : 10.165 87.426 4830 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.50 % Allowed : 12.18 % Favored : 86.31 % 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: 2.19 (0.14), residues: 3953 helix: 2.13 (0.11), residues: 2142 sheet: 1.00 (0.27), residues: 365 loop : 0.66 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 128 TYR 0.022 0.001 TYR P 214 PHE 0.018 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 0.00249 / 0.11 (33377) covalent geometry : angle 0.51712 / 0.25 (45363) SS BOND : bond 0.00278 / 0.16 ( 5) SS BOND : angle 1.25926 / 0.67 ( 10) hydrogen bonds : bond 0.04037 / 2.70 ( 1882) hydrogen bonds : angle 4.21566 / 3.08 ( 5304) metal coordination : bond 0.00550 / 0.27 ( 4) metal coordination : angle 5.66801 / 3.08 ( 3) Misc. bond : bond 0.22593 / 12.19 ( 6) *********************** 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 346 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8859 (tttt) cc_final: 0.8652 (ttmt) REVERT: P 106 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7889 (mmtm) REVERT: P 129 HIS cc_start: 0.6602 (t-170) cc_final: 0.6091 (t-90) REVERT: P 147 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.4932 (ttm170) REVERT: G 9 LYS cc_start: 0.8989 (mttp) cc_final: 0.8535 (tttm) REVERT: A 120 LYS cc_start: 0.8835 (tttt) cc_final: 0.8580 (ptmt) REVERT: A 390 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8665 (mttt) REVERT: B 134 GLU cc_start: 0.8792 (tt0) cc_final: 0.8537 (tt0) REVERT: B 139 LYS cc_start: 0.9104 (tttt) cc_final: 0.8866 (tppt) REVERT: B 388 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 163 ASP cc_start: 0.8968 (m-30) cc_final: 0.8501 (p0) REVERT: H 78 GLU cc_start: 0.8965 (tt0) cc_final: 0.8468 (mt-10) REVERT: I 54 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8736 (ttp80) REVERT: J 69 GLU cc_start: 0.7588 (pp20) cc_final: 0.7388 (pp20) REVERT: R 85 LYS cc_start: 0.9043 (mttm) cc_final: 0.8769 (mmtt) REVERT: R 117 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8601 (t0) REVERT: Q 103 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8207 (tm-30) REVERT: L 240 GLN cc_start: 0.8628 (mp10) cc_final: 0.8279 (mm110) REVERT: M 388 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 50 outliers final: 17 residues processed: 328 average time/residue: 0.7312 time to fit residues: 278.9331 Evaluate side-chains 301 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 107 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 361 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN B 377 ASN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.055039 restraints weight = 60479.014| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 1.80 r_work: 0.2532 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9340 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.310 33392 Z= 0.189 Angle : 0.577 15.457 45376 Z= 0.278 Chirality : 0.043 0.223 4959 Planarity : 0.004 0.057 5699 Dihedral : 10.270 89.154 4827 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 12.36 % Favored : 86.04 % 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: 2.14 (0.14), residues: 3953 helix: 2.09 (0.11), residues: 2142 sheet: 1.00 (0.27), residues: 364 loop : 0.63 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 55 TYR 0.021 0.002 TYR Q 114 PHE 0.021 0.002 PHE A 334 TRP 0.021 0.001 TRP C 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (33377) covalent geometry : angle 0.57506 / 0.28 (45363) SS BOND : bond 0.00361 / 0.20 ( 5) SS BOND : angle 1.44579 / 0.76 ( 10) hydrogen bonds : bond 0.04667 / 3.13 ( 1882) hydrogen bonds : angle 4.28319 / 3.13 ( 5304) metal coordination : bond 0.01314 / 0.66 ( 4) metal coordination : angle 5.89539 / 3.19 ( 3) Misc. bond : bond 0.24314 / 13.27 ( 6) *********************** 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 339 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8883 (tttt) cc_final: 0.8671 (ttmt) REVERT: C 159 GLU cc_start: 0.7646 (pm20) cc_final: 0.7392 (pm20) REVERT: P 106 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (mmtm) REVERT: P 129 HIS cc_start: 0.6461 (t-170) cc_final: 0.5946 (t-90) REVERT: P 147 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.4944 (ttm170) REVERT: P 196 ILE cc_start: 0.7074 (mm) cc_final: 0.6568 (tp) REVERT: P 199 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6636 (mtt-85) REVERT: G 9 LYS cc_start: 0.8978 (mttp) cc_final: 0.8551 (tttm) REVERT: A 120 LYS cc_start: 0.8826 (tttt) cc_final: 0.8570 (ptmt) REVERT: A 390 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8673 (mttt) REVERT: B 134 GLU cc_start: 0.8827 (tt0) cc_final: 0.8552 (tt0) REVERT: B 139 LYS cc_start: 0.9106 (tttt) cc_final: 0.8865 (tppt) REVERT: B 170 TYR cc_start: 0.8330 (p90) cc_final: 0.7915 (p90) REVERT: B 388 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7980 (tm-30) REVERT: D 163 ASP cc_start: 0.8996 (m-30) cc_final: 0.8511 (p0) REVERT: D 248 MET cc_start: 0.9376 (ttp) cc_final: 0.8925 (ttm) REVERT: H 78 GLU cc_start: 0.8965 (tt0) cc_final: 0.8752 (tt0) REVERT: I 54 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (ttp80) REVERT: R 85 LYS cc_start: 0.9055 (mttm) cc_final: 0.8758 (mmtt) REVERT: R 117 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8650 (t0) REVERT: Q 103 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8225 (tm-30) REVERT: L 240 GLN cc_start: 0.8677 (mp10) cc_final: 0.8326 (mm110) REVERT: M 236 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7961 (ttp-170) REVERT: M 388 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8042 (tm-30) REVERT: U 55 ARG cc_start: 0.8917 (tpp-160) cc_final: 0.8657 (ttp-170) outliers start: 53 outliers final: 23 residues processed: 323 average time/residue: 0.7489 time to fit residues: 279.9473 Evaluate side-chains 308 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 199 ARG Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 163 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 358 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN M 295 ASN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.055128 restraints weight = 60301.257| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.80 r_work: 0.2537 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9339 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.320 33392 Z= 0.177 Angle : 0.566 15.182 45376 Z= 0.274 Chirality : 0.042 0.188 4959 Planarity : 0.004 0.057 5699 Dihedral : 10.202 89.331 4827 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 12.61 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.14), residues: 3953 helix: 2.10 (0.11), residues: 2140 sheet: 1.02 (0.27), residues: 364 loop : 0.64 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 55 TYR 0.023 0.002 TYR Q 114 PHE 0.021 0.001 PHE A 334 TRP 0.020 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (33377) covalent geometry : angle 0.56313 / 0.27 (45363) SS BOND : bond 0.00338 / 0.19 ( 5) SS BOND : angle 1.41787 / 0.75 ( 10) hydrogen bonds : bond 0.04593 / 3.08 ( 1882) hydrogen bonds : angle 4.28601 / 3.14 ( 5304) metal coordination : bond 0.01093 / 0.55 ( 4) metal coordination : angle 6.04038 / 3.26 ( 3) Misc. bond : bond 0.24239 / 13.50 ( 6) *********************** 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 327 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8877 (tttt) cc_final: 0.8667 (ttmt) REVERT: C 159 GLU cc_start: 0.7625 (pm20) cc_final: 0.7325 (pm20) REVERT: P 106 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7915 (mmtm) REVERT: P 196 ILE cc_start: 0.7109 (mm) cc_final: 0.6565 (tp) REVERT: G 9 LYS cc_start: 0.8994 (mttp) cc_final: 0.8563 (tttm) REVERT: F 126 GLU cc_start: 0.9003 (mp0) cc_final: 0.8444 (mp0) REVERT: A 120 LYS cc_start: 0.8823 (tttt) cc_final: 0.8574 (ptmt) REVERT: A 230 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8363 (tp30) REVERT: A 390 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8660 (mttt) REVERT: B 134 GLU cc_start: 0.8823 (tt0) cc_final: 0.8546 (tt0) REVERT: B 139 LYS cc_start: 0.9098 (tttt) cc_final: 0.8865 (tppt) REVERT: B 170 TYR cc_start: 0.8333 (p90) cc_final: 0.7969 (p90) REVERT: B 388 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 163 ASP cc_start: 0.8987 (m-30) cc_final: 0.8474 (p0) REVERT: D 248 MET cc_start: 0.9357 (ttp) cc_final: 0.8937 (ttm) REVERT: H 78 GLU cc_start: 0.8967 (tt0) cc_final: 0.8746 (tt0) REVERT: R 85 LYS cc_start: 0.9052 (mttm) cc_final: 0.8758 (mmtt) REVERT: R 117 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (t0) REVERT: Q 103 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8171 (tm-30) REVERT: L 240 GLN cc_start: 0.8673 (mp10) cc_final: 0.8318 (mm110) REVERT: M 236 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7951 (ttp-170) REVERT: M 388 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7954 (tm-30) REVERT: M 392 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: U 55 ARG cc_start: 0.8946 (tpp-160) cc_final: 0.8667 (ttp-170) outliers start: 47 outliers final: 25 residues processed: 313 average time/residue: 0.7471 time to fit residues: 270.4986 Evaluate side-chains 307 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 392 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 259 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN U 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.056531 restraints weight = 60045.443| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.80 r_work: 0.2572 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9316 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.307 33392 Z= 0.119 Angle : 0.527 13.973 45376 Z= 0.255 Chirality : 0.040 0.188 4959 Planarity : 0.004 0.056 5699 Dihedral : 9.886 88.621 4827 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 12.91 % Favored : 85.98 % 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: 2.31 (0.14), residues: 3953 helix: 2.23 (0.11), residues: 2130 sheet: 1.11 (0.27), residues: 364 loop : 0.70 (0.18), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 155 TYR 0.025 0.001 TYR Q 114 PHE 0.019 0.001 PHE A 334 TRP 0.015 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (33377) covalent geometry : angle 0.52447 / 0.26 (45363) SS BOND : bond 0.00250 / 0.14 ( 5) SS BOND : angle 1.18223 / 0.62 ( 10) hydrogen bonds : bond 0.04117 / 2.75 ( 1882) hydrogen bonds : angle 4.20923 / 3.08 ( 5304) metal coordination : bond 0.00612 / 0.31 ( 4) metal coordination : angle 5.96924 / 3.26 ( 3) Misc. bond : bond 0.22410 / 12.34 ( 6) *********************** 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 322 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7678 (pm20) cc_final: 0.7366 (pm20) REVERT: P 106 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7881 (mmtm) REVERT: P 129 HIS cc_start: 0.6797 (t-170) cc_final: 0.6263 (t-90) REVERT: G 9 LYS cc_start: 0.8979 (mttp) cc_final: 0.8555 (tttm) REVERT: F 126 GLU cc_start: 0.8999 (mp0) cc_final: 0.8411 (mp0) REVERT: A 120 LYS cc_start: 0.8823 (tttt) cc_final: 0.8579 (ptmt) REVERT: A 390 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8658 (mttt) REVERT: B 134 GLU cc_start: 0.8799 (tt0) cc_final: 0.8533 (tt0) REVERT: B 139 LYS cc_start: 0.9099 (tttt) cc_final: 0.8868 (tppt) REVERT: B 170 TYR cc_start: 0.8343 (p90) cc_final: 0.8028 (p90) REVERT: B 179 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8823 (mttp) REVERT: B 388 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 85 MET cc_start: 0.7905 (ttp) cc_final: 0.7274 (ttm) REVERT: D 163 ASP cc_start: 0.8937 (m-30) cc_final: 0.8439 (p0) REVERT: H 78 GLU cc_start: 0.8941 (tt0) cc_final: 0.8730 (tt0) REVERT: R 85 LYS cc_start: 0.9021 (mttm) cc_final: 0.8734 (mmtt) REVERT: R 117 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8599 (t0) REVERT: Q 103 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8182 (tm-30) REVERT: L 240 GLN cc_start: 0.8680 (mp10) cc_final: 0.8313 (mm110) REVERT: M 236 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7792 (ttp-170) REVERT: M 388 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8021 (tm-30) REVERT: U 15 LYS cc_start: 0.9205 (pttm) cc_final: 0.8953 (pttp) REVERT: U 55 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8677 (ttp-170) outliers start: 37 outliers final: 21 residues processed: 313 average time/residue: 0.7112 time to fit residues: 259.1342 Evaluate side-chains 305 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 21 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 333 optimal weight: 0.2980 chunk 141 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN M 184 GLN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.074725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.056837 restraints weight = 60265.185| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.80 r_work: 0.2578 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 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 0.305 33392 Z= 0.117 Angle : 0.520 13.801 45376 Z= 0.251 Chirality : 0.040 0.183 4959 Planarity : 0.004 0.055 5699 Dihedral : 9.655 89.813 4827 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.90 % Allowed : 13.24 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.14), residues: 3953 helix: 2.23 (0.11), residues: 2142 sheet: 1.15 (0.27), residues: 364 loop : 0.75 (0.18), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 61 TYR 0.024 0.001 TYR Q 114 PHE 0.019 0.001 PHE A 334 TRP 0.014 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33377) covalent geometry : angle 0.51782 / 0.25 (45363) SS BOND : bond 0.00275 / 0.16 ( 5) SS BOND : angle 1.11068 / 0.58 ( 10) hydrogen bonds : bond 0.04040 / 2.70 ( 1882) hydrogen bonds : angle 4.16859 / 3.05 ( 5304) metal coordination : bond 0.00560 / 0.28 ( 4) metal coordination : angle 5.96003 / 3.27 ( 3) Misc. bond : bond 0.21634 / 11.73 ( 6) ********************** 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 319 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7698 (pm20) cc_final: 0.7383 (pm20) REVERT: P 106 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7901 (mmtm) REVERT: P 129 HIS cc_start: 0.6772 (t-170) cc_final: 0.6296 (t-90) REVERT: P 196 ILE cc_start: 0.6981 (mm) cc_final: 0.6455 (tp) REVERT: G 9 LYS cc_start: 0.8993 (mttp) cc_final: 0.8560 (tttm) REVERT: F 126 GLU cc_start: 0.8986 (mp0) cc_final: 0.8383 (mp0) REVERT: A 120 LYS cc_start: 0.8827 (tttt) cc_final: 0.8572 (ptmt) REVERT: A 230 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8392 (tp30) REVERT: A 390 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8669 (mttt) REVERT: B 134 GLU cc_start: 0.8799 (tt0) cc_final: 0.8531 (tt0) REVERT: B 139 LYS cc_start: 0.9094 (tttt) cc_final: 0.8866 (tppt) REVERT: B 170 TYR cc_start: 0.8334 (p90) cc_final: 0.8046 (p90) REVERT: B 179 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8818 (mttp) REVERT: B 388 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7964 (tm-30) REVERT: D 85 MET cc_start: 0.7909 (ttp) cc_final: 0.7299 (ttm) REVERT: D 163 ASP cc_start: 0.8946 (m-30) cc_final: 0.8420 (p0) REVERT: H 78 GLU cc_start: 0.8952 (tt0) cc_final: 0.8736 (tt0) REVERT: I 43 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.8240 (ttp-170) REVERT: I 54 ARG cc_start: 0.9014 (tmm-80) cc_final: 0.8783 (ttp80) REVERT: R 85 LYS cc_start: 0.9001 (mttm) cc_final: 0.8712 (mmtp) REVERT: R 117 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (t0) REVERT: Q 103 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8171 (tm-30) REVERT: Q 138 THR cc_start: 0.9063 (m) cc_final: 0.8753 (p) REVERT: L 240 GLN cc_start: 0.8715 (mp10) cc_final: 0.8343 (mm110) REVERT: M 236 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7802 (ttp-170) REVERT: M 388 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8035 (tm-30) REVERT: U 10 LYS cc_start: 0.9001 (tptm) cc_final: 0.8726 (mmmt) REVERT: U 15 LYS cc_start: 0.9209 (pttm) cc_final: 0.9005 (pttp) REVERT: U 55 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8700 (ttp-170) outliers start: 30 outliers final: 20 residues processed: 312 average time/residue: 0.7418 time to fit residues: 268.3893 Evaluate side-chains 309 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 230 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 370 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN N 11 ASN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.055105 restraints weight = 60639.499| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 1.80 r_work: 0.2534 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9339 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.301 33392 Z= 0.185 Angle : 0.573 15.350 45376 Z= 0.277 Chirality : 0.042 0.183 4959 Planarity : 0.004 0.055 5699 Dihedral : 9.896 88.780 4827 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.99 % Allowed : 13.51 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.14), residues: 3953 helix: 2.15 (0.11), residues: 2142 sheet: 1.02 (0.27), residues: 362 loop : 0.67 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 51 TYR 0.036 0.002 TYR M 170 PHE 0.022 0.002 PHE A 334 TRP 0.021 0.001 TRP C 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (33377) covalent geometry : angle 0.57069 / 0.28 (45363) SS BOND : bond 0.00358 / 0.20 ( 5) SS BOND : angle 1.36202 / 0.72 ( 10) hydrogen bonds : bond 0.04608 / 3.09 ( 1882) hydrogen bonds : angle 4.26131 / 3.12 ( 5304) metal coordination : bond 0.01182 / 0.60 ( 4) metal coordination : angle 6.02413 / 3.27 ( 3) Misc. bond : bond 0.23842 / 12.96 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9588.91 seconds wall clock time: 164 minutes 21.02 seconds (9861.02 seconds total)