Starting phenix.real_space_refine on Mon Jul 6 06:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ac5_15334/07_2026/8ac5_15334.cif" } resolution = 3.1 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 21022 2.51 5 N 5294 2.21 5 O 6071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s 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: 32527 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: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'CDL': 2, 'HEC': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 129 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'FES': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 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: "N" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 250 Unusual residues: {'CDL': 1, 'HEC': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.132 49.735 34.434 1.00153.46 S ATOM 4207 SG CYS P 187 32.693 47.027 33.382 1.00159.22 S Time building chain proxies: 6.98, per 1000 atoms: 0.21 Number of scatterers: 32527 At special positions: 0 Unit cell: (119.691, 129.735, 164.889, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6071 8.00 N 5294 7.00 C 21022 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=2.06 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7482 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 61.5% alpha, 8.6% 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: 3.762A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.892A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.802A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.821A 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: 4.099A 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: 3.617A 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: 3.736A 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 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: 4.181A 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: 3.606A 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: 3.534A 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: 4.000A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.075A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.502A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.955A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.644A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.576A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.384A 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: 3.660A 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: 3.610A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.586A 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: 3.824A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.784A 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: 3.687A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.567A 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: 3.969A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.882A 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 219 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.370A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.509A 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: 3.572A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.571A 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 removed outlier: 3.512A pdb=" N ILE J 64 " --> pdb=" O LEU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.791A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.652A 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: 3.758A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.515A 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: 6.855A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.795A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.839A 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: 4.092A 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: 3.640A 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 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: 4.134A 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: 3.619A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.992A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.081A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.574A 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: 3.507A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.946A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 328 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.655A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.671A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.310A 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: 3.658A 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: 3.604A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.844A 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 141 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.598A 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: 3.839A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.787A 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: 3.922A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.558A 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: 3.972A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.916A 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 219 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 321 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 31 through 34 Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.367A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.502A 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: 3.644A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.582A 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 removed outlier: 3.517A pdb=" N ILE U 64 " --> pdb=" O LEU U 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 61 through 64' Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.810A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.645A 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: 3.852A 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: 3.644A 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: 6.533A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.308A 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: 4.008A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.567A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.574A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.632A 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: 6.525A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.295A 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: 4.083A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.544A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.556A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.608A 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 1880 hydrogen bonds defined for protein. 5298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13461 1.40 - 1.61: 19671 1.61 - 1.82: 172 1.82 - 2.03: 30 2.03 - 2.24: 20 Bond restraints: 33354 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.297 0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sigma weight residual 1.544 1.307 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.307 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sigma weight residual 1.544 1.310 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" CAB HEC N 501 " pdb=" CBB HEC N 501 " ideal model delta sigma weight residual 1.544 1.314 0.230 2.00e-02 2.50e+03 1.33e+02 ... (remaining 33349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 44020 4.29 - 8.58: 1197 8.58 - 12.86: 102 12.86 - 17.15: 11 17.15 - 21.44: 4 Bond angle restraints: 45334 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 96.26 15.01 1.47e+00 4.63e-01 1.04e+02 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 90.56 21.44 2.20e+00 2.07e-01 9.50e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 97.55 13.72 1.47e+00 4.63e-01 8.71e+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 94.03 10.30 1.14e+00 7.69e-01 8.16e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 92.60 19.40 2.20e+00 2.07e-01 7.78e+01 ... (remaining 45329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 18444 31.31 - 62.61: 958 62.61 - 93.91: 103 93.91 - 125.22: 1 125.22 - 156.52: 1 Dihedral angle restraints: 19507 sinusoidal: 7894 harmonic: 11613 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C2B HEC C 502 " pdb=" C3B HEC C 502 " pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sinusoidal sigma weight residual 60.00 -21.70 81.70 2 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" C2B HEC N 502 " pdb=" C3B HEC N 502 " pdb=" CAB HEC N 502 " pdb=" CBB HEC N 502 " ideal model delta sinusoidal sigma weight residual 60.00 -19.86 79.86 2 1.00e+01 1.00e-02 4.65e+01 ... (remaining 19504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4344 0.174 - 0.347: 579 0.347 - 0.521: 30 0.521 - 0.695: 2 0.695 - 0.868: 4 Chirality restraints: 4959 Sorted by residual: chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.71 -0.87 2.00e-01 2.50e+01 1.89e+01 chirality pdb=" CB4 CDL D 402 " pdb=" CB3 CDL D 402 " pdb=" CB6 CDL D 402 " pdb=" OB6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.74 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.77 -0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 4956 not shown) Planarity restraints: 5698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " -0.032 2.00e-02 2.50e+03 3.27e-02 2.41e+01 pdb=" C2C HEC C 502 " -0.009 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " -0.033 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " 0.023 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " 0.058 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " 0.042 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " 0.003 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC C 502 " 0.026 2.00e-02 2.50e+03 3.14e-02 2.22e+01 pdb=" C1B HEC C 502 " 0.020 2.00e-02 2.50e+03 pdb=" C2B HEC C 502 " 0.018 2.00e-02 2.50e+03 pdb=" C3B HEC C 502 " 0.023 2.00e-02 2.50e+03 pdb=" C4B HEC C 502 " 0.041 2.00e-02 2.50e+03 pdb=" CAB HEC C 502 " -0.022 2.00e-02 2.50e+03 pdb=" CHB HEC C 502 " -0.049 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " -0.049 2.00e-02 2.50e+03 pdb=" CMB HEC C 502 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 502 " 0.024 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" C2C HEC N 502 " 0.005 2.00e-02 2.50e+03 pdb=" C3C HEC N 502 " 0.023 2.00e-02 2.50e+03 pdb=" C4C HEC N 502 " 0.020 2.00e-02 2.50e+03 pdb=" CAC HEC N 502 " -0.014 2.00e-02 2.50e+03 pdb=" CHC HEC N 502 " -0.051 2.00e-02 2.50e+03 pdb=" CHD HEC N 502 " -0.045 2.00e-02 2.50e+03 pdb=" CMC HEC N 502 " -0.002 2.00e-02 2.50e+03 pdb=" NC HEC N 502 " 0.041 2.00e-02 2.50e+03 ... (remaining 5695 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 277 2.63 - 3.20: 28613 3.20 - 3.77: 53393 3.77 - 4.33: 77708 4.33 - 4.90: 120631 Nonbonded interactions: 280622 Sorted by model distance: nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEC C 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEC N 501 " model vdw 2.071 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.078 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEC N 502 " model vdw 2.221 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEC C 502 " model vdw 2.236 3.080 ... (remaining 280617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 503 or resid 506)) selection = (chain 'N' and (resid 1 through 503 or resid 506)) } ncs_group { reference = (chain 'D' and resid 85 through 401) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = (chain 'U' and resid 8 through 82) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 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: 0.060 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.790 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9383 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 : 0.012 0.467 33370 Z= 0.707 Angle : 1.773 21.441 45347 Z= 1.097 Chirality : 0.116 0.868 4959 Planarity : 0.007 0.060 5698 Dihedral : 17.864 156.524 12010 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.61 % Allowed : 7.28 % Favored : 89.11 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.12), residues: 3953 helix: -0.99 (0.09), residues: 2118 sheet: 0.06 (0.25), residues: 359 loop : -0.62 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 283 TYR 0.050 0.008 TYR O 177 PHE 0.050 0.007 PHE C 234 TRP 0.057 0.007 TRP A 474 HIS 0.022 0.005 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01121 / 0.66 (33354) covalent geometry : angle 1.76981 / 1.10 (45334) SS BOND : bond 0.03311 / 1.89 ( 5) SS BOND : angle 2.90789 / 1.55 ( 10) hydrogen bonds : bond 0.19196 / 12.96 ( 1880) hydrogen bonds : angle 6.99162 / 5.06 ( 5298) metal coordination : bond 0.07617 / 3.89 ( 4) metal coordination : angle 13.41082 / 7.21 ( 3) Misc. bond : bond 0.21405 / 9.05 ( 7) *********************** 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 531 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 411 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9202 (m) REVERT: C 239 MET cc_start: 0.9073 (ttp) cc_final: 0.8421 (mmt) REVERT: P 104 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8724 (tp30) REVERT: P 119 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7479 (tttt) REVERT: P 158 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7705 (mtpp) REVERT: P 178 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7327 (mp0) REVERT: G 97 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8785 (mt-10) REVERT: G 112 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8880 (mt-10) REVERT: F 84 GLU cc_start: 0.9140 (tt0) cc_final: 0.8846 (tp30) REVERT: F 107 LYS cc_start: 0.9349 (tttt) cc_final: 0.9090 (tmmt) REVERT: F 114 TYR cc_start: 0.8438 (t80) cc_final: 0.8231 (t80) REVERT: F 119 TYR cc_start: 0.9060 (t80) cc_final: 0.8723 (t80) REVERT: F 137 ASN cc_start: 0.9206 (m-40) cc_final: 0.8962 (m-40) REVERT: A 87 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: A 97 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9152 (mm-30) REVERT: B 134 GLU cc_start: 0.9248 (tt0) cc_final: 0.9024 (tp30) REVERT: B 345 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9030 (ttmt) REVERT: B 372 ARG cc_start: 0.8490 (ptt-90) cc_final: 0.8146 (ptt90) REVERT: B 373 ILE cc_start: 0.9309 (mm) cc_final: 0.9020 (tt) REVERT: D 85 MET cc_start: 0.8836 (mtt) cc_final: 0.8585 (mtp) REVERT: H 78 GLU cc_start: 0.9352 (tt0) cc_final: 0.9126 (pp20) REVERT: J 55 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8533 (ttm-80) REVERT: N 255 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9227 (m-30) REVERT: E 55 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8347 (p0) REVERT: R 29 LYS cc_start: 0.9345 (mttt) cc_final: 0.9137 (mmtt) REVERT: Q 77 ASP cc_start: 0.9041 (t0) cc_final: 0.8782 (t0) REVERT: Q 80 ILE cc_start: 0.9452 (mt) cc_final: 0.9245 (mt) REVERT: Q 113 ASP cc_start: 0.9331 (m-30) cc_final: 0.8725 (t0) REVERT: M 236 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8616 (mtt180) REVERT: M 309 ASP cc_start: 0.9330 (m-30) cc_final: 0.9019 (p0) REVERT: M 341 TYR cc_start: 0.9136 (t80) cc_final: 0.8932 (t80) REVERT: M 356 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8886 (t0) REVERT: M 377 ASN cc_start: 0.9324 (m-40) cc_final: 0.8793 (m110) REVERT: O 291 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9139 (tttt) REVERT: S 78 GLU cc_start: 0.9313 (tt0) cc_final: 0.9069 (tp30) REVERT: T 7 PHE cc_start: 0.8960 (t80) cc_final: 0.8623 (m-80) REVERT: U 51 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8865 (tm-30) REVERT: U 69 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9067 (mp0) outliers start: 120 outliers final: 21 residues processed: 487 average time/residue: 0.2217 time to fit residues: 166.3795 Evaluate side-chains 292 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 85 GLN P 90 ASN P 157 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN L 177 ASN L 332 ASN L 371 ASN M 87 HIS M 215 GLN M 241 ASN U 58 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.046953 restraints weight = 93030.684| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.31 r_work: 0.2574 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 33370 Z= 0.134 Angle : 0.624 14.951 45347 Z= 0.308 Chirality : 0.042 0.170 4959 Planarity : 0.004 0.038 5698 Dihedral : 12.258 131.408 4892 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.59 % Allowed : 8.97 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 3953 helix: 1.12 (0.11), residues: 2139 sheet: 0.58 (0.27), residues: 363 loop : 0.07 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 104 TYR 0.018 0.001 TYR D 237 PHE 0.020 0.002 PHE A 334 TRP 0.026 0.001 TRP C 156 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (33354) covalent geometry : angle 0.62331 / 0.31 (45334) SS BOND : bond 0.00226 / 0.12 ( 5) SS BOND : angle 0.75639 / 0.39 ( 10) hydrogen bonds : bond 0.05113 / 3.38 ( 1880) hydrogen bonds : angle 4.75238 / 3.40 ( 5298) metal coordination : bond 0.02169 / 1.09 ( 4) metal coordination : angle 2.23531 / 1.27 ( 3) Misc. bond : bond 0.24863 / 12.53 ( 7) *********************** 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 329 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.8982 (ttp) cc_final: 0.8302 (mmt) REVERT: C 282 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8811 (tt) REVERT: C 287 ASP cc_start: 0.7854 (t0) cc_final: 0.7611 (t0) REVERT: P 62 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8674 (mtm110) REVERT: P 164 MET cc_start: 0.8758 (mtm) cc_final: 0.8554 (mpp) REVERT: G 19 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8415 (mm) REVERT: G 22 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8454 (ptpt) REVERT: G 97 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8353 (mt-10) REVERT: G 112 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: G 123 GLU cc_start: 0.8824 (tt0) cc_final: 0.8567 (tt0) REVERT: F 107 LYS cc_start: 0.9121 (tttt) cc_final: 0.8903 (tmmt) REVERT: F 137 ASN cc_start: 0.8793 (m-40) cc_final: 0.8424 (m-40) REVERT: A 87 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8384 (ptp90) REVERT: A 97 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8792 (mm-30) REVERT: B 134 GLU cc_start: 0.8822 (tt0) cc_final: 0.8566 (tp30) REVERT: B 345 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9007 (ttmt) REVERT: B 373 ILE cc_start: 0.9117 (mm) cc_final: 0.8852 (tp) REVERT: H 78 GLU cc_start: 0.9163 (tt0) cc_final: 0.8852 (pp20) REVERT: J 51 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8810 (tm-30) REVERT: J 55 ARG cc_start: 0.8648 (ttm-80) cc_final: 0.8422 (ttm-80) REVERT: N 255 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8770 (m-30) REVERT: E 55 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7588 (p0) REVERT: R 29 LYS cc_start: 0.9175 (mttt) cc_final: 0.8774 (mmtt) REVERT: R 39 GLN cc_start: 0.9163 (mm110) cc_final: 0.8957 (mm110) REVERT: Q 103 GLU cc_start: 0.8659 (tp30) cc_final: 0.8382 (tm-30) REVERT: L 183 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8950 (t) REVERT: O 248 MET cc_start: 0.9088 (ttp) cc_final: 0.8859 (ttp) REVERT: S 51 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7226 (ptm160) REVERT: S 78 GLU cc_start: 0.9075 (tt0) cc_final: 0.8752 (tp30) REVERT: S 88 GLU cc_start: 0.8548 (mp0) cc_final: 0.8333 (mm-30) REVERT: U 51 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8835 (tm-30) outliers start: 53 outliers final: 19 residues processed: 313 average time/residue: 0.2089 time to fit residues: 104.8169 Evaluate side-chains 269 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 197 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 279 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 167 optimal weight: 0.0000 chunk 33 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 387 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 GLN D 93 HIS R 39 GLN R 84 HIS M 316 GLN U 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.044987 restraints weight = 94127.484| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.29 r_work: 0.2527 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.428 33370 Z= 0.205 Angle : 0.596 14.092 45347 Z= 0.289 Chirality : 0.043 0.149 4959 Planarity : 0.004 0.042 5698 Dihedral : 11.090 106.291 4852 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.47 % Allowed : 9.99 % Favored : 88.54 % 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: 1.58 (0.14), residues: 3953 helix: 1.66 (0.11), residues: 2157 sheet: 0.62 (0.27), residues: 367 loop : 0.34 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.025 0.002 TYR F 119 PHE 0.020 0.002 PHE C 164 TRP 0.020 0.001 TRP C 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (33354) covalent geometry : angle 0.59509 / 0.29 (45334) SS BOND : bond 0.00229 / 0.13 ( 5) SS BOND : angle 0.58749 / 0.27 ( 10) hydrogen bonds : bond 0.04845 / 3.21 ( 1880) hydrogen bonds : angle 4.48386 / 3.20 ( 5298) metal coordination : bond 0.02602 / 1.30 ( 4) metal coordination : angle 3.78315 / 2.16 ( 3) Misc. bond : bond 0.27593 / 13.92 ( 7) *********************** 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 295 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.8997 (ttp) cc_final: 0.8326 (mmt) REVERT: C 282 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8880 (tt) REVERT: P 62 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8755 (mtm110) REVERT: P 130 ARG cc_start: 0.7123 (ttp-170) cc_final: 0.6749 (ttp-170) REVERT: P 196 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7742 (tp) REVERT: G 55 MET cc_start: 0.9137 (tpp) cc_final: 0.8932 (tpp) REVERT: G 97 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8410 (mt-10) REVERT: G 112 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: F 107 LYS cc_start: 0.9105 (tttt) cc_final: 0.8591 (tmmt) REVERT: F 113 ASP cc_start: 0.8150 (p0) cc_final: 0.7521 (p0) REVERT: A 94 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 97 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8742 (mm-30) REVERT: B 134 GLU cc_start: 0.8810 (tt0) cc_final: 0.8523 (tp30) REVERT: B 345 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9036 (ttmt) REVERT: B 373 ILE cc_start: 0.9126 (mm) cc_final: 0.8897 (tp) REVERT: D 248 MET cc_start: 0.9176 (ttp) cc_final: 0.8950 (ttp) REVERT: H 78 GLU cc_start: 0.9187 (tt0) cc_final: 0.8936 (tm-30) REVERT: J 15 LYS cc_start: 0.9334 (ptpt) cc_final: 0.9123 (ptmm) REVERT: J 58 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: N 255 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: E 55 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7647 (p0) REVERT: R 29 LYS cc_start: 0.9185 (mttt) cc_final: 0.8786 (mmtt) REVERT: R 115 GLU cc_start: 0.8855 (tt0) cc_final: 0.8629 (tt0) REVERT: Q 103 GLU cc_start: 0.8644 (tp30) cc_final: 0.8392 (tm-30) REVERT: Q 107 LYS cc_start: 0.9063 (pttt) cc_final: 0.8802 (pttp) REVERT: L 183 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9013 (t) REVERT: S 78 GLU cc_start: 0.9114 (tt0) cc_final: 0.8793 (tp30) REVERT: S 88 GLU cc_start: 0.8620 (mp0) cc_final: 0.8371 (mm-30) REVERT: U 51 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8889 (tm-30) outliers start: 49 outliers final: 20 residues processed: 285 average time/residue: 0.1930 time to fit residues: 89.5502 Evaluate side-chains 264 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 269 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 370 optimal weight: 0.7980 chunk 290 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.045897 restraints weight = 93493.204| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.29 r_work: 0.2552 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.345 33370 Z= 0.139 Angle : 0.532 12.619 45347 Z= 0.258 Chirality : 0.041 0.141 4959 Planarity : 0.004 0.045 5698 Dihedral : 10.485 99.071 4837 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.14 % Allowed : 10.53 % Favored : 88.33 % 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: 1.93 (0.14), residues: 3953 helix: 1.97 (0.11), residues: 2147 sheet: 0.76 (0.27), residues: 369 loop : 0.49 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 55 TYR 0.026 0.001 TYR Q 119 PHE 0.017 0.001 PHE C 164 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 0.00319 / 0.14 (33354) covalent geometry : angle 0.53095 / 0.26 (45334) SS BOND : bond 0.00145 / 0.08 ( 5) SS BOND : angle 0.49289 / 0.24 ( 10) hydrogen bonds : bond 0.04221 / 2.78 ( 1880) hydrogen bonds : angle 4.31762 / 3.07 ( 5298) metal coordination : bond 0.01443 / 0.72 ( 4) metal coordination : angle 3.94057 / 2.21 ( 3) Misc. bond : bond 0.22727 / 11.17 ( 7) *********************** 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 286 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.075 Fit side-chains REVERT: C 239 MET cc_start: 0.8976 (ttp) cc_final: 0.8294 (mmt) REVERT: C 282 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8803 (tt) REVERT: C 287 ASP cc_start: 0.7892 (t0) cc_final: 0.7596 (t0) REVERT: P 62 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8728 (mtm110) REVERT: P 118 ILE cc_start: 0.8676 (mt) cc_final: 0.8364 (tt) REVERT: P 162 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7929 (tp) REVERT: P 196 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7835 (tp) REVERT: G 22 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8615 (ptpt) REVERT: G 55 MET cc_start: 0.9047 (tpp) cc_final: 0.8810 (tpp) REVERT: G 97 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8446 (mt-10) REVERT: G 112 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: F 114 TYR cc_start: 0.8169 (t80) cc_final: 0.7963 (t80) REVERT: F 125 GLU cc_start: 0.8680 (mp0) cc_final: 0.8457 (mp0) REVERT: A 94 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 97 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8694 (mm-30) REVERT: A 390 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8805 (mtmt) REVERT: B 134 GLU cc_start: 0.8807 (tt0) cc_final: 0.8554 (tp30) REVERT: B 345 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8979 (ttmt) REVERT: B 373 ILE cc_start: 0.9139 (mm) cc_final: 0.8925 (tp) REVERT: D 248 MET cc_start: 0.9255 (ttp) cc_final: 0.8899 (ttp) REVERT: H 78 GLU cc_start: 0.9198 (tt0) cc_final: 0.8929 (tm-30) REVERT: J 15 LYS cc_start: 0.9324 (ptpt) cc_final: 0.9116 (ptmm) REVERT: J 58 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: N 97 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: N 255 ASP cc_start: 0.9217 (m-30) cc_final: 0.8778 (m-30) REVERT: N 322 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9146 (m) REVERT: E 55 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7663 (p0) REVERT: R 29 LYS cc_start: 0.9197 (mttt) cc_final: 0.8863 (mmtt) REVERT: R 115 GLU cc_start: 0.8874 (tt0) cc_final: 0.8605 (tt0) REVERT: Q 103 GLU cc_start: 0.8690 (tp30) cc_final: 0.8388 (tm-30) REVERT: Q 107 LYS cc_start: 0.9104 (pttt) cc_final: 0.8855 (pttp) REVERT: S 78 GLU cc_start: 0.9097 (tt0) cc_final: 0.8794 (tp30) REVERT: S 88 GLU cc_start: 0.8642 (mp0) cc_final: 0.8343 (mm-30) REVERT: U 10 LYS cc_start: 0.9001 (tppt) cc_final: 0.8728 (ttpp) outliers start: 38 outliers final: 18 residues processed: 277 average time/residue: 0.1936 time to fit residues: 87.8191 Evaluate side-chains 264 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 294 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 381 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 92 HIS F 109 GLN U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.045985 restraints weight = 93407.022| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.28 r_work: 0.2559 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.325 33370 Z= 0.134 Angle : 0.519 12.495 45347 Z= 0.250 Chirality : 0.040 0.175 4959 Planarity : 0.004 0.046 5698 Dihedral : 10.027 86.578 4835 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.41 % Allowed : 10.74 % Favored : 87.85 % 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: 2.16 (0.14), residues: 3953 helix: 2.13 (0.11), residues: 2159 sheet: 0.85 (0.27), residues: 369 loop : 0.63 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 55 TYR 0.033 0.001 TYR Q 119 PHE 0.017 0.001 PHE C 164 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 0.00309 / 0.13 (33354) covalent geometry : angle 0.51780 / 0.25 (45334) SS BOND : bond 0.00202 / 0.13 ( 5) SS BOND : angle 0.57884 / 0.29 ( 10) hydrogen bonds : bond 0.04065 / 2.68 ( 1880) hydrogen bonds : angle 4.22395 / 3.00 ( 5298) metal coordination : bond 0.01461 / 0.72 ( 4) metal coordination : angle 4.68220 / 2.64 ( 3) Misc. bond : bond 0.22437 / 10.90 ( 7) *********************** 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 294 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.8948 (ttp) cc_final: 0.8251 (mmt) REVERT: P 62 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8716 (mtm110) REVERT: P 118 ILE cc_start: 0.8623 (mt) cc_final: 0.8362 (tt) REVERT: P 162 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7796 (tp) REVERT: P 196 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7879 (tp) REVERT: G 55 MET cc_start: 0.9055 (tpp) cc_final: 0.8811 (tpp) REVERT: G 97 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8449 (mt-10) REVERT: G 112 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: F 125 GLU cc_start: 0.8689 (mp0) cc_final: 0.8477 (mp0) REVERT: A 94 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 97 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: A 390 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8829 (mtmt) REVERT: A 395 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 134 GLU cc_start: 0.8810 (tt0) cc_final: 0.8554 (tp30) REVERT: B 373 ILE cc_start: 0.9139 (mm) cc_final: 0.8923 (tp) REVERT: H 78 GLU cc_start: 0.9220 (tt0) cc_final: 0.8934 (tm-30) REVERT: J 58 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: J 80 ASN cc_start: 0.8761 (t0) cc_final: 0.7896 (p0) REVERT: N 255 ASP cc_start: 0.9232 (m-30) cc_final: 0.8778 (m-30) REVERT: N 322 SER cc_start: 0.9381 (OUTLIER) cc_final: 0.9114 (m) REVERT: E 55 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7587 (p0) REVERT: E 68 MET cc_start: 0.9121 (mmt) cc_final: 0.8900 (mmt) REVERT: R 29 LYS cc_start: 0.9185 (mttt) cc_final: 0.8880 (mmtt) REVERT: R 115 GLU cc_start: 0.8870 (tt0) cc_final: 0.8586 (tt0) REVERT: Q 103 GLU cc_start: 0.8749 (tp30) cc_final: 0.8431 (tm-30) REVERT: Q 107 LYS cc_start: 0.9084 (pttt) cc_final: 0.8849 (pttp) REVERT: L 183 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9014 (t) REVERT: S 78 GLU cc_start: 0.9090 (tt0) cc_final: 0.8814 (tp30) REVERT: U 10 LYS cc_start: 0.8976 (tppt) cc_final: 0.8715 (ttpp) outliers start: 47 outliers final: 24 residues processed: 284 average time/residue: 0.1848 time to fit residues: 86.4548 Evaluate side-chains 275 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 153 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 219 optimal weight: 0.0060 chunk 40 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 357 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 332 ASN G 84 HIS A 317 GLN R 56 GLN L 317 GLN U 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.045939 restraints weight = 93493.668| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.29 r_work: 0.2554 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9232 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 33370 Z= 0.138 Angle : 0.522 15.592 45347 Z= 0.248 Chirality : 0.040 0.161 4959 Planarity : 0.004 0.050 5698 Dihedral : 9.706 86.205 4831 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.35 % Allowed : 10.86 % Favored : 87.79 % 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: 2.26 (0.14), residues: 3953 helix: 2.21 (0.11), residues: 2162 sheet: 0.90 (0.27), residues: 369 loop : 0.66 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 130 TYR 0.025 0.001 TYR Q 119 PHE 0.016 0.001 PHE C 164 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 0.00318 / 0.14 (33354) covalent geometry : angle 0.52048 / 0.25 (45334) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.51042 / 0.26 ( 10) hydrogen bonds : bond 0.04011 / 2.64 ( 1880) hydrogen bonds : angle 4.17902 / 2.97 ( 5298) metal coordination : bond 0.01448 / 0.72 ( 4) metal coordination : angle 5.18280 / 2.91 ( 3) Misc. bond : bond 0.23556 / 11.36 ( 7) *********************** 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 291 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 1.287 Fit side-chains REVERT: C 287 ASP cc_start: 0.7891 (t0) cc_final: 0.7684 (t0) REVERT: P 118 ILE cc_start: 0.8674 (mt) cc_final: 0.8415 (tt) REVERT: P 162 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.8000 (tp) REVERT: G 22 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8626 (ptpt) REVERT: G 55 MET cc_start: 0.9070 (tpp) cc_final: 0.8818 (tpp) REVERT: G 112 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: F 114 TYR cc_start: 0.8034 (t80) cc_final: 0.7689 (t80) REVERT: F 125 GLU cc_start: 0.8730 (mp0) cc_final: 0.8527 (mp0) REVERT: A 97 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8713 (mm-30) REVERT: A 390 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8828 (mtmt) REVERT: A 395 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8702 (mp) REVERT: H 78 GLU cc_start: 0.9217 (tt0) cc_final: 0.8946 (tm-30) REVERT: J 58 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: J 80 ASN cc_start: 0.8776 (t0) cc_final: 0.7931 (p0) REVERT: N 221 MET cc_start: 0.9473 (tpp) cc_final: 0.9237 (ttm) REVERT: N 255 ASP cc_start: 0.9240 (m-30) cc_final: 0.8788 (m-30) REVERT: N 322 SER cc_start: 0.9407 (OUTLIER) cc_final: 0.9155 (m) REVERT: E 55 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7569 (p0) REVERT: R 29 LYS cc_start: 0.9195 (mttt) cc_final: 0.8903 (mmtt) REVERT: R 115 GLU cc_start: 0.8891 (tt0) cc_final: 0.8614 (tt0) REVERT: Q 103 GLU cc_start: 0.8784 (tp30) cc_final: 0.8471 (tm-30) REVERT: Q 107 LYS cc_start: 0.9101 (pttt) cc_final: 0.8811 (pttp) REVERT: L 183 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.9010 (t) REVERT: M 292 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8962 (p) REVERT: S 78 GLU cc_start: 0.9092 (tt0) cc_final: 0.8850 (tp30) REVERT: U 10 LYS cc_start: 0.8971 (tppt) cc_final: 0.8717 (ttpp) outliers start: 45 outliers final: 28 residues processed: 281 average time/residue: 0.1810 time to fit residues: 84.3576 Evaluate side-chains 277 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 218 optimal weight: 0.8980 chunk 217 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 325 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 379 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN A 364 HIS U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.046125 restraints weight = 93631.432| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.29 r_work: 0.2563 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9223 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 33370 Z= 0.130 Angle : 0.520 17.581 45347 Z= 0.246 Chirality : 0.040 0.146 4959 Planarity : 0.004 0.051 5698 Dihedral : 9.456 85.988 4829 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.35 % Allowed : 11.25 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.14), residues: 3953 helix: 2.26 (0.11), residues: 2163 sheet: 0.89 (0.27), residues: 365 loop : 0.69 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 130 TYR 0.027 0.001 TYR Q 119 PHE 0.016 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (33354) covalent geometry : angle 0.51783 / 0.25 (45334) SS BOND : bond 0.00174 / 0.10 ( 5) SS BOND : angle 0.50157 / 0.26 ( 10) hydrogen bonds : bond 0.03926 / 2.59 ( 1880) hydrogen bonds : angle 4.15171 / 2.95 ( 5298) metal coordination : bond 0.01237 / 0.61 ( 4) metal coordination : angle 5.41610 / 3.05 ( 3) Misc. bond : bond 0.22696 / 10.80 ( 7) *********************** 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 291 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 1.129 Fit side-chains REVERT: C 282 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8815 (tt) REVERT: C 287 ASP cc_start: 0.7983 (t0) cc_final: 0.7758 (t0) REVERT: P 62 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8666 (mtm110) REVERT: P 118 ILE cc_start: 0.8679 (mt) cc_final: 0.8413 (tt) REVERT: G 22 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8629 (ptpt) REVERT: G 55 MET cc_start: 0.9058 (tpp) cc_final: 0.8799 (tpp) REVERT: G 112 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: F 114 TYR cc_start: 0.7967 (t80) cc_final: 0.7712 (t80) REVERT: F 125 GLU cc_start: 0.8748 (mp0) cc_final: 0.8489 (mp0) REVERT: A 390 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8823 (mtmt) REVERT: A 395 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (mp) REVERT: B 117 GLU cc_start: 0.8695 (mp0) cc_final: 0.8451 (mp0) REVERT: H 78 GLU cc_start: 0.9242 (tt0) cc_final: 0.8953 (tm-30) REVERT: J 80 ASN cc_start: 0.8768 (t0) cc_final: 0.7920 (p0) REVERT: N 221 MET cc_start: 0.9458 (tpp) cc_final: 0.9242 (ttm) REVERT: N 255 ASP cc_start: 0.9250 (m-30) cc_final: 0.8797 (m-30) REVERT: N 322 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9160 (m) REVERT: E 55 ASP cc_start: 0.8342 (m-30) cc_final: 0.7566 (p0) REVERT: R 29 LYS cc_start: 0.9194 (mttt) cc_final: 0.8905 (mmtt) REVERT: R 115 GLU cc_start: 0.8863 (tt0) cc_final: 0.8582 (tt0) REVERT: Q 103 GLU cc_start: 0.8795 (tp30) cc_final: 0.8502 (tm-30) REVERT: Q 107 LYS cc_start: 0.9126 (pttt) cc_final: 0.8885 (pttp) REVERT: L 183 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8994 (t) REVERT: M 292 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8935 (p) REVERT: S 78 GLU cc_start: 0.9064 (tt0) cc_final: 0.8844 (tp30) outliers start: 45 outliers final: 28 residues processed: 281 average time/residue: 0.1826 time to fit residues: 83.8669 Evaluate side-chains 275 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 278 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 167 optimal weight: 0.0070 chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 274 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.045603 restraints weight = 93866.226| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.29 r_work: 0.2547 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 33370 Z= 0.155 Angle : 0.523 14.395 45347 Z= 0.252 Chirality : 0.041 0.156 4959 Planarity : 0.004 0.051 5698 Dihedral : 9.313 85.979 4824 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.05 % Allowed : 11.43 % Favored : 87.52 % 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: 2.33 (0.14), residues: 3953 helix: 2.26 (0.11), residues: 2167 sheet: 0.93 (0.27), residues: 369 loop : 0.72 (0.18), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 201 TYR 0.025 0.001 TYR Q 119 PHE 0.018 0.001 PHE N 240 TRP 0.015 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (33354) covalent geometry : angle 0.52054 / 0.25 (45334) SS BOND : bond 0.00184 / 0.11 ( 5) SS BOND : angle 0.52811 / 0.27 ( 10) hydrogen bonds : bond 0.04060 / 2.68 ( 1880) hydrogen bonds : angle 4.15690 / 2.96 ( 5298) metal coordination : bond 0.01455 / 0.72 ( 4) metal coordination : angle 5.77239 / 3.25 ( 3) Misc. bond : bond 0.21370 / 10.60 ( 7) *********************** 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 275 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: C 282 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 287 ASP cc_start: 0.8044 (t0) cc_final: 0.7823 (t0) REVERT: P 62 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8687 (mtm110) REVERT: P 118 ILE cc_start: 0.8745 (mt) cc_final: 0.8445 (tt) REVERT: G 22 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8636 (ptpt) REVERT: G 55 MET cc_start: 0.9068 (tpp) cc_final: 0.8816 (tpp) REVERT: G 112 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: F 114 TYR cc_start: 0.7971 (t80) cc_final: 0.7769 (t80) REVERT: F 125 GLU cc_start: 0.8698 (mp0) cc_final: 0.8496 (mp0) REVERT: A 390 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8825 (mtmt) REVERT: A 395 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8703 (mp) REVERT: B 117 GLU cc_start: 0.8694 (mp0) cc_final: 0.8490 (mp0) REVERT: H 78 GLU cc_start: 0.9233 (tt0) cc_final: 0.8965 (tm-30) REVERT: N 221 MET cc_start: 0.9470 (tpp) cc_final: 0.9267 (ttm) REVERT: N 255 ASP cc_start: 0.9244 (m-30) cc_final: 0.8812 (m-30) REVERT: E 55 ASP cc_start: 0.8398 (m-30) cc_final: 0.7662 (p0) REVERT: R 29 LYS cc_start: 0.9205 (mttt) cc_final: 0.8920 (mmtt) REVERT: R 115 GLU cc_start: 0.8871 (tt0) cc_final: 0.8587 (tt0) REVERT: Q 103 GLU cc_start: 0.8794 (tp30) cc_final: 0.8527 (tm-30) REVERT: Q 107 LYS cc_start: 0.9166 (pttt) cc_final: 0.8941 (pttp) REVERT: L 183 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (t) REVERT: M 292 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8940 (p) REVERT: S 78 GLU cc_start: 0.9079 (tt0) cc_final: 0.8870 (tp30) outliers start: 35 outliers final: 26 residues processed: 270 average time/residue: 0.1872 time to fit residues: 83.2375 Evaluate side-chains 269 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 102 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.045958 restraints weight = 93135.007| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.27 r_work: 0.2557 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9232 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.315 33370 Z= 0.136 Angle : 0.512 13.836 45347 Z= 0.247 Chirality : 0.040 0.139 4959 Planarity : 0.004 0.053 5698 Dihedral : 9.163 86.173 4824 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.17 % Allowed : 11.55 % Favored : 87.27 % 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: 2.36 (0.14), residues: 3953 helix: 2.28 (0.11), residues: 2167 sheet: 0.93 (0.27), residues: 365 loop : 0.72 (0.18), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 201 TYR 0.025 0.001 TYR Q 119 PHE 0.016 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (33354) covalent geometry : angle 0.51018 / 0.25 (45334) SS BOND : bond 0.00179 / 0.10 ( 5) SS BOND : angle 0.49707 / 0.24 ( 10) hydrogen bonds : bond 0.03928 / 2.59 ( 1880) hydrogen bonds : angle 4.13033 / 2.94 ( 5298) metal coordination : bond 0.01130 / 0.55 ( 4) metal coordination : angle 5.87575 / 3.31 ( 3) Misc. bond : bond 0.20076 / 9.98 ( 7) *********************** 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 277 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.891 Fit side-chains REVERT: C 282 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 287 ASP cc_start: 0.8039 (t0) cc_final: 0.7818 (t0) REVERT: P 62 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8662 (mtm110) REVERT: P 118 ILE cc_start: 0.8728 (mt) cc_final: 0.8463 (tt) REVERT: G 55 MET cc_start: 0.9070 (tpp) cc_final: 0.8819 (tpp) REVERT: G 112 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: F 114 TYR cc_start: 0.7958 (t80) cc_final: 0.7737 (t80) REVERT: F 125 GLU cc_start: 0.8696 (mp0) cc_final: 0.8492 (mp0) REVERT: A 390 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8828 (mtmt) REVERT: A 395 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8699 (mp) REVERT: H 78 GLU cc_start: 0.9228 (tt0) cc_final: 0.8964 (tm-30) REVERT: H 88 GLU cc_start: 0.8712 (mp0) cc_final: 0.8456 (mp0) REVERT: N 255 ASP cc_start: 0.9240 (m-30) cc_final: 0.8808 (m-30) REVERT: E 55 ASP cc_start: 0.8412 (m-30) cc_final: 0.7686 (p0) REVERT: R 29 LYS cc_start: 0.9204 (mttt) cc_final: 0.8929 (mmtt) REVERT: R 115 GLU cc_start: 0.8892 (tt0) cc_final: 0.8594 (tt0) REVERT: Q 100 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8434 (mt-10) REVERT: Q 103 GLU cc_start: 0.8816 (tp30) cc_final: 0.8549 (tm-30) REVERT: Q 107 LYS cc_start: 0.9146 (pttt) cc_final: 0.8897 (pttp) REVERT: L 183 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.9000 (t) REVERT: M 292 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8942 (p) REVERT: S 78 GLU cc_start: 0.9068 (tt0) cc_final: 0.8861 (tp30) outliers start: 39 outliers final: 27 residues processed: 271 average time/residue: 0.1856 time to fit residues: 82.0642 Evaluate side-chains 270 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 313 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 347 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.046096 restraints weight = 93817.802| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.29 r_work: 0.2560 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9227 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.308 33370 Z= 0.130 Angle : 0.512 13.555 45347 Z= 0.248 Chirality : 0.040 0.139 4959 Planarity : 0.004 0.055 5698 Dihedral : 9.067 86.301 4824 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 11.58 % Favored : 87.24 % 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: 2.39 (0.14), residues: 3953 helix: 2.30 (0.11), residues: 2167 sheet: 0.99 (0.27), residues: 367 loop : 0.75 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 201 TYR 0.026 0.001 TYR Q 119 PHE 0.016 0.001 PHE A 334 TRP 0.013 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (33354) covalent geometry : angle 0.51007 / 0.25 (45334) SS BOND : bond 0.00163 / 0.10 ( 5) SS BOND : angle 0.49935 / 0.25 ( 10) hydrogen bonds : bond 0.03883 / 2.56 ( 1880) hydrogen bonds : angle 4.10641 / 2.92 ( 5298) metal coordination : bond 0.00986 / 0.48 ( 4) metal coordination : angle 5.75391 / 3.24 ( 3) Misc. bond : bond 0.19789 / 9.91 ( 7) ********************** 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 276 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 1.366 Fit side-chains REVERT: C 282 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8711 (tp) REVERT: C 287 ASP cc_start: 0.8034 (t0) cc_final: 0.7817 (t0) REVERT: P 62 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8664 (mtm110) REVERT: P 118 ILE cc_start: 0.8723 (mt) cc_final: 0.8465 (tt) REVERT: G 55 MET cc_start: 0.9075 (tpp) cc_final: 0.8821 (tpp) REVERT: G 112 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: F 113 ASP cc_start: 0.8083 (p0) cc_final: 0.7594 (p0) REVERT: F 114 TYR cc_start: 0.7940 (t80) cc_final: 0.7716 (t80) REVERT: F 119 TYR cc_start: 0.8238 (t80) cc_final: 0.7957 (t80) REVERT: A 390 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8845 (mtmt) REVERT: A 395 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8694 (mp) REVERT: H 78 GLU cc_start: 0.9229 (tt0) cc_final: 0.8959 (tm-30) REVERT: H 88 GLU cc_start: 0.8713 (mp0) cc_final: 0.8473 (mp0) REVERT: N 255 ASP cc_start: 0.9240 (m-30) cc_final: 0.8806 (m-30) REVERT: E 55 ASP cc_start: 0.8412 (m-30) cc_final: 0.7676 (p0) REVERT: R 29 LYS cc_start: 0.9209 (mttt) cc_final: 0.8938 (mmtt) REVERT: R 115 GLU cc_start: 0.8886 (tt0) cc_final: 0.8586 (tt0) REVERT: Q 100 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8451 (mt-10) REVERT: Q 103 GLU cc_start: 0.8800 (tp30) cc_final: 0.8527 (tm-30) REVERT: Q 107 LYS cc_start: 0.9149 (pttt) cc_final: 0.8890 (pttp) REVERT: L 183 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8995 (t) REVERT: M 292 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8934 (p) REVERT: S 78 GLU cc_start: 0.9085 (tt0) cc_final: 0.8874 (tp30) REVERT: U 10 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8826 (ttpp) outliers start: 39 outliers final: 28 residues processed: 267 average time/residue: 0.2110 time to fit residues: 92.9569 Evaluate side-chains 270 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 166 optimal weight: 0.6980 chunk 305 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 chunk 291 optimal weight: 0.4980 chunk 361 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.047418 restraints weight = 93303.684| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.30 r_work: 0.2597 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 33370 Z= 0.100 Angle : 0.492 12.274 45347 Z= 0.239 Chirality : 0.039 0.144 4959 Planarity : 0.004 0.056 5698 Dihedral : 8.815 87.160 4824 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.99 % Allowed : 11.88 % 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: 2.48 (0.14), residues: 3953 helix: 2.35 (0.11), residues: 2172 sheet: 1.04 (0.27), residues: 367 loop : 0.81 (0.18), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 201 TYR 0.025 0.001 TYR Q 119 PHE 0.017 0.001 PHE I 7 TRP 0.010 0.001 TRP C 142 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (33354) covalent geometry : angle 0.48959 / 0.24 (45334) SS BOND : bond 0.00156 / 0.10 ( 5) SS BOND : angle 0.49816 / 0.25 ( 10) hydrogen bonds : bond 0.03544 / 2.33 ( 1880) hydrogen bonds : angle 4.02718 / 2.86 ( 5298) metal coordination : bond 0.00525 / 0.26 ( 4) metal coordination : angle 5.49600 / 3.10 ( 3) Misc. bond : bond 0.20230 / 10.14 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.39 seconds wall clock time: 128 minutes 52.37 seconds (7732.37 seconds total)