Starting phenix.real_space_refine on Mon Jul 6 10:58:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.map" model { file = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ab7_15313/07_2026/8ab7_15313.cif" } resolution = 3.3 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= 0.004 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: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 P 30 5.49 5 S 110 5.16 5 Cl 2 4.86 5 C 21754 2.51 5 N 5472 2.21 5 O 6276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33654 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} 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: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 313 Unusual residues: {'AOQ': 1, 'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'FES': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'HEC': 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: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 363 Unusual residues: {'AOQ': 1, 'AWB': 1, 'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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 29.588 51.844 37.435 1.00 54.19 S ATOM 4207 SG CYS P 187 32.328 49.243 37.027 1.00 36.86 S ATOM 20227 SG CYS E 168 87.591 77.054 37.439 1.00 54.82 S ATOM 20364 SG CYS E 187 84.854 79.657 37.028 1.00 36.40 S Time building chain proxies: 7.19, per 1000 atoms: 0.21 Number of scatterers: 33654 At special positions: 0 Unit cell: (118.017, 128.898, 162.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 10 26.01 Cl 2 17.00 S 110 16.00 P 30 15.00 O 6276 8.00 N 5472 7.00 C 21754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.09 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 189 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 170 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 190 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 168 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 187 " 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 : 6 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 24 sheets defined 59.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 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: 3.629A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.547A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 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: 6.698A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.730A 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 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.908A 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: 4.053A 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: 3.575A 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 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.528A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.145A 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: 3.601A 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: 3.523A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.968A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.559A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.023A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.811A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.553A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.395A 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 467 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' 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 78 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.609A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.804A 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: 3.561A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.521A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.697A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.795A 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: 3.569A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.593A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.339A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.513A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 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: 3.509A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.725A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.661A 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: 3.622A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.711A 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 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: 6.732A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.740A 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 Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.924A 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: 4.053A 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: 3.589A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 131 through 139 Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.527A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.118A 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: 3.600A 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 removed outlier: 3.506A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 3.971A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.007A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.560A 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 206 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.021A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.818A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.584A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.382A 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 467 Processing helix chain 'L' and resid 468 through 470 No H-bonds generated for 'chain 'L' and resid 468 through 470' 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: 3.809A 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: 3.555A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 removed outlier: 3.522A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.712A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.858A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 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: 3.887A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.312A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.516A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 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: 3.573A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.724A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.661A 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: 3.861A 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: 3.543A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.566A 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: 6.479A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.789A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.037A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.702A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.550A 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 'E' and resid 103 through 106 Processing sheet with id=AB7, first strand: chain 'E' and resid 114 through 120 removed outlier: 3.861A pdb=" N LYS E 114 " --> pdb=" O HIS E 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 176 through 177 removed outlier: 3.538A pdb=" N SER E 192 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 202 " --> pdb=" O HIS E 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.479A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 306 through 308 removed outlier: 3.789A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.536A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.680A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC5, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC6, first strand: chain 'U' and resid 19 through 20 1907 hydrogen bonds defined for protein. 5376 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: 7.38 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 10690 1.35 - 1.57: 23526 1.57 - 1.78: 90 1.78 - 2.00: 186 2.00 - 2.22: 22 Bond restraints: 34514 Sorted by residual: bond pdb=" C32 CDL A3001 " pdb=" C33 CDL A3001 " ideal model delta sigma weight residual 1.517 1.705 -0.188 1.70e-02 3.46e+03 1.22e+02 bond pdb=" C14 CDL N 504 " pdb=" C15 CDL N 504 " ideal model delta sigma weight residual 1.517 1.764 -0.247 2.70e-02 1.37e+03 8.40e+01 bond pdb=" C34 CDL A3001 " pdb=" C35 CDL A3001 " ideal model delta sigma weight residual 1.517 1.764 -0.247 2.70e-02 1.37e+03 8.35e+01 bond pdb=" C55 CDL L3002 " pdb=" C56 CDL L3002 " ideal model delta sigma weight residual 1.517 1.743 -0.226 2.70e-02 1.37e+03 7.01e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.480 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 34509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 45688 5.02 - 10.03: 1138 10.03 - 15.05: 71 15.05 - 20.06: 13 20.06 - 25.08: 4 Bond angle restraints: 46914 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.52 15.81 1.14e+00 7.69e-01 1.92e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 88.55 15.78 1.14e+00 7.69e-01 1.92e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 89.65 14.68 1.20e+00 6.94e-01 1.50e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 89.71 14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" CG ARG P 62 " pdb=" CD ARG P 62 " pdb=" NE ARG P 62 " ideal model delta sigma weight residual 112.00 137.08 -25.08 2.20e+00 2.07e-01 1.30e+02 ... (remaining 46909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.10: 19029 31.10 - 62.20: 1108 62.20 - 93.30: 115 93.30 - 124.40: 3 124.40 - 155.51: 1 Dihedral angle restraints: 20256 sinusoidal: 8284 harmonic: 11972 Sorted by residual: dihedral pdb=" C HIS Q 96 " pdb=" N HIS Q 96 " pdb=" CA HIS Q 96 " pdb=" CB HIS Q 96 " ideal model delta harmonic sigma weight residual -122.60 -98.06 -24.54 0 2.50e+00 1.60e-01 9.64e+01 dihedral pdb=" C GLU Q 100 " pdb=" N GLU Q 100 " pdb=" CA GLU Q 100 " pdb=" CB GLU Q 100 " ideal model delta harmonic sigma weight residual -122.60 -101.43 -21.17 0 2.50e+00 1.60e-01 7.17e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -102.46 -20.14 0 2.50e+00 1.60e-01 6.49e+01 ... (remaining 20253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.814: 5120 0.814 - 1.628: 2 1.628 - 2.442: 0 2.442 - 3.257: 0 3.257 - 4.071: 2 Chirality restraints: 5124 Sorted by residual: chirality pdb=" C16 AOQ C 508 " pdb=" C11 AOQ C 508 " pdb=" C15 AOQ C 508 " pdb=" C2 AOQ C 508 " both_signs ideal model delta sigma weight residual False -2.36 1.71 -4.07 2.00e-01 2.50e+01 4.14e+02 chirality pdb=" C16 AOQ N 509 " pdb=" C11 AOQ N 509 " pdb=" C15 AOQ N 509 " pdb=" C2 AOQ N 509 " both_signs ideal model delta sigma weight residual False -2.36 1.63 -3.99 2.00e-01 2.50e+01 3.99e+02 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 -1.68 -0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 5121 not shown) Planarity restraints: 5896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 508 " -0.132 2.00e-02 2.50e+03 1.49e-01 2.21e+02 pdb=" C21 AWB N 508 " 0.173 2.00e-02 2.50e+03 pdb=" N1 AWB N 508 " 0.121 2.00e-02 2.50e+03 pdb=" O5 AWB N 508 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 507 " 0.127 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C21 AWB C 507 " -0.154 2.00e-02 2.50e+03 pdb=" N1 AWB C 507 " -0.124 2.00e-02 2.50e+03 pdb=" O5 AWB C 507 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 96 " -0.090 2.00e-02 2.50e+03 7.57e-02 8.60e+01 pdb=" CG HIS F 96 " 0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS F 96 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 HIS F 96 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 HIS F 96 " -0.055 2.00e-02 2.50e+03 pdb=" NE2 HIS F 96 " -0.075 2.00e-02 2.50e+03 ... (remaining 5893 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 63 2.48 - 3.08: 23539 3.08 - 3.69: 54733 3.69 - 4.29: 87673 4.29 - 4.90: 136187 Nonbonded interactions: 302195 Sorted by model distance: nonbonded pdb=" OG SER N 152 " pdb=" NZ LYS N 288 " model vdw 1.874 3.120 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.060 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.112 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.164 3.120 ... (remaining 302190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = (chain 'D' and resid 85 through 401) selection = chain 'O' } ncs_group { reference = chain 'E' selection = (chain 'P' and resid 39 through 301) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 36.060 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.013 0.483 34536 Z= 0.838 Angle : 2.004 26.227 46932 Z= 1.256 Chirality : 0.142 4.071 5124 Planarity : 0.008 0.149 5896 Dihedral : 18.459 155.505 12526 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 5.54 % Allowed : 8.60 % Favored : 85.86 % Cbeta Deviations : 2.02 % Peptide Plane: Cis-proline : 2.73 % 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: -1.88 (0.11), residues: 4080 helix: -1.49 (0.09), residues: 2134 sheet: -0.24 (0.24), residues: 358 loop : -0.86 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG P 62 TYR 0.057 0.008 TYR G 101 PHE 0.100 0.008 PHE N 129 TRP 0.073 0.009 TRP N 142 HIS 0.056 0.005 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01252 / 0.75 (34514) covalent geometry : angle 1.99409 / 1.26 (46914) SS BOND : bond 0.04187 / 2.26 ( 6) SS BOND : angle 3.29029 / 1.79 ( 12) hydrogen bonds : bond 0.17975 / 12.37 ( 1907) hydrogen bonds : angle 7.25058 / 5.22 ( 5376) metal coordination : bond 0.12703 / 5.78 ( 8) metal coordination : angle 17.11058 / 8.50 ( 6) Misc. bond : bond 0.27728 / 13.19 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 900 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7525 (tttt) cc_final: 0.7118 (tttp) REVERT: C 186 MET cc_start: 0.8532 (tpp) cc_final: 0.8304 (mmm) REVERT: C 217 ASP cc_start: 0.7626 (t0) cc_final: 0.6980 (p0) REVERT: C 221 MET cc_start: 0.9020 (tpt) cc_final: 0.8675 (tpp) REVERT: C 239 MET cc_start: 0.7525 (ttp) cc_final: 0.7204 (ttt) REVERT: C 247 SER cc_start: 0.8549 (t) cc_final: 0.8342 (p) REVERT: C 250 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7265 (tptp) REVERT: C 255 ASP cc_start: 0.8559 (m-30) cc_final: 0.7984 (t0) REVERT: C 289 LEU cc_start: 0.7816 (tp) cc_final: 0.7541 (tp) REVERT: C 309 ASP cc_start: 0.8070 (t0) cc_final: 0.7836 (t0) REVERT: C 341 GLN cc_start: 0.8720 (pp30) cc_final: 0.8505 (pp30) REVERT: C 365 ILE cc_start: 0.7758 (mt) cc_final: 0.7350 (mt) REVERT: C 369 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7484 (mmt) REVERT: C 376 ILE cc_start: 0.8416 (mt) cc_final: 0.8142 (mm) REVERT: P 40 LYS cc_start: 0.6000 (tttt) cc_final: 0.5629 (tttp) REVERT: P 91 MET cc_start: 0.8334 (mtp) cc_final: 0.8052 (mtp) REVERT: P 106 LYS cc_start: 0.7524 (mmtp) cc_final: 0.7057 (mmtt) REVERT: P 114 LYS cc_start: 0.7222 (mptp) cc_final: 0.6833 (mmtm) REVERT: P 119 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7511 (ptmm) REVERT: P 123 LYS cc_start: 0.7926 (mttt) cc_final: 0.7634 (mttp) REVERT: P 129 HIS cc_start: 0.6782 (t70) cc_final: 0.6338 (t70) REVERT: P 136 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6494 (mm-30) REVERT: P 150 GLN cc_start: 0.7239 (tt0) cc_final: 0.6482 (tp40) REVERT: P 154 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7313 (mt-10) REVERT: P 215 ASP cc_start: 0.7620 (m-30) cc_final: 0.7333 (p0) REVERT: P 218 ASP cc_start: 0.6406 (t70) cc_final: 0.6151 (t0) REVERT: G 3 SER cc_start: 0.7470 (OUTLIER) cc_final: 0.7172 (t) REVERT: G 50 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: G 56 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7800 (mm-40) REVERT: G 94 LYS cc_start: 0.7241 (mttp) cc_final: 0.6763 (mmmt) REVERT: G 97 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6695 (mt-10) REVERT: F 96 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6772 (t-90) REVERT: F 125 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: F 145 VAL cc_start: 0.8187 (m) cc_final: 0.7987 (p) REVERT: A 32 THR cc_start: 0.8015 (m) cc_final: 0.7810 (p) REVERT: A 103 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 141 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: A 145 ASP cc_start: 0.7964 (m-30) cc_final: 0.7357 (m-30) REVERT: A 148 ARG cc_start: 0.7095 (ttp-170) cc_final: 0.6371 (ttt90) REVERT: A 164 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7334 (mm-30) REVERT: A 191 ILE cc_start: 0.7774 (mt) cc_final: 0.7546 (mm) REVERT: A 201 LYS cc_start: 0.7677 (tttm) cc_final: 0.7392 (ttmt) REVERT: A 247 THR cc_start: 0.6982 (m) cc_final: 0.6324 (p) REVERT: A 260 ILE cc_start: 0.4373 (mm) cc_final: 0.4088 (tt) REVERT: A 327 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7301 (mm-30) REVERT: A 354 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7495 (pt0) REVERT: A 381 GLN cc_start: 0.7249 (mp10) cc_final: 0.6874 (mp10) REVERT: A 390 LYS cc_start: 0.7549 (tptt) cc_final: 0.7154 (mtpp) REVERT: A 409 ARG cc_start: 0.6870 (tmm160) cc_final: 0.6625 (ttp80) REVERT: B 34 ILE cc_start: 0.7767 (mm) cc_final: 0.7533 (mt) REVERT: B 58 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: B 60 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8635 (t80) REVERT: B 77 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7932 (tp) REVERT: B 117 GLU cc_start: 0.6887 (mp0) cc_final: 0.6485 (mm-30) REVERT: B 119 LYS cc_start: 0.6601 (mtpp) cc_final: 0.6312 (mttt) REVERT: B 136 ASP cc_start: 0.8413 (t70) cc_final: 0.8176 (t70) REVERT: B 154 GLU cc_start: 0.7878 (tp30) cc_final: 0.7628 (tt0) REVERT: B 168 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: B 171 SER cc_start: 0.7720 (t) cc_final: 0.7517 (p) REVERT: B 176 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6985 (tp30) REVERT: B 197 ASN cc_start: 0.8119 (t0) cc_final: 0.7612 (t0) REVERT: B 220 VAL cc_start: 0.8140 (t) cc_final: 0.7908 (m) REVERT: B 232 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7037 (pm20) REVERT: B 251 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6577 (pm20) REVERT: B 268 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7428 (m) REVERT: B 271 TRP cc_start: 0.7708 (m100) cc_final: 0.7497 (m100) REVERT: B 307 LYS cc_start: 0.7909 (pttm) cc_final: 0.7613 (ptmt) REVERT: B 345 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7468 (ttmm) REVERT: B 355 PRO cc_start: 0.6665 (Cg_exo) cc_final: 0.6459 (Cg_endo) REVERT: B 376 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: B 379 GLN cc_start: 0.6201 (tt0) cc_final: 0.5374 (mp10) REVERT: B 385 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 85 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5518 (mtp) REVERT: D 90 HIS cc_start: 0.7524 (m-70) cc_final: 0.7145 (t70) REVERT: D 169 LYS cc_start: 0.7145 (mmtp) cc_final: 0.6708 (mptt) REVERT: D 185 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7588 (tt0) REVERT: D 224 GLU cc_start: 0.7153 (tt0) cc_final: 0.6917 (pm20) REVERT: D 283 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8188 (mp0) REVERT: D 291 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8184 (ttpp) REVERT: D 292 LEU cc_start: 0.8384 (mt) cc_final: 0.8157 (mp) REVERT: I 27 PHE cc_start: 0.7493 (t80) cc_final: 0.7094 (t80) REVERT: I 42 ASP cc_start: 0.8029 (m-30) cc_final: 0.7589 (t70) REVERT: I 49 GLN cc_start: 0.7840 (mt0) cc_final: 0.7083 (pt0) REVERT: J 11 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6711 (ttpp) REVERT: J 13 SER cc_start: 0.6919 (t) cc_final: 0.6707 (t) REVERT: J 15 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7021 (pttm) REVERT: J 27 THR cc_start: 0.8134 (m) cc_final: 0.7676 (p) REVERT: N 6 LYS cc_start: 0.7470 (tttt) cc_final: 0.7084 (tttp) REVERT: N 160 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: N 186 MET cc_start: 0.8528 (tpp) cc_final: 0.8314 (mmm) REVERT: N 217 ASP cc_start: 0.7515 (t0) cc_final: 0.6939 (p0) REVERT: N 221 MET cc_start: 0.9033 (tpt) cc_final: 0.8688 (tpp) REVERT: N 239 MET cc_start: 0.7541 (ttp) cc_final: 0.7218 (ttt) REVERT: N 247 SER cc_start: 0.8563 (t) cc_final: 0.8354 (p) REVERT: N 250 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7154 (tptp) REVERT: N 255 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8345 (t0) REVERT: N 287 ASP cc_start: 0.7720 (t70) cc_final: 0.7055 (m-30) REVERT: N 309 ASP cc_start: 0.8034 (t0) cc_final: 0.7782 (t0) REVERT: N 332 ASN cc_start: 0.8379 (t0) cc_final: 0.8059 (t0) REVERT: N 341 GLN cc_start: 0.8698 (pp30) cc_final: 0.8443 (pp30) REVERT: N 365 ILE cc_start: 0.7763 (mt) cc_final: 0.7360 (mt) REVERT: N 369 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7493 (mmt) REVERT: N 376 ILE cc_start: 0.8414 (mt) cc_final: 0.8147 (mm) REVERT: E 40 LYS cc_start: 0.6027 (tttt) cc_final: 0.5648 (tttp) REVERT: E 55 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (p0) REVERT: E 91 MET cc_start: 0.8324 (mtp) cc_final: 0.8028 (mtp) REVERT: E 100 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6291 (ttp) REVERT: E 106 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7052 (mmtt) REVERT: E 114 LYS cc_start: 0.7181 (mptp) cc_final: 0.6754 (mmtm) REVERT: E 119 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7519 (ptmm) REVERT: E 123 LYS cc_start: 0.7937 (mttt) cc_final: 0.7662 (mttp) REVERT: E 129 HIS cc_start: 0.6837 (t70) cc_final: 0.6401 (t70) REVERT: E 136 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6496 (mm-30) REVERT: E 150 GLN cc_start: 0.7236 (tt0) cc_final: 0.6476 (tp40) REVERT: E 154 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7325 (mt-10) REVERT: E 215 ASP cc_start: 0.7628 (m-30) cc_final: 0.7330 (p0) REVERT: E 218 ASP cc_start: 0.6391 (t70) cc_final: 0.6135 (t0) REVERT: R 6 SER cc_start: 0.7690 (m) cc_final: 0.7377 (p) REVERT: R 50 GLU cc_start: 0.7975 (pt0) cc_final: 0.7749 (pt0) REVERT: R 55 MET cc_start: 0.8434 (mmm) cc_final: 0.8111 (tpp) REVERT: R 56 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7704 (mm-40) REVERT: R 94 LYS cc_start: 0.7238 (mttp) cc_final: 0.6735 (mmmt) REVERT: R 97 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6795 (mt-10) REVERT: L 32 THR cc_start: 0.8028 (m) cc_final: 0.7819 (p) REVERT: L 48 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.6077 (tp) REVERT: L 87 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6620 (ptp90) REVERT: L 99 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6914 (mtm) REVERT: L 145 ASP cc_start: 0.7967 (m-30) cc_final: 0.7578 (m-30) REVERT: L 164 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7337 (mm-30) REVERT: L 201 LYS cc_start: 0.7671 (tttm) cc_final: 0.7390 (ttmt) REVERT: L 247 THR cc_start: 0.6962 (m) cc_final: 0.6396 (p) REVERT: L 260 ILE cc_start: 0.4370 (mm) cc_final: 0.4032 (tt) REVERT: L 327 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7277 (mm-30) REVERT: L 354 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7482 (pt0) REVERT: L 381 GLN cc_start: 0.7035 (mp10) cc_final: 0.6747 (mp10) REVERT: L 383 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8103 (tp30) REVERT: L 390 LYS cc_start: 0.7429 (tptt) cc_final: 0.7041 (mtpp) REVERT: L 396 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.5818 (t) REVERT: L 406 ASP cc_start: 0.8263 (t70) cc_final: 0.8060 (t0) REVERT: L 409 ARG cc_start: 0.6843 (tmm160) cc_final: 0.6603 (ttp80) REVERT: M 58 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: M 77 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7897 (tp) REVERT: M 117 GLU cc_start: 0.6882 (mp0) cc_final: 0.6483 (mm-30) REVERT: M 119 LYS cc_start: 0.6610 (mtpp) cc_final: 0.6319 (mttt) REVERT: M 154 GLU cc_start: 0.7882 (tp30) cc_final: 0.7637 (tt0) REVERT: M 176 GLU cc_start: 0.7243 (mm-30) cc_final: 0.7010 (tp30) REVERT: M 197 ASN cc_start: 0.8113 (t0) cc_final: 0.7678 (t0) REVERT: M 216 GLU cc_start: 0.7562 (tp30) cc_final: 0.7224 (tm-30) REVERT: M 232 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7032 (pm20) REVERT: M 236 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6753 (mtt90) REVERT: M 251 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6605 (pm20) REVERT: M 271 TRP cc_start: 0.7701 (m100) cc_final: 0.7451 (m100) REVERT: M 292 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7920 (p) REVERT: M 307 LYS cc_start: 0.7855 (pttm) cc_final: 0.7640 (ptmt) REVERT: M 331 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: M 345 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7507 (ttmm) REVERT: M 356 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6816 (t0) REVERT: M 376 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: M 379 GLN cc_start: 0.6228 (tt0) cc_final: 0.5393 (mp10) REVERT: O 90 HIS cc_start: 0.7519 (m-70) cc_final: 0.6938 (t70) REVERT: O 169 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6691 (mptt) REVERT: O 185 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7575 (tt0) REVERT: O 224 GLU cc_start: 0.7171 (tt0) cc_final: 0.6927 (pm20) REVERT: O 291 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8193 (ttpp) REVERT: O 292 LEU cc_start: 0.8272 (mt) cc_final: 0.8045 (mp) REVERT: T 27 PHE cc_start: 0.7612 (t80) cc_final: 0.7201 (t80) REVERT: T 42 ASP cc_start: 0.8006 (m-30) cc_final: 0.7562 (t70) REVERT: T 49 GLN cc_start: 0.7849 (mt0) cc_final: 0.7087 (pt0) REVERT: U 11 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6276 (ttpt) REVERT: U 13 SER cc_start: 0.6952 (t) cc_final: 0.6731 (t) REVERT: U 15 LYS cc_start: 0.7409 (pttt) cc_final: 0.6987 (pttt) REVERT: U 27 THR cc_start: 0.8190 (m) cc_final: 0.7704 (p) outliers start: 190 outliers final: 30 residues processed: 1014 average time/residue: 0.2233 time to fit residues: 359.2353 Evaluate side-chains 626 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 556 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 PRO Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain N residue 109 PRO Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 250 LYS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 331 GLU Chi-restraints excluded: chain M residue 345 LYS Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain M residue 376 GLU Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 163 HIS C 173 ASN C 253 HIS C 332 ASN P 115 ASN F 96 HIS F 132 HIS A 70 ASN A 74 HIS A 102 HIS A 177 ASN A 192 GLN A 196 ASN A 222 HIS A 371 ASN A 433 HIS B 28 GLN B 87 HIS B 92 HIS B 121 GLN B 354 ASN D 90 HIS D 118 GLN D 269 GLN D 326 ASN I 49 GLN N 14 ASN N 332 ASN E 115 ASN Q 132 HIS L 70 ASN L 102 HIS L 177 ASN L 192 GLN L 196 ASN L 323 ASN L 371 ASN L 433 HIS M 87 HIS M 92 HIS M 121 GLN O 90 HIS O 118 GLN O 208 HIS O 269 GLN O 326 ASN T 49 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091572 restraints weight = 47959.480| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.93 r_work: 0.2798 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.534 34536 Z= 0.159 Angle : 0.667 17.138 46932 Z= 0.329 Chirality : 0.044 0.286 5124 Planarity : 0.005 0.082 5896 Dihedral : 13.285 119.400 5247 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.45 % Favored : 98.50 % Rotamer: Outliers : 2.92 % Allowed : 12.57 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.21 (0.13), residues: 4080 helix: 0.48 (0.10), residues: 2172 sheet: 0.19 (0.26), residues: 352 loop : -0.16 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 14 TYR 0.021 0.002 TYR N 16 PHE 0.025 0.002 PHE M 62 TRP 0.031 0.002 TRP N 142 HIS 0.013 0.001 HIS P 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (34514) covalent geometry : angle 0.66631 / 0.33 (46914) SS BOND : bond 0.00255 / 0.15 ( 6) SS BOND : angle 1.40131 / 0.76 ( 12) hydrogen bonds : bond 0.04881 / 3.23 ( 1907) hydrogen bonds : angle 5.06709 / 3.63 ( 5376) metal coordination : bond 0.01631 / 0.75 ( 8) metal coordination : angle 2.89370 / 1.23 ( 6) Misc. bond : bond 0.33972 / 19.65 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 672 time to evaluate : 1.432 Fit side-chains REVERT: C 6 LYS cc_start: 0.7826 (tttt) cc_final: 0.7453 (tttp) REVERT: C 186 MET cc_start: 0.8869 (tpp) cc_final: 0.8533 (mmm) REVERT: C 221 MET cc_start: 0.8829 (tpt) cc_final: 0.8622 (tpp) REVERT: C 250 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7667 (tptp) REVERT: C 255 ASP cc_start: 0.8626 (m-30) cc_final: 0.8185 (t0) REVERT: C 287 ASP cc_start: 0.7883 (t70) cc_final: 0.7094 (m-30) REVERT: C 296 VAL cc_start: 0.8474 (t) cc_final: 0.8020 (m) REVERT: C 341 GLN cc_start: 0.8676 (pp30) cc_final: 0.8288 (pp30) REVERT: C 365 ILE cc_start: 0.8439 (mt) cc_final: 0.8117 (mt) REVERT: C 369 MET cc_start: 0.8092 (mmm) cc_final: 0.7650 (mmt) REVERT: C 372 THR cc_start: 0.8828 (m) cc_final: 0.8416 (p) REVERT: P 40 LYS cc_start: 0.6247 (tttt) cc_final: 0.5970 (tttp) REVERT: P 91 MET cc_start: 0.8287 (mtp) cc_final: 0.8052 (mtp) REVERT: P 100 MET cc_start: 0.5526 (mmm) cc_final: 0.4627 (ttm) REVERT: P 107 LEU cc_start: 0.7965 (mt) cc_final: 0.7599 (mt) REVERT: P 114 LYS cc_start: 0.7132 (mptp) cc_final: 0.6798 (mmtm) REVERT: P 123 LYS cc_start: 0.8240 (mttt) cc_final: 0.7847 (mttp) REVERT: P 160 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7809 (mm-30) REVERT: G 55 MET cc_start: 0.7973 (tpp) cc_final: 0.7652 (tpp) REVERT: G 56 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7699 (mm-40) REVERT: G 110 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7747 (mm-30) REVERT: F 97 HIS cc_start: 0.6771 (m90) cc_final: 0.5995 (m-70) REVERT: F 100 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6686 (pt0) REVERT: A 32 THR cc_start: 0.8149 (m) cc_final: 0.7753 (p) REVERT: A 59 ASP cc_start: 0.7650 (t0) cc_final: 0.7202 (t0) REVERT: A 97 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6830 (mt-10) REVERT: A 117 LYS cc_start: 0.7576 (tttp) cc_final: 0.7246 (ttmt) REVERT: A 135 GLN cc_start: 0.6832 (mt0) cc_final: 0.6446 (mp10) REVERT: A 141 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6319 (tp30) REVERT: A 145 ASP cc_start: 0.8086 (m-30) cc_final: 0.7446 (m-30) REVERT: A 148 ARG cc_start: 0.7228 (ttp-170) cc_final: 0.6944 (ptp-110) REVERT: A 247 THR cc_start: 0.7635 (m) cc_final: 0.6990 (p) REVERT: A 260 ILE cc_start: 0.4506 (mm) cc_final: 0.4298 (tt) REVERT: A 327 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7011 (mm-30) REVERT: A 390 LYS cc_start: 0.7828 (tptt) cc_final: 0.7546 (mtpp) REVERT: A 409 ARG cc_start: 0.7064 (tmm160) cc_final: 0.6653 (ttp-170) REVERT: B 47 TYR cc_start: 0.8490 (m-80) cc_final: 0.8056 (m-10) REVERT: B 58 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: B 60 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8940 (t80) REVERT: B 88 THR cc_start: 0.8616 (m) cc_final: 0.8317 (t) REVERT: B 116 LYS cc_start: 0.7387 (mtpt) cc_final: 0.7024 (mtmt) REVERT: B 137 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7472 (tp) REVERT: B 159 THR cc_start: 0.7314 (p) cc_final: 0.6988 (t) REVERT: B 168 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: B 197 ASN cc_start: 0.8342 (t0) cc_final: 0.7869 (t0) REVERT: B 271 TRP cc_start: 0.7925 (m100) cc_final: 0.7624 (m100) REVERT: B 290 LYS cc_start: 0.8133 (tptm) cc_final: 0.7873 (tptt) REVERT: B 307 LYS cc_start: 0.8121 (pttm) cc_final: 0.7890 (ptmt) REVERT: B 339 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6968 (ttp80) REVERT: B 345 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7680 (ttmm) REVERT: B 372 ARG cc_start: 0.6528 (ptt-90) cc_final: 0.5479 (ptt-90) REVERT: B 379 GLN cc_start: 0.6419 (tt0) cc_final: 0.5846 (mp10) REVERT: B 385 GLU cc_start: 0.7143 (mt-10) cc_final: 0.5915 (mm-30) REVERT: B 406 GLN cc_start: 0.7315 (mm110) cc_final: 0.7028 (mp10) REVERT: D 86 THR cc_start: 0.6744 (m) cc_final: 0.6495 (p) REVERT: D 154 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6881 (mt-10) REVERT: D 168 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7243 (mtp180) REVERT: D 169 LYS cc_start: 0.7375 (mmtp) cc_final: 0.7031 (mptt) REVERT: D 173 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7726 (mmmt) REVERT: D 283 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7900 (mp0) REVERT: D 291 LYS cc_start: 0.8701 (tttt) cc_final: 0.8395 (ttpp) REVERT: H 88 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6615 (mm-30) REVERT: I 14 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7997 (mtt-85) REVERT: I 27 PHE cc_start: 0.8023 (t80) cc_final: 0.7489 (t80) REVERT: I 42 ASP cc_start: 0.7768 (m-30) cc_final: 0.7547 (t70) REVERT: I 49 GLN cc_start: 0.7601 (mt0) cc_final: 0.7356 (mt0) REVERT: J 11 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6399 (ttpt) REVERT: J 13 SER cc_start: 0.7344 (t) cc_final: 0.7096 (t) REVERT: J 15 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7587 (pttm) REVERT: N 6 LYS cc_start: 0.7838 (tttt) cc_final: 0.7513 (tttp) REVERT: N 221 MET cc_start: 0.8806 (tpt) cc_final: 0.8562 (tpp) REVERT: N 250 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7474 (tptp) REVERT: N 255 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: N 287 ASP cc_start: 0.7870 (t70) cc_final: 0.7274 (m-30) REVERT: N 289 LEU cc_start: 0.8133 (tp) cc_final: 0.7866 (tp) REVERT: N 296 VAL cc_start: 0.8452 (t) cc_final: 0.8016 (m) REVERT: N 365 ILE cc_start: 0.8449 (mt) cc_final: 0.8133 (mt) REVERT: N 369 MET cc_start: 0.8056 (mmm) cc_final: 0.7617 (mmt) REVERT: N 372 THR cc_start: 0.8830 (m) cc_final: 0.8396 (p) REVERT: E 40 LYS cc_start: 0.6289 (tttt) cc_final: 0.5872 (tttp) REVERT: E 91 MET cc_start: 0.8242 (mtp) cc_final: 0.7997 (mtp) REVERT: E 107 LEU cc_start: 0.7989 (mt) cc_final: 0.7635 (mt) REVERT: E 114 LYS cc_start: 0.7227 (mptp) cc_final: 0.6857 (mmtm) REVERT: R 50 GLU cc_start: 0.7174 (pt0) cc_final: 0.6756 (pt0) REVERT: R 55 MET cc_start: 0.8527 (mmm) cc_final: 0.8324 (tpp) REVERT: R 56 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7799 (mm-40) REVERT: R 112 GLU cc_start: 0.7571 (tt0) cc_final: 0.7355 (tt0) REVERT: Q 97 HIS cc_start: 0.7069 (m170) cc_final: 0.6865 (m90) REVERT: Q 125 GLU cc_start: 0.7173 (mp0) cc_final: 0.6967 (mp0) REVERT: L 32 THR cc_start: 0.8153 (m) cc_final: 0.7756 (p) REVERT: L 59 ASP cc_start: 0.7626 (t0) cc_final: 0.7188 (t0) REVERT: L 135 GLN cc_start: 0.6892 (mt0) cc_final: 0.6483 (mp10) REVERT: L 136 HIS cc_start: 0.6414 (m-70) cc_final: 0.6037 (m-70) REVERT: L 138 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5874 (ttmm) REVERT: L 145 ASP cc_start: 0.8016 (m-30) cc_final: 0.7430 (m-30) REVERT: L 147 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7105 (mm-30) REVERT: L 247 THR cc_start: 0.7546 (m) cc_final: 0.6898 (p) REVERT: L 390 LYS cc_start: 0.7802 (tptt) cc_final: 0.7532 (mtpp) REVERT: L 409 ARG cc_start: 0.7055 (tmm160) cc_final: 0.6669 (ttp-170) REVERT: M 47 TYR cc_start: 0.8243 (m-80) cc_final: 0.7876 (m-80) REVERT: M 58 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: M 60 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8898 (t80) REVERT: M 77 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (tp) REVERT: M 116 LYS cc_start: 0.7368 (mtpt) cc_final: 0.7015 (mtmt) REVERT: M 159 THR cc_start: 0.7316 (p) cc_final: 0.7023 (t) REVERT: M 184 GLN cc_start: 0.7602 (mt0) cc_final: 0.7367 (mp10) REVERT: M 197 ASN cc_start: 0.8195 (t0) cc_final: 0.7811 (t0) REVERT: M 236 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6743 (mtt180) REVERT: M 271 TRP cc_start: 0.7915 (m100) cc_final: 0.7470 (m100) REVERT: M 273 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6923 (p) REVERT: M 307 LYS cc_start: 0.8077 (pttm) cc_final: 0.7845 (ptmt) REVERT: M 356 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: M 379 GLN cc_start: 0.6214 (tt0) cc_final: 0.5680 (mp10) REVERT: M 392 GLN cc_start: 0.7455 (tt0) cc_final: 0.7194 (mm110) REVERT: M 406 GLN cc_start: 0.7355 (mm110) cc_final: 0.7046 (mp10) REVERT: O 118 GLN cc_start: 0.8431 (tt0) cc_final: 0.8177 (tt0) REVERT: O 154 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6872 (mt-10) REVERT: O 168 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7250 (mtp180) REVERT: O 169 LYS cc_start: 0.7419 (mmtp) cc_final: 0.7042 (mptt) REVERT: O 173 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7770 (mmmt) REVERT: O 291 LYS cc_start: 0.8688 (tttt) cc_final: 0.8400 (ttpp) REVERT: S 88 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6617 (mm-30) REVERT: T 27 PHE cc_start: 0.8071 (t80) cc_final: 0.7568 (t80) REVERT: T 42 ASP cc_start: 0.7763 (m-30) cc_final: 0.7496 (t70) REVERT: T 49 GLN cc_start: 0.7572 (mt0) cc_final: 0.7331 (mt0) REVERT: U 11 LYS cc_start: 0.6572 (tttt) cc_final: 0.6088 (ttpt) REVERT: U 13 SER cc_start: 0.7391 (t) cc_final: 0.7181 (t) REVERT: U 15 LYS cc_start: 0.7796 (pttt) cc_final: 0.7374 (pttm) REVERT: U 20 PHE cc_start: 0.7871 (t80) cc_final: 0.7616 (t80) outliers start: 100 outliers final: 44 residues processed: 738 average time/residue: 0.2294 time to fit residues: 270.4665 Evaluate side-chains 581 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 523 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 370 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 441 LYS Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain U residue 25 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 173 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 290 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN P 115 ASN F 132 HIS A 317 GLN B 316 GLN B 354 ASN D 118 GLN E 115 ASN L 317 GLN M 184 GLN M 316 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093033 restraints weight = 47938.895| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.83 r_work: 0.2847 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.395 34536 Z= 0.131 Angle : 0.579 11.601 46932 Z= 0.284 Chirality : 0.042 0.241 5124 Planarity : 0.004 0.059 5896 Dihedral : 11.857 100.512 5126 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Rotamer: Outliers : 2.59 % Allowed : 14.20 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 4080 helix: 1.14 (0.11), residues: 2162 sheet: 0.30 (0.26), residues: 384 loop : 0.14 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 14 TYR 0.019 0.001 TYR N 16 PHE 0.018 0.001 PHE I 40 TRP 0.020 0.001 TRP N 142 HIS 0.008 0.001 HIS P 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (34514) covalent geometry : angle 0.57540 / 0.28 (46914) SS BOND : bond 0.01092 / 0.69 ( 6) SS BOND : angle 2.85953 / 1.47 ( 12) hydrogen bonds : bond 0.04248 / 2.80 ( 1907) hydrogen bonds : angle 4.74832 / 3.40 ( 5376) metal coordination : bond 0.01518 / 0.69 ( 8) metal coordination : angle 4.34828 / 1.89 ( 6) Misc. bond : bond 0.27877 / 15.59 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 591 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7757 (tttt) cc_final: 0.7486 (tttp) REVERT: C 186 MET cc_start: 0.8819 (tpp) cc_final: 0.8468 (mmm) REVERT: C 239 MET cc_start: 0.8242 (ttt) cc_final: 0.8008 (ttm) REVERT: C 250 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7708 (tptp) REVERT: C 255 ASP cc_start: 0.8656 (m-30) cc_final: 0.8342 (t0) REVERT: C 287 ASP cc_start: 0.7941 (t70) cc_final: 0.7113 (m-30) REVERT: C 289 LEU cc_start: 0.8284 (tp) cc_final: 0.7841 (tp) REVERT: C 322 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8222 (m) REVERT: C 369 MET cc_start: 0.8137 (mmm) cc_final: 0.7712 (mmt) REVERT: C 372 THR cc_start: 0.8727 (m) cc_final: 0.8489 (p) REVERT: P 40 LYS cc_start: 0.6373 (tttt) cc_final: 0.6035 (tttp) REVERT: P 55 ASP cc_start: 0.8208 (p0) cc_final: 0.7907 (p0) REVERT: P 90 ASN cc_start: 0.8702 (p0) cc_final: 0.8497 (p0) REVERT: P 100 MET cc_start: 0.5342 (mmm) cc_final: 0.4879 (ttm) REVERT: P 107 LEU cc_start: 0.7615 (mt) cc_final: 0.7386 (mt) REVERT: P 114 LYS cc_start: 0.7012 (mptp) cc_final: 0.6687 (mmtm) REVERT: P 123 LYS cc_start: 0.8181 (mttt) cc_final: 0.7750 (mttm) REVERT: P 139 ASN cc_start: 0.7021 (m-40) cc_final: 0.6680 (m-40) REVERT: G 55 MET cc_start: 0.7861 (tpp) cc_final: 0.7534 (tpp) REVERT: G 56 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7806 (mm-40) REVERT: G 94 LYS cc_start: 0.7560 (mttp) cc_final: 0.7066 (mmmt) REVERT: F 97 HIS cc_start: 0.6350 (m90) cc_final: 0.6083 (m-70) REVERT: F 100 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6690 (pt0) REVERT: A 32 THR cc_start: 0.8029 (m) cc_final: 0.7639 (p) REVERT: A 59 ASP cc_start: 0.7552 (t0) cc_final: 0.7130 (t0) REVERT: A 148 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6841 (ptp-110) REVERT: A 247 THR cc_start: 0.7563 (m) cc_final: 0.6901 (p) REVERT: A 390 LYS cc_start: 0.7786 (tptt) cc_final: 0.7531 (mtpp) REVERT: A 409 ARG cc_start: 0.7072 (tmm160) cc_final: 0.6682 (ttp-170) REVERT: B 47 TYR cc_start: 0.8469 (m-80) cc_final: 0.8205 (m-10) REVERT: B 60 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (t80) REVERT: B 116 LYS cc_start: 0.7404 (mtpt) cc_final: 0.7084 (mtmt) REVERT: B 154 GLU cc_start: 0.8610 (tt0) cc_final: 0.8279 (tt0) REVERT: B 159 THR cc_start: 0.7349 (p) cc_final: 0.7013 (t) REVERT: B 168 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: B 197 ASN cc_start: 0.8242 (t0) cc_final: 0.7851 (t0) REVERT: B 213 ASP cc_start: 0.6979 (m-30) cc_final: 0.6757 (t0) REVERT: B 232 GLU cc_start: 0.6269 (pm20) cc_final: 0.6005 (pm20) REVERT: B 271 TRP cc_start: 0.7948 (m100) cc_final: 0.7716 (m100) REVERT: B 290 LYS cc_start: 0.8086 (tptm) cc_final: 0.7730 (tptt) REVERT: B 323 GLN cc_start: 0.5648 (mm-40) cc_final: 0.5430 (mm110) REVERT: B 339 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6941 (ttp-110) REVERT: B 345 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7721 (ttmm) REVERT: B 357 SER cc_start: 0.7365 (OUTLIER) cc_final: 0.7107 (t) REVERT: B 372 ARG cc_start: 0.6617 (ptt-90) cc_final: 0.5526 (ptt-90) REVERT: B 379 GLN cc_start: 0.6379 (tt0) cc_final: 0.5911 (mp10) REVERT: B 385 GLU cc_start: 0.7029 (mt-10) cc_final: 0.5919 (mm-30) REVERT: B 392 GLN cc_start: 0.7418 (mt0) cc_final: 0.7147 (mm110) REVERT: B 406 GLN cc_start: 0.7336 (mm110) cc_final: 0.7042 (mp10) REVERT: D 86 THR cc_start: 0.7056 (m) cc_final: 0.6371 (p) REVERT: D 154 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6575 (pt0) REVERT: D 166 ASN cc_start: 0.7239 (m110) cc_final: 0.6742 (m-40) REVERT: D 169 LYS cc_start: 0.7387 (mmtp) cc_final: 0.7010 (mptt) REVERT: D 173 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7748 (mmmt) REVERT: D 208 HIS cc_start: 0.8341 (m-70) cc_final: 0.8126 (m-70) REVERT: D 283 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7965 (mp0) REVERT: D 291 LYS cc_start: 0.8687 (tttt) cc_final: 0.8418 (ttpp) REVERT: H 57 LEU cc_start: 0.8208 (mt) cc_final: 0.7724 (tt) REVERT: H 88 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6635 (mm-30) REVERT: I 14 ARG cc_start: 0.8258 (mtt90) cc_final: 0.8035 (mtt-85) REVERT: I 27 PHE cc_start: 0.8021 (t80) cc_final: 0.7538 (t80) REVERT: I 49 GLN cc_start: 0.7588 (mt0) cc_final: 0.7266 (mt0) REVERT: J 11 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6304 (ttpt) REVERT: J 13 SER cc_start: 0.7394 (t) cc_final: 0.7146 (t) REVERT: J 15 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7529 (pttm) REVERT: J 78 SER cc_start: 0.8193 (p) cc_final: 0.7896 (p) REVERT: N 6 LYS cc_start: 0.7776 (tttt) cc_final: 0.7552 (tttp) REVERT: N 107 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7627 (mtpt) REVERT: N 186 MET cc_start: 0.8795 (tpp) cc_final: 0.8462 (mmm) REVERT: N 239 MET cc_start: 0.8233 (ttt) cc_final: 0.7998 (ttm) REVERT: N 250 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7529 (tptp) REVERT: N 255 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: N 287 ASP cc_start: 0.7860 (t70) cc_final: 0.7246 (m-30) REVERT: N 289 LEU cc_start: 0.8109 (tp) cc_final: 0.7856 (tp) REVERT: N 322 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8208 (m) REVERT: N 369 MET cc_start: 0.8113 (mmm) cc_final: 0.7718 (mmt) REVERT: N 372 THR cc_start: 0.8761 (m) cc_final: 0.8502 (p) REVERT: E 90 ASN cc_start: 0.8696 (p0) cc_final: 0.8493 (p0) REVERT: E 107 LEU cc_start: 0.7636 (mt) cc_final: 0.7405 (mt) REVERT: E 139 ASN cc_start: 0.7014 (m-40) cc_final: 0.6671 (m-40) REVERT: R 50 GLU cc_start: 0.7001 (pt0) cc_final: 0.6737 (pt0) REVERT: R 52 THR cc_start: 0.8110 (m) cc_final: 0.7670 (p) REVERT: R 55 MET cc_start: 0.8354 (mmm) cc_final: 0.8104 (tpp) REVERT: R 56 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7714 (mm-40) REVERT: R 94 LYS cc_start: 0.7672 (mttp) cc_final: 0.7126 (mmmt) REVERT: Q 97 HIS cc_start: 0.6987 (m170) cc_final: 0.6785 (m90) REVERT: Q 125 GLU cc_start: 0.7257 (mp0) cc_final: 0.7007 (mp0) REVERT: L 32 THR cc_start: 0.8076 (m) cc_final: 0.7679 (p) REVERT: L 59 ASP cc_start: 0.7529 (t0) cc_final: 0.7114 (t0) REVERT: L 136 HIS cc_start: 0.6469 (m-70) cc_final: 0.6268 (m-70) REVERT: L 138 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5975 (mtmm) REVERT: L 147 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6876 (mm-30) REVERT: L 247 THR cc_start: 0.7409 (m) cc_final: 0.6789 (p) REVERT: L 390 LYS cc_start: 0.7786 (tptt) cc_final: 0.7544 (mtpp) REVERT: L 409 ARG cc_start: 0.7081 (tmm160) cc_final: 0.6651 (ttp-170) REVERT: M 47 TYR cc_start: 0.8215 (m-80) cc_final: 0.7972 (m-10) REVERT: M 58 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: M 60 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8891 (t80) REVERT: M 116 LYS cc_start: 0.7391 (mtpt) cc_final: 0.7064 (mtmt) REVERT: M 159 THR cc_start: 0.7369 (p) cc_final: 0.7052 (t) REVERT: M 184 GLN cc_start: 0.7637 (mt0) cc_final: 0.7374 (mp10) REVERT: M 197 ASN cc_start: 0.8135 (t0) cc_final: 0.7799 (t0) REVERT: M 232 GLU cc_start: 0.6397 (pm20) cc_final: 0.6139 (pm20) REVERT: M 271 TRP cc_start: 0.7919 (m100) cc_final: 0.7448 (m100) REVERT: M 273 VAL cc_start: 0.7087 (t) cc_final: 0.6858 (p) REVERT: M 307 LYS cc_start: 0.8091 (pttm) cc_final: 0.7873 (ptmt) REVERT: M 335 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7142 (mm-30) REVERT: M 345 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7698 (ttmm) REVERT: M 356 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6195 (m-30) REVERT: M 379 GLN cc_start: 0.6339 (tt0) cc_final: 0.5754 (mp10) REVERT: M 406 GLN cc_start: 0.7331 (mm110) cc_final: 0.7034 (mp10) REVERT: O 154 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6559 (pt0) REVERT: O 166 ASN cc_start: 0.7278 (m110) cc_final: 0.6813 (m-40) REVERT: O 169 LYS cc_start: 0.7418 (mmtp) cc_final: 0.6942 (mptt) REVERT: O 173 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7775 (mmmt) REVERT: O 208 HIS cc_start: 0.8208 (m-70) cc_final: 0.8005 (m-70) REVERT: O 291 LYS cc_start: 0.8689 (tttt) cc_final: 0.8411 (ttpp) REVERT: S 57 LEU cc_start: 0.8225 (mt) cc_final: 0.7764 (tt) REVERT: S 88 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6635 (mm-30) REVERT: T 27 PHE cc_start: 0.8074 (t80) cc_final: 0.7596 (t80) REVERT: T 49 GLN cc_start: 0.7574 (mt0) cc_final: 0.7255 (mt0) REVERT: U 11 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6072 (ttpt) REVERT: U 13 SER cc_start: 0.7371 (t) cc_final: 0.7116 (t) REVERT: U 15 LYS cc_start: 0.7847 (pttt) cc_final: 0.7425 (pttm) REVERT: U 78 SER cc_start: 0.8226 (p) cc_final: 0.7921 (p) outliers start: 89 outliers final: 43 residues processed: 652 average time/residue: 0.2311 time to fit residues: 241.1830 Evaluate side-chains 565 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 508 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 370 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 345 LYS Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 371 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 267 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN P 85 GLN G 84 HIS F 96 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 410 GLN I 55 HIS N 177 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 317 GLN L 410 GLN M 121 GLN M 204 GLN T 55 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089684 restraints weight = 48519.938| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.75 r_work: 0.2777 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.477 34536 Z= 0.267 Angle : 0.716 20.679 46932 Z= 0.339 Chirality : 0.047 0.248 5124 Planarity : 0.005 0.056 5896 Dihedral : 11.744 87.400 5113 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 3.56 % Allowed : 14.81 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.72 (0.13), residues: 4080 helix: 1.00 (0.11), residues: 2148 sheet: -0.04 (0.26), residues: 372 loop : 0.05 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.030 0.002 TYR P 66 PHE 0.023 0.002 PHE N 90 TRP 0.022 0.002 TRP N 142 HIS 0.011 0.002 HIS P 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (34514) covalent geometry : angle 0.71438 / 0.34 (46914) SS BOND : bond 0.00408 / 0.21 ( 6) SS BOND : angle 1.69943 / 0.86 ( 12) hydrogen bonds : bond 0.04742 / 3.16 ( 1907) hydrogen bonds : angle 4.89759 / 3.50 ( 5376) metal coordination : bond 0.03684 / 1.72 ( 8) metal coordination : angle 3.78077 / 1.72 ( 6) Misc. bond : bond 0.32737 / 17.80 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 489 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7815 (tttt) cc_final: 0.7484 (tttp) REVERT: C 250 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7755 (tptp) REVERT: C 287 ASP cc_start: 0.7953 (t70) cc_final: 0.7146 (m-30) REVERT: C 289 LEU cc_start: 0.8287 (tp) cc_final: 0.7871 (tp) REVERT: C 322 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8330 (m) REVERT: C 334 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 341 GLN cc_start: 0.8595 (pp30) cc_final: 0.8211 (pp30) REVERT: C 369 MET cc_start: 0.8187 (mmm) cc_final: 0.7652 (mmt) REVERT: C 372 THR cc_start: 0.8799 (m) cc_final: 0.8433 (p) REVERT: C 374 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7312 (mt-10) REVERT: P 55 ASP cc_start: 0.8258 (p0) cc_final: 0.7968 (p0) REVERT: P 100 MET cc_start: 0.5708 (mmm) cc_final: 0.5484 (ttm) REVERT: P 107 LEU cc_start: 0.7823 (mt) cc_final: 0.7600 (mt) REVERT: G 56 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7835 (mm-40) REVERT: G 108 ASP cc_start: 0.7792 (m-30) cc_final: 0.7527 (m-30) REVERT: A 59 ASP cc_start: 0.7562 (t0) cc_final: 0.7206 (t0) REVERT: A 148 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6842 (ptp-110) REVERT: A 351 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 390 LYS cc_start: 0.7765 (tptt) cc_final: 0.7523 (mtpp) REVERT: A 409 ARG cc_start: 0.7292 (tmm160) cc_final: 0.6768 (ttp80) REVERT: B 60 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8862 (t80) REVERT: B 117 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: B 168 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: B 197 ASN cc_start: 0.8305 (t0) cc_final: 0.7909 (t0) REVERT: B 323 GLN cc_start: 0.5691 (mm-40) cc_final: 0.5468 (mm110) REVERT: B 345 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7674 (ttmm) REVERT: B 357 SER cc_start: 0.7500 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 379 GLN cc_start: 0.6576 (tt0) cc_final: 0.5873 (mp10) REVERT: B 385 GLU cc_start: 0.7196 (mt-10) cc_final: 0.5958 (mm-30) REVERT: B 392 GLN cc_start: 0.7333 (mt0) cc_final: 0.7120 (mm110) REVERT: D 85 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5834 (ptm) REVERT: D 86 THR cc_start: 0.7228 (m) cc_final: 0.6947 (p) REVERT: D 154 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6806 (mt-10) REVERT: D 166 ASN cc_start: 0.7140 (m110) cc_final: 0.6675 (m-40) REVERT: D 169 LYS cc_start: 0.7566 (mmtp) cc_final: 0.7233 (mptt) REVERT: D 173 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7738 (mmmt) REVERT: D 283 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7977 (mp0) REVERT: H 57 LEU cc_start: 0.8234 (mt) cc_final: 0.7784 (tt) REVERT: H 68 TYR cc_start: 0.7739 (t80) cc_final: 0.7254 (t80) REVERT: H 88 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6740 (mm-30) REVERT: I 27 PHE cc_start: 0.8093 (t80) cc_final: 0.7573 (t80) REVERT: I 49 GLN cc_start: 0.7802 (mt0) cc_final: 0.7428 (mt0) REVERT: J 11 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6205 (ttpt) REVERT: J 13 SER cc_start: 0.7612 (t) cc_final: 0.7340 (t) REVERT: J 20 PHE cc_start: 0.8026 (t80) cc_final: 0.7797 (t80) REVERT: N 6 LYS cc_start: 0.7826 (tttt) cc_final: 0.7508 (tttp) REVERT: N 250 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7656 (tptp) REVERT: N 287 ASP cc_start: 0.7968 (t70) cc_final: 0.7297 (m-30) REVERT: N 295 MET cc_start: 0.8105 (ttp) cc_final: 0.7720 (ttp) REVERT: N 322 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8337 (m) REVERT: N 334 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8474 (mp) REVERT: N 341 GLN cc_start: 0.8603 (pp30) cc_final: 0.8347 (pp30) REVERT: N 369 MET cc_start: 0.8196 (mmm) cc_final: 0.7692 (mmt) REVERT: N 372 THR cc_start: 0.8831 (m) cc_final: 0.8460 (p) REVERT: N 374 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7310 (mt-10) REVERT: E 107 LEU cc_start: 0.7835 (mt) cc_final: 0.7611 (mt) REVERT: R 50 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: R 51 GLU cc_start: 0.8164 (mp0) cc_final: 0.7814 (mp0) REVERT: R 55 MET cc_start: 0.8452 (mmm) cc_final: 0.8173 (tpp) REVERT: R 56 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7638 (mm-40) REVERT: Q 125 GLU cc_start: 0.7297 (mp0) cc_final: 0.7026 (mp0) REVERT: L 59 ASP cc_start: 0.7516 (t0) cc_final: 0.7149 (t0) REVERT: L 138 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6327 (ttmm) REVERT: L 351 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8423 (mt) REVERT: L 390 LYS cc_start: 0.7762 (tptt) cc_final: 0.7548 (mtpp) REVERT: L 409 ARG cc_start: 0.7230 (tmm160) cc_final: 0.6743 (ttp80) REVERT: M 47 TYR cc_start: 0.8267 (m-80) cc_final: 0.8026 (m-10) REVERT: M 60 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8826 (t80) REVERT: M 117 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6635 (mt-10) REVERT: M 184 GLN cc_start: 0.7586 (mt0) cc_final: 0.7368 (mp10) REVERT: M 197 ASN cc_start: 0.8159 (t0) cc_final: 0.7529 (t0) REVERT: M 356 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.6098 (m-30) REVERT: M 379 GLN cc_start: 0.6475 (tt0) cc_final: 0.5765 (mp10) REVERT: M 406 GLN cc_start: 0.7298 (mm110) cc_final: 0.6750 (mm-40) REVERT: O 154 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6791 (mt-10) REVERT: O 166 ASN cc_start: 0.7165 (m110) cc_final: 0.6727 (m-40) REVERT: O 169 LYS cc_start: 0.7602 (mmtp) cc_final: 0.7254 (mptt) REVERT: O 173 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7763 (mmmt) REVERT: S 57 LEU cc_start: 0.8182 (mt) cc_final: 0.7756 (tt) REVERT: S 68 TYR cc_start: 0.7759 (t80) cc_final: 0.7284 (t80) REVERT: S 88 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6764 (mm-30) REVERT: T 27 PHE cc_start: 0.8100 (t80) cc_final: 0.7520 (t80) REVERT: T 49 GLN cc_start: 0.7796 (mt0) cc_final: 0.7407 (mt0) REVERT: U 11 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5885 (ttpt) REVERT: U 13 SER cc_start: 0.7540 (t) cc_final: 0.7269 (t) REVERT: U 15 LYS cc_start: 0.7899 (pttt) cc_final: 0.7415 (pttt) outliers start: 122 outliers final: 73 residues processed: 574 average time/residue: 0.2314 time to fit residues: 215.3662 Evaluate side-chains 546 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 453 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 296 VAL Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 370 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 291 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 95 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 361 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 381 optimal weight: 0.8980 chunk 387 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 96 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS A 317 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Q 97 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 317 GLN O 118 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.098420 restraints weight = 46918.186| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.62 r_work: 0.2846 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.409 34536 Z= 0.139 Angle : 0.557 12.223 46932 Z= 0.271 Chirality : 0.042 0.231 5124 Planarity : 0.004 0.049 5896 Dihedral : 11.033 89.892 5108 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Rotamer: Outliers : 2.97 % Allowed : 16.65 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.15 (0.13), residues: 4080 helix: 1.38 (0.11), residues: 2142 sheet: 0.16 (0.26), residues: 376 loop : 0.20 (0.17), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 153 TYR 0.019 0.001 TYR E 66 PHE 0.018 0.001 PHE A 334 TRP 0.016 0.001 TRP N 142 HIS 0.010 0.001 HIS Q 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (34514) covalent geometry : angle 0.55561 / 0.27 (46914) SS BOND : bond 0.00282 / 0.14 ( 6) SS BOND : angle 1.48074 / 0.75 ( 12) hydrogen bonds : bond 0.04037 / 2.64 ( 1907) hydrogen bonds : angle 4.66981 / 3.34 ( 5376) metal coordination : bond 0.01476 / 0.70 ( 8) metal coordination : angle 3.09672 / 1.48 ( 6) Misc. bond : bond 0.25596 / 14.88 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 484 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7741 (tttt) cc_final: 0.7501 (tttp) REVERT: C 74 PHE cc_start: 0.8126 (m-80) cc_final: 0.7875 (m-80) REVERT: C 250 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7700 (tptp) REVERT: C 255 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: C 287 ASP cc_start: 0.7990 (t70) cc_final: 0.7179 (m-30) REVERT: C 289 LEU cc_start: 0.8232 (tp) cc_final: 0.7811 (tp) REVERT: C 322 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8201 (m) REVERT: C 369 MET cc_start: 0.8049 (mmm) cc_final: 0.7634 (mmt) REVERT: C 372 THR cc_start: 0.8727 (m) cc_final: 0.8447 (p) REVERT: P 90 ASN cc_start: 0.8735 (p0) cc_final: 0.8500 (p0) REVERT: P 107 LEU cc_start: 0.7781 (mt) cc_final: 0.7576 (mt) REVERT: P 201 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7157 (mmm160) REVERT: G 56 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7690 (mm-40) REVERT: G 108 ASP cc_start: 0.7658 (m-30) cc_final: 0.7376 (m-30) REVERT: A 59 ASP cc_start: 0.7485 (t0) cc_final: 0.7220 (t0) REVERT: A 203 ILE cc_start: 0.8229 (pt) cc_final: 0.7946 (mp) REVERT: A 270 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 351 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 390 LYS cc_start: 0.7760 (tptt) cc_final: 0.7466 (mtpp) REVERT: A 409 ARG cc_start: 0.7197 (tmm160) cc_final: 0.6744 (ttp80) REVERT: B 60 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8958 (t80) REVERT: B 117 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: B 197 ASN cc_start: 0.8317 (t0) cc_final: 0.7865 (t0) REVERT: B 357 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7228 (p) REVERT: B 379 GLN cc_start: 0.6551 (tt0) cc_final: 0.5911 (mp10) REVERT: B 385 GLU cc_start: 0.7178 (mt-10) cc_final: 0.5930 (mm-30) REVERT: B 392 GLN cc_start: 0.7265 (mt0) cc_final: 0.7057 (mm110) REVERT: B 406 GLN cc_start: 0.7183 (mp10) cc_final: 0.6493 (mm-40) REVERT: D 86 THR cc_start: 0.7192 (m) cc_final: 0.6913 (p) REVERT: D 154 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6864 (mt-10) REVERT: D 166 ASN cc_start: 0.7120 (m110) cc_final: 0.6742 (m-40) REVERT: D 169 LYS cc_start: 0.7561 (mmtp) cc_final: 0.7176 (mptt) REVERT: D 173 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7712 (mmmt) REVERT: D 283 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7894 (mp0) REVERT: H 57 LEU cc_start: 0.8203 (mt) cc_final: 0.7763 (tt) REVERT: H 88 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6689 (mm-30) REVERT: I 27 PHE cc_start: 0.8049 (t80) cc_final: 0.7488 (t80) REVERT: I 43 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7194 (mtm110) REVERT: I 49 GLN cc_start: 0.7872 (mt0) cc_final: 0.7470 (mt0) REVERT: J 11 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6236 (ttpt) REVERT: J 13 SER cc_start: 0.7529 (t) cc_final: 0.7266 (t) REVERT: N 6 LYS cc_start: 0.7744 (tttt) cc_final: 0.7514 (tttp) REVERT: N 107 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7796 (mtpt) REVERT: N 250 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7623 (tptp) REVERT: N 287 ASP cc_start: 0.7829 (t70) cc_final: 0.7184 (m-30) REVERT: N 295 MET cc_start: 0.7927 (ttp) cc_final: 0.7512 (ttp) REVERT: N 322 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8210 (m) REVERT: N 369 MET cc_start: 0.8018 (mmm) cc_final: 0.7629 (mmt) REVERT: N 372 THR cc_start: 0.8752 (m) cc_final: 0.8455 (p) REVERT: E 90 ASN cc_start: 0.8685 (p0) cc_final: 0.8481 (p0) REVERT: E 107 LEU cc_start: 0.7739 (mt) cc_final: 0.7519 (mt) REVERT: E 201 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7157 (mmm160) REVERT: R 51 GLU cc_start: 0.8093 (mp0) cc_final: 0.7745 (mp0) REVERT: R 55 MET cc_start: 0.8319 (mmm) cc_final: 0.8025 (tpp) REVERT: R 56 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7624 (mm-40) REVERT: L 32 THR cc_start: 0.7956 (m) cc_final: 0.7510 (p) REVERT: L 59 ASP cc_start: 0.7332 (t0) cc_final: 0.7018 (t0) REVERT: L 203 ILE cc_start: 0.8191 (pt) cc_final: 0.7907 (mp) REVERT: L 351 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8421 (mt) REVERT: L 390 LYS cc_start: 0.7811 (tptt) cc_final: 0.7554 (mtpp) REVERT: L 409 ARG cc_start: 0.7224 (tmm160) cc_final: 0.6728 (ttp80) REVERT: M 60 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8787 (t80) REVERT: M 116 LYS cc_start: 0.7495 (mtpt) cc_final: 0.7144 (mtmt) REVERT: M 117 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: M 184 GLN cc_start: 0.7579 (mt0) cc_final: 0.7356 (mp10) REVERT: M 197 ASN cc_start: 0.8114 (t0) cc_final: 0.7753 (t0) REVERT: M 271 TRP cc_start: 0.7850 (m100) cc_final: 0.7446 (m100) REVERT: M 356 ASP cc_start: 0.6616 (t70) cc_final: 0.6210 (m-30) REVERT: M 379 GLN cc_start: 0.6348 (tt0) cc_final: 0.5680 (mp10) REVERT: M 406 GLN cc_start: 0.7242 (mm110) cc_final: 0.6669 (mm-40) REVERT: O 154 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6855 (mt-10) REVERT: O 166 ASN cc_start: 0.7161 (m110) cc_final: 0.6800 (m-40) REVERT: O 169 LYS cc_start: 0.7589 (mmtp) cc_final: 0.7201 (mptt) REVERT: O 173 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7734 (mmmt) REVERT: S 57 LEU cc_start: 0.8210 (mt) cc_final: 0.7792 (tt) REVERT: S 88 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6730 (mm-30) REVERT: T 27 PHE cc_start: 0.8067 (t80) cc_final: 0.7521 (t80) REVERT: T 43 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7238 (mtm110) REVERT: T 49 GLN cc_start: 0.7806 (mt0) cc_final: 0.7405 (mt0) REVERT: U 11 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5860 (ttpt) REVERT: U 13 SER cc_start: 0.7535 (t) cc_final: 0.7248 (t) REVERT: U 15 LYS cc_start: 0.7858 (pttt) cc_final: 0.7378 (pttt) outliers start: 102 outliers final: 59 residues processed: 559 average time/residue: 0.2299 time to fit residues: 208.5611 Evaluate side-chains 517 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 442 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 28 GLN Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 279 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 379 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN F 96 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091722 restraints weight = 47713.176| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.78 r_work: 0.2807 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.402 34536 Z= 0.185 Angle : 0.591 13.628 46932 Z= 0.285 Chirality : 0.043 0.160 5124 Planarity : 0.004 0.050 5896 Dihedral : 10.875 89.770 5098 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 3.62 % Allowed : 16.12 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.13 (0.13), residues: 4080 helix: 1.37 (0.11), residues: 2142 sheet: 0.11 (0.25), residues: 384 loop : 0.20 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.022 0.002 TYR P 66 PHE 0.029 0.002 PHE B 62 TRP 0.016 0.001 TRP N 142 HIS 0.006 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (34514) covalent geometry : angle 0.58849 / 0.28 (46914) SS BOND : bond 0.00364 / 0.22 ( 6) SS BOND : angle 1.70496 / 0.85 ( 12) hydrogen bonds : bond 0.04173 / 2.75 ( 1907) hydrogen bonds : angle 4.68861 / 3.35 ( 5376) metal coordination : bond 0.02517 / 1.18 ( 8) metal coordination : angle 4.03579 / 1.78 ( 6) Misc. bond : bond 0.25488 / 14.81 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 449 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7764 (tttt) cc_final: 0.7502 (tttp) REVERT: C 250 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7726 (tptp) REVERT: C 289 LEU cc_start: 0.8316 (tp) cc_final: 0.7948 (tp) REVERT: C 322 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 341 GLN cc_start: 0.8504 (pp30) cc_final: 0.8233 (pp30) REVERT: C 369 MET cc_start: 0.8168 (mmm) cc_final: 0.7814 (mmt) REVERT: C 372 THR cc_start: 0.8736 (m) cc_final: 0.8452 (p) REVERT: P 55 ASP cc_start: 0.8367 (p0) cc_final: 0.8140 (p0) REVERT: P 62 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7341 (mtm110) REVERT: P 139 ASN cc_start: 0.6869 (m-40) cc_final: 0.6523 (m-40) REVERT: P 201 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7441 (mmt90) REVERT: G 56 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7744 (mm-40) REVERT: G 108 ASP cc_start: 0.7700 (m-30) cc_final: 0.7420 (m-30) REVERT: A 59 ASP cc_start: 0.7537 (t0) cc_final: 0.7227 (t0) REVERT: A 203 ILE cc_start: 0.8253 (pt) cc_final: 0.8005 (mp) REVERT: A 390 LYS cc_start: 0.7786 (tptt) cc_final: 0.7486 (mtpp) REVERT: A 409 ARG cc_start: 0.7284 (tmm160) cc_final: 0.6758 (ttp80) REVERT: B 60 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (t80) REVERT: B 197 ASN cc_start: 0.8274 (t0) cc_final: 0.7848 (t0) REVERT: B 335 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: B 357 SER cc_start: 0.7444 (OUTLIER) cc_final: 0.7213 (p) REVERT: B 379 GLN cc_start: 0.6560 (tt0) cc_final: 0.5883 (mp10) REVERT: B 385 GLU cc_start: 0.7228 (mt-10) cc_final: 0.5974 (mm-30) REVERT: B 392 GLN cc_start: 0.7284 (mt0) cc_final: 0.7054 (mm110) REVERT: B 406 GLN cc_start: 0.7232 (mp10) cc_final: 0.6569 (mm-40) REVERT: D 85 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5552 (ttm) REVERT: D 86 THR cc_start: 0.7257 (m) cc_final: 0.7018 (p) REVERT: D 154 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6914 (mt-10) REVERT: D 166 ASN cc_start: 0.7119 (m110) cc_final: 0.6743 (m-40) REVERT: D 169 LYS cc_start: 0.7543 (mmtp) cc_final: 0.7128 (mptt) REVERT: D 173 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7705 (mmmt) REVERT: D 283 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7944 (mp0) REVERT: H 57 LEU cc_start: 0.8246 (mt) cc_final: 0.7774 (tt) REVERT: H 72 GLN cc_start: 0.7900 (mm110) cc_final: 0.7494 (pt0) REVERT: H 88 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6832 (mm-30) REVERT: I 27 PHE cc_start: 0.8106 (t80) cc_final: 0.7573 (t80) REVERT: I 43 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7191 (mtm110) REVERT: I 49 GLN cc_start: 0.7945 (mt0) cc_final: 0.7516 (mt0) REVERT: J 11 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6342 (ttpt) REVERT: J 13 SER cc_start: 0.7515 (t) cc_final: 0.7229 (t) REVERT: N 6 LYS cc_start: 0.7761 (tttt) cc_final: 0.7502 (tttp) REVERT: N 250 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7621 (tptp) REVERT: N 287 ASP cc_start: 0.7892 (t70) cc_final: 0.7188 (m-30) REVERT: N 295 MET cc_start: 0.7994 (ttp) cc_final: 0.7642 (ttp) REVERT: N 322 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8354 (m) REVERT: N 341 GLN cc_start: 0.8458 (pp30) cc_final: 0.8202 (pp30) REVERT: N 369 MET cc_start: 0.8117 (mmm) cc_final: 0.7782 (mmt) REVERT: N 372 THR cc_start: 0.8762 (m) cc_final: 0.8470 (p) REVERT: N 374 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7354 (mt-10) REVERT: E 90 ASN cc_start: 0.8745 (p0) cc_final: 0.8519 (p0) REVERT: E 139 ASN cc_start: 0.6862 (m-40) cc_final: 0.6513 (m-40) REVERT: E 201 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7460 (mmt90) REVERT: R 50 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6434 (pt0) REVERT: R 51 GLU cc_start: 0.8103 (mp0) cc_final: 0.7763 (mp0) REVERT: R 55 MET cc_start: 0.8443 (mmm) cc_final: 0.8165 (tpp) REVERT: R 56 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7774 (mm-40) REVERT: L 59 ASP cc_start: 0.7468 (t0) cc_final: 0.7182 (t0) REVERT: L 203 ILE cc_start: 0.8257 (pt) cc_final: 0.7975 (mp) REVERT: L 390 LYS cc_start: 0.7802 (tptt) cc_final: 0.7526 (mtpp) REVERT: L 409 ARG cc_start: 0.7244 (tmm160) cc_final: 0.6682 (ttp80) REVERT: M 60 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8848 (t80) REVERT: M 117 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: M 184 GLN cc_start: 0.7557 (mt0) cc_final: 0.7346 (mp10) REVERT: M 197 ASN cc_start: 0.8157 (t0) cc_final: 0.7877 (t0) REVERT: M 271 TRP cc_start: 0.7830 (m100) cc_final: 0.7455 (m100) REVERT: M 356 ASP cc_start: 0.6689 (t70) cc_final: 0.6265 (m-30) REVERT: M 357 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.7029 (p) REVERT: M 379 GLN cc_start: 0.6437 (tt0) cc_final: 0.5751 (mp10) REVERT: M 406 GLN cc_start: 0.7298 (mm110) cc_final: 0.6716 (mm-40) REVERT: O 154 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6882 (mt-10) REVERT: O 166 ASN cc_start: 0.7125 (m110) cc_final: 0.6755 (m-40) REVERT: O 169 LYS cc_start: 0.7542 (mmtp) cc_final: 0.7118 (mptt) REVERT: O 173 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7688 (mmmt) REVERT: S 57 LEU cc_start: 0.8290 (mt) cc_final: 0.7830 (tt) REVERT: S 72 GLN cc_start: 0.7861 (mm110) cc_final: 0.7470 (pt0) REVERT: S 88 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6850 (mm-30) REVERT: T 27 PHE cc_start: 0.8113 (t80) cc_final: 0.7593 (t80) REVERT: T 42 ASP cc_start: 0.7823 (t70) cc_final: 0.7591 (t70) REVERT: T 43 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7227 (mtm110) REVERT: T 49 GLN cc_start: 0.7927 (mt0) cc_final: 0.7488 (mt0) REVERT: U 13 SER cc_start: 0.7526 (t) cc_final: 0.7225 (t) REVERT: U 15 LYS cc_start: 0.7829 (pttt) cc_final: 0.7311 (pttt) REVERT: U 57 ARG cc_start: 0.6689 (mtt-85) cc_final: 0.6361 (mtt-85) outliers start: 124 outliers final: 85 residues processed: 541 average time/residue: 0.2277 time to fit residues: 201.5435 Evaluate side-chains 539 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 439 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 104 GLU Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 203 THR Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 296 VAL Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 370 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain U residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 340 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 251 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 196 optimal weight: 0.0570 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN F 96 HIS A 135 GLN A 317 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN L 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094306 restraints weight = 47746.019| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.83 r_work: 0.2846 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.382 34536 Z= 0.117 Angle : 0.534 14.934 46932 Z= 0.256 Chirality : 0.041 0.157 5124 Planarity : 0.004 0.051 5896 Dihedral : 10.399 89.083 5098 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 2.68 % Allowed : 17.26 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.13), residues: 4080 helix: 1.64 (0.11), residues: 2144 sheet: 0.25 (0.26), residues: 374 loop : 0.33 (0.17), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 148 TYR 0.023 0.001 TYR M 47 PHE 0.022 0.001 PHE B 62 TRP 0.021 0.001 TRP B 271 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (34514) covalent geometry : angle 0.53327 / 0.26 (46914) SS BOND : bond 0.00244 / 0.12 ( 6) SS BOND : angle 1.55045 / 0.77 ( 12) hydrogen bonds : bond 0.03764 / 2.44 ( 1907) hydrogen bonds : angle 4.54094 / 3.24 ( 5376) metal coordination : bond 0.01021 / 0.47 ( 8) metal coordination : angle 2.38547 / 1.14 ( 6) Misc. bond : bond 0.25037 / 14.37 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 476 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7691 (tttt) cc_final: 0.7466 (tttp) REVERT: C 250 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7688 (tptp) REVERT: C 287 ASP cc_start: 0.7994 (t70) cc_final: 0.7164 (m-30) REVERT: C 289 LEU cc_start: 0.8321 (tp) cc_final: 0.7928 (tp) REVERT: C 322 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8270 (m) REVERT: C 369 MET cc_start: 0.8159 (mmm) cc_final: 0.7696 (mmt) REVERT: C 372 THR cc_start: 0.8693 (m) cc_final: 0.8484 (p) REVERT: P 67 PHE cc_start: 0.8283 (t80) cc_final: 0.8027 (t80) REVERT: P 71 SER cc_start: 0.8880 (m) cc_final: 0.8659 (t) REVERT: P 92 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8652 (p) REVERT: P 139 ASN cc_start: 0.6947 (m-40) cc_final: 0.6603 (m-40) REVERT: P 201 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7080 (mmm160) REVERT: G 21 SER cc_start: 0.8136 (t) cc_final: 0.7193 (m) REVERT: G 56 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7714 (mm-40) REVERT: G 65 THR cc_start: 0.8412 (m) cc_final: 0.8109 (p) REVERT: G 108 ASP cc_start: 0.7645 (m-30) cc_final: 0.7362 (m-30) REVERT: A 32 THR cc_start: 0.7862 (m) cc_final: 0.7314 (p) REVERT: A 59 ASP cc_start: 0.7376 (t0) cc_final: 0.7148 (t0) REVERT: A 148 ARG cc_start: 0.6951 (ttm110) cc_final: 0.6658 (ttm110) REVERT: A 203 ILE cc_start: 0.8214 (pt) cc_final: 0.7997 (mp) REVERT: A 351 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 390 LYS cc_start: 0.7766 (tptt) cc_final: 0.7466 (mtpp) REVERT: A 409 ARG cc_start: 0.7201 (tmm160) cc_final: 0.6754 (ttp80) REVERT: B 58 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: B 168 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: B 197 ASN cc_start: 0.8304 (t0) cc_final: 0.7895 (t0) REVERT: B 357 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 379 GLN cc_start: 0.6468 (tt0) cc_final: 0.5847 (mp10) REVERT: B 385 GLU cc_start: 0.7197 (mt-10) cc_final: 0.5939 (mm-30) REVERT: B 392 GLN cc_start: 0.7306 (mt0) cc_final: 0.7034 (mm110) REVERT: B 406 GLN cc_start: 0.7209 (mp10) cc_final: 0.6526 (mm-40) REVERT: D 154 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6989 (mt-10) REVERT: D 166 ASN cc_start: 0.7140 (m110) cc_final: 0.6780 (m-40) REVERT: D 169 LYS cc_start: 0.7527 (mmtp) cc_final: 0.7155 (mptt) REVERT: D 173 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7751 (mmmt) REVERT: D 283 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7924 (mp0) REVERT: H 57 LEU cc_start: 0.8283 (mt) cc_final: 0.7811 (tt) REVERT: H 72 GLN cc_start: 0.7838 (mm110) cc_final: 0.7529 (pt0) REVERT: H 88 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6828 (mm-30) REVERT: I 14 ARG cc_start: 0.8358 (mtt90) cc_final: 0.8148 (mtt-85) REVERT: I 27 PHE cc_start: 0.8070 (t80) cc_final: 0.7551 (t80) REVERT: I 43 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7190 (mtm110) REVERT: I 49 GLN cc_start: 0.7950 (mt0) cc_final: 0.7553 (mt0) REVERT: N 6 LYS cc_start: 0.7736 (tttt) cc_final: 0.7497 (tttp) REVERT: N 107 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7747 (mtpt) REVERT: N 217 ASP cc_start: 0.7159 (t0) cc_final: 0.6854 (t70) REVERT: N 250 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7597 (tptp) REVERT: N 287 ASP cc_start: 0.7987 (t70) cc_final: 0.7304 (m-30) REVERT: N 322 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8280 (m) REVERT: N 369 MET cc_start: 0.8083 (mmm) cc_final: 0.7674 (mmt) REVERT: N 372 THR cc_start: 0.8713 (m) cc_final: 0.8475 (p) REVERT: E 74 MET cc_start: 0.8324 (ttp) cc_final: 0.8001 (ttp) REVERT: E 86 ASP cc_start: 0.8417 (m-30) cc_final: 0.8181 (m-30) REVERT: E 90 ASN cc_start: 0.8642 (p0) cc_final: 0.8440 (p0) REVERT: E 139 ASN cc_start: 0.6941 (m-40) cc_final: 0.6603 (m-40) REVERT: E 201 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7095 (mmm160) REVERT: R 21 SER cc_start: 0.8131 (t) cc_final: 0.7215 (m) REVERT: R 50 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6448 (pt0) REVERT: R 51 GLU cc_start: 0.8019 (mp0) cc_final: 0.7729 (mp0) REVERT: R 55 MET cc_start: 0.8380 (mmm) cc_final: 0.8138 (tpp) REVERT: R 56 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7729 (mm-40) REVERT: L 32 THR cc_start: 0.7936 (m) cc_final: 0.7425 (p) REVERT: L 59 ASP cc_start: 0.7413 (t0) cc_final: 0.7113 (t0) REVERT: L 203 ILE cc_start: 0.8175 (pt) cc_final: 0.7944 (mp) REVERT: L 390 LYS cc_start: 0.7781 (tptt) cc_final: 0.7490 (mtpp) REVERT: L 409 ARG cc_start: 0.7232 (tmm160) cc_final: 0.6734 (ttp80) REVERT: M 60 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8818 (t80) REVERT: M 184 GLN cc_start: 0.7559 (mt0) cc_final: 0.7358 (mp10) REVERT: M 197 ASN cc_start: 0.8101 (t0) cc_final: 0.7855 (t0) REVERT: M 198 VAL cc_start: 0.8723 (t) cc_final: 0.8463 (p) REVERT: M 271 TRP cc_start: 0.7785 (m100) cc_final: 0.7391 (m100) REVERT: M 356 ASP cc_start: 0.6635 (t70) cc_final: 0.6291 (m-30) REVERT: M 357 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6980 (p) REVERT: M 379 GLN cc_start: 0.6338 (tt0) cc_final: 0.5793 (pm20) REVERT: M 406 GLN cc_start: 0.7304 (mm110) cc_final: 0.6722 (mm-40) REVERT: O 154 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6973 (mt-10) REVERT: O 166 ASN cc_start: 0.7150 (m110) cc_final: 0.6793 (m-40) REVERT: O 169 LYS cc_start: 0.7496 (mmtp) cc_final: 0.7097 (mptt) REVERT: O 173 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7769 (mmmt) REVERT: S 57 LEU cc_start: 0.8288 (mt) cc_final: 0.7804 (tt) REVERT: S 72 GLN cc_start: 0.7783 (mm110) cc_final: 0.7502 (pt0) REVERT: S 88 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6853 (mm-30) REVERT: T 27 PHE cc_start: 0.8090 (t80) cc_final: 0.7561 (t80) REVERT: T 43 ARG cc_start: 0.7403 (mtm-85) cc_final: 0.7155 (mtm110) REVERT: T 49 GLN cc_start: 0.7909 (mt0) cc_final: 0.7519 (mt0) REVERT: U 15 LYS cc_start: 0.7828 (pttt) cc_final: 0.7329 (pttt) REVERT: U 57 ARG cc_start: 0.6695 (mtt-85) cc_final: 0.6414 (mtt-85) outliers start: 92 outliers final: 58 residues processed: 544 average time/residue: 0.2188 time to fit residues: 194.4466 Evaluate side-chains 523 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 203 THR Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 230 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 233 optimal weight: 10.0000 chunk 384 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 383 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN A 135 GLN B 241 ASN D 118 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN L 64 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 118 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094753 restraints weight = 47479.682| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.76 r_work: 0.2856 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.372 34536 Z= 0.128 Angle : 0.535 12.120 46932 Z= 0.259 Chirality : 0.041 0.149 5124 Planarity : 0.004 0.050 5896 Dihedral : 10.205 89.352 5092 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 17.49 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.50 (0.13), residues: 4080 helix: 1.65 (0.11), residues: 2158 sheet: 0.23 (0.26), residues: 380 loop : 0.39 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 148 TYR 0.027 0.001 TYR B 47 PHE 0.020 0.001 PHE B 62 TRP 0.021 0.001 TRP B 271 HIS 0.006 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (34514) covalent geometry : angle 0.53326 / 0.26 (46914) SS BOND : bond 0.00200 / 0.10 ( 6) SS BOND : angle 1.29482 / 0.65 ( 12) hydrogen bonds : bond 0.03786 / 2.47 ( 1907) hydrogen bonds : angle 4.50909 / 3.22 ( 5376) metal coordination : bond 0.01482 / 0.70 ( 8) metal coordination : angle 2.88774 / 1.30 ( 6) Misc. bond : bond 0.22732 / 13.47 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 470 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7669 (tttt) cc_final: 0.7438 (tttp) REVERT: C 250 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7685 (tptp) REVERT: C 287 ASP cc_start: 0.7985 (t70) cc_final: 0.7145 (m-30) REVERT: C 289 LEU cc_start: 0.8317 (tp) cc_final: 0.7931 (tp) REVERT: C 322 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 369 MET cc_start: 0.8146 (mmm) cc_final: 0.7667 (mmt) REVERT: C 372 THR cc_start: 0.8691 (m) cc_final: 0.8471 (p) REVERT: P 67 PHE cc_start: 0.8250 (t80) cc_final: 0.7951 (t80) REVERT: P 71 SER cc_start: 0.8869 (m) cc_final: 0.8609 (t) REVERT: P 139 ASN cc_start: 0.7059 (m-40) cc_final: 0.6746 (m-40) REVERT: P 201 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7068 (mmm160) REVERT: G 55 MET cc_start: 0.8440 (tpp) cc_final: 0.8181 (tpp) REVERT: G 56 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7683 (mm-40) REVERT: G 65 THR cc_start: 0.8380 (m) cc_final: 0.8089 (p) REVERT: G 108 ASP cc_start: 0.7652 (m-30) cc_final: 0.7379 (m-30) REVERT: A 32 THR cc_start: 0.7827 (m) cc_final: 0.7274 (p) REVERT: A 59 ASP cc_start: 0.7308 (t0) cc_final: 0.7075 (t0) REVERT: A 148 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6227 (ttm-80) REVERT: A 203 ILE cc_start: 0.8176 (pt) cc_final: 0.7971 (mp) REVERT: A 390 LYS cc_start: 0.7752 (tptt) cc_final: 0.7460 (mtpt) REVERT: B 58 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: B 197 ASN cc_start: 0.8279 (t0) cc_final: 0.7870 (t0) REVERT: B 335 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: B 357 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7038 (t) REVERT: B 379 GLN cc_start: 0.6493 (tt0) cc_final: 0.5857 (mp10) REVERT: B 385 GLU cc_start: 0.7198 (mt-10) cc_final: 0.5931 (mm-30) REVERT: B 392 GLN cc_start: 0.7305 (mt0) cc_final: 0.7012 (mm110) REVERT: B 406 GLN cc_start: 0.7118 (mp10) cc_final: 0.6778 (mp10) REVERT: D 154 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7026 (mt-10) REVERT: D 166 ASN cc_start: 0.7115 (m110) cc_final: 0.6765 (m-40) REVERT: D 169 LYS cc_start: 0.7516 (mmtp) cc_final: 0.7210 (mptt) REVERT: D 173 LYS cc_start: 0.8413 (mtmt) cc_final: 0.7730 (mmmt) REVERT: D 283 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7935 (mp0) REVERT: H 27 TYR cc_start: 0.9147 (m-80) cc_final: 0.8895 (m-80) REVERT: H 57 LEU cc_start: 0.8284 (mt) cc_final: 0.7793 (tt) REVERT: H 72 GLN cc_start: 0.7827 (mm110) cc_final: 0.7523 (pt0) REVERT: H 88 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6817 (mm-30) REVERT: I 14 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8128 (mtt-85) REVERT: I 27 PHE cc_start: 0.8052 (t80) cc_final: 0.7541 (t80) REVERT: I 43 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7173 (mtm110) REVERT: I 49 GLN cc_start: 0.7933 (mt0) cc_final: 0.7567 (mt0) REVERT: N 217 ASP cc_start: 0.7137 (t0) cc_final: 0.6853 (t70) REVERT: N 250 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7589 (tptp) REVERT: N 322 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8254 (m) REVERT: N 369 MET cc_start: 0.8038 (mmm) cc_final: 0.7585 (mmt) REVERT: N 372 THR cc_start: 0.8725 (m) cc_final: 0.8499 (p) REVERT: E 74 MET cc_start: 0.8300 (ttp) cc_final: 0.7958 (ttp) REVERT: E 86 ASP cc_start: 0.8352 (m-30) cc_final: 0.8127 (m-30) REVERT: E 139 ASN cc_start: 0.7058 (m-40) cc_final: 0.6743 (m-40) REVERT: E 201 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7058 (mmm160) REVERT: R 21 SER cc_start: 0.8161 (t) cc_final: 0.7229 (m) REVERT: R 51 GLU cc_start: 0.8041 (mp0) cc_final: 0.7735 (mp0) REVERT: R 55 MET cc_start: 0.8349 (mmm) cc_final: 0.8085 (tpp) REVERT: R 56 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7644 (mm-40) REVERT: L 32 THR cc_start: 0.7922 (m) cc_final: 0.7412 (p) REVERT: L 59 ASP cc_start: 0.7372 (t0) cc_final: 0.7063 (t0) REVERT: L 203 ILE cc_start: 0.8155 (pt) cc_final: 0.7949 (mp) REVERT: L 390 LYS cc_start: 0.7788 (tptt) cc_final: 0.7490 (mtpt) REVERT: L 409 ARG cc_start: 0.7217 (tmm160) cc_final: 0.6714 (ttp80) REVERT: M 60 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8793 (t80) REVERT: M 95 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (mt) REVERT: M 116 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7426 (mtmt) REVERT: M 197 ASN cc_start: 0.8077 (t0) cc_final: 0.7794 (t0) REVERT: M 198 VAL cc_start: 0.8697 (t) cc_final: 0.8459 (p) REVERT: M 271 TRP cc_start: 0.7777 (m100) cc_final: 0.7447 (m100) REVERT: M 356 ASP cc_start: 0.6545 (t70) cc_final: 0.6308 (m-30) REVERT: M 357 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6945 (p) REVERT: M 379 GLN cc_start: 0.6387 (tt0) cc_final: 0.5858 (pm20) REVERT: M 392 GLN cc_start: 0.6891 (mm110) cc_final: 0.6475 (mm110) REVERT: M 406 GLN cc_start: 0.7247 (mm110) cc_final: 0.6666 (mm-40) REVERT: O 154 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6967 (mt-10) REVERT: O 166 ASN cc_start: 0.7134 (m110) cc_final: 0.6791 (m-40) REVERT: O 169 LYS cc_start: 0.7498 (mmtp) cc_final: 0.7190 (mptt) REVERT: O 173 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7734 (mmmt) REVERT: S 57 LEU cc_start: 0.8276 (mt) cc_final: 0.7790 (tt) REVERT: S 72 GLN cc_start: 0.7776 (mm110) cc_final: 0.7491 (pt0) REVERT: S 88 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6846 (mm-30) REVERT: T 27 PHE cc_start: 0.8067 (t80) cc_final: 0.7566 (t80) REVERT: T 43 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7183 (mtm110) REVERT: T 49 GLN cc_start: 0.7906 (mt0) cc_final: 0.7537 (mt0) REVERT: U 15 LYS cc_start: 0.7818 (pttt) cc_final: 0.7316 (pttt) REVERT: U 57 ARG cc_start: 0.6628 (mtt-85) cc_final: 0.6330 (mtt-85) outliers start: 83 outliers final: 61 residues processed: 533 average time/residue: 0.2202 time to fit residues: 191.3785 Evaluate side-chains 524 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 453 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 203 THR Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 173 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 chunk 334 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 253 HIS P 115 ASN F 96 HIS A 135 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN L 64 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093930 restraints weight = 47566.758| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.76 r_work: 0.2847 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.375 34536 Z= 0.152 Angle : 0.553 12.930 46932 Z= 0.269 Chirality : 0.042 0.150 5124 Planarity : 0.004 0.049 5896 Dihedral : 10.221 89.831 5088 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 17.87 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.13), residues: 4080 helix: 1.64 (0.11), residues: 2148 sheet: 0.32 (0.26), residues: 374 loop : 0.37 (0.17), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 409 TYR 0.029 0.002 TYR B 47 PHE 0.020 0.001 PHE B 62 TRP 0.024 0.001 TRP B 271 HIS 0.005 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (34514) covalent geometry : angle 0.55149 / 0.27 (46914) SS BOND : bond 0.00261 / 0.14 ( 6) SS BOND : angle 1.25304 / 0.63 ( 12) hydrogen bonds : bond 0.03897 / 2.55 ( 1907) hydrogen bonds : angle 4.54478 / 3.25 ( 5376) metal coordination : bond 0.01842 / 0.87 ( 8) metal coordination : angle 3.12812 / 1.41 ( 6) Misc. bond : bond 0.21111 / 12.89 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 458 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7680 (tttt) cc_final: 0.7458 (tttp) REVERT: C 250 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7684 (tptp) REVERT: C 289 LEU cc_start: 0.8329 (tp) cc_final: 0.7964 (tp) REVERT: C 322 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8254 (m) REVERT: C 369 MET cc_start: 0.8159 (mmm) cc_final: 0.7663 (mmt) REVERT: C 372 THR cc_start: 0.8700 (m) cc_final: 0.8457 (p) REVERT: P 42 THR cc_start: 0.8919 (m) cc_final: 0.8683 (t) REVERT: P 67 PHE cc_start: 0.8291 (t80) cc_final: 0.7978 (t80) REVERT: P 71 SER cc_start: 0.8858 (m) cc_final: 0.8623 (t) REVERT: P 201 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7355 (mmt90) REVERT: G 56 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7655 (mm-40) REVERT: G 108 ASP cc_start: 0.7683 (m-30) cc_final: 0.7411 (m-30) REVERT: A 32 THR cc_start: 0.7818 (m) cc_final: 0.7278 (p) REVERT: A 59 ASP cc_start: 0.7314 (t0) cc_final: 0.7095 (t0) REVERT: A 145 ASP cc_start: 0.7810 (m-30) cc_final: 0.7348 (m-30) REVERT: A 148 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6295 (ttm-80) REVERT: A 390 LYS cc_start: 0.7728 (tptt) cc_final: 0.7427 (mtpt) REVERT: A 409 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7538 (ttp80) REVERT: B 58 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: B 168 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: B 197 ASN cc_start: 0.8303 (t0) cc_final: 0.7915 (t0) REVERT: B 335 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6369 (mm-30) REVERT: B 357 SER cc_start: 0.7425 (OUTLIER) cc_final: 0.7039 (t) REVERT: B 379 GLN cc_start: 0.6527 (tt0) cc_final: 0.5875 (mp10) REVERT: B 385 GLU cc_start: 0.7229 (mt-10) cc_final: 0.5986 (mm-30) REVERT: B 392 GLN cc_start: 0.7325 (mt0) cc_final: 0.7030 (mm110) REVERT: B 406 GLN cc_start: 0.7165 (mp10) cc_final: 0.6534 (mm-40) REVERT: D 154 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7024 (mt-10) REVERT: D 166 ASN cc_start: 0.7082 (m110) cc_final: 0.6747 (m-40) REVERT: D 169 LYS cc_start: 0.7464 (mmtp) cc_final: 0.7208 (mmtm) REVERT: D 173 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7705 (mmmt) REVERT: D 283 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7933 (mp0) REVERT: H 57 LEU cc_start: 0.8285 (mt) cc_final: 0.7800 (tt) REVERT: H 72 GLN cc_start: 0.7822 (mm110) cc_final: 0.7503 (pt0) REVERT: H 88 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6850 (mm-30) REVERT: I 27 PHE cc_start: 0.8075 (t80) cc_final: 0.7563 (t80) REVERT: I 43 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7233 (mtm110) REVERT: I 49 GLN cc_start: 0.7962 (mt0) cc_final: 0.7596 (mt0) REVERT: N 217 ASP cc_start: 0.7195 (t0) cc_final: 0.6905 (t70) REVERT: N 250 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7597 (tptp) REVERT: N 322 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8255 (m) REVERT: N 369 MET cc_start: 0.8054 (mmm) cc_final: 0.7735 (mmt) REVERT: N 372 THR cc_start: 0.8737 (m) cc_final: 0.8489 (p) REVERT: E 67 PHE cc_start: 0.8331 (t80) cc_final: 0.8040 (t80) REVERT: E 74 MET cc_start: 0.8311 (ttp) cc_final: 0.7969 (ttp) REVERT: E 86 ASP cc_start: 0.8367 (m-30) cc_final: 0.8132 (m-30) REVERT: E 201 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7321 (mmt90) REVERT: R 21 SER cc_start: 0.8165 (t) cc_final: 0.7223 (m) REVERT: R 51 GLU cc_start: 0.8026 (mp0) cc_final: 0.7750 (mp0) REVERT: R 55 MET cc_start: 0.8387 (mmm) cc_final: 0.8114 (tpp) REVERT: R 56 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7654 (mm-40) REVERT: L 32 THR cc_start: 0.7890 (m) cc_final: 0.7393 (p) REVERT: L 59 ASP cc_start: 0.7344 (t0) cc_final: 0.7035 (t0) REVERT: L 221 ASP cc_start: 0.5024 (t70) cc_final: 0.4823 (t70) REVERT: L 390 LYS cc_start: 0.7765 (tptt) cc_final: 0.7476 (mtpt) REVERT: L 409 ARG cc_start: 0.7248 (tmm160) cc_final: 0.6719 (ttp80) REVERT: M 60 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8803 (t80) REVERT: M 95 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8494 (mt) REVERT: M 197 ASN cc_start: 0.8087 (t0) cc_final: 0.7811 (t0) REVERT: M 198 VAL cc_start: 0.8691 (t) cc_final: 0.8455 (p) REVERT: M 271 TRP cc_start: 0.7775 (m100) cc_final: 0.7437 (m100) REVERT: M 356 ASP cc_start: 0.6504 (t70) cc_final: 0.6287 (m-30) REVERT: M 357 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.6956 (p) REVERT: M 379 GLN cc_start: 0.6452 (tt0) cc_final: 0.5921 (pm20) REVERT: M 406 GLN cc_start: 0.7249 (mm110) cc_final: 0.6685 (mm-40) REVERT: O 154 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7021 (mt-10) REVERT: O 166 ASN cc_start: 0.7101 (m110) cc_final: 0.6755 (m-40) REVERT: O 169 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7211 (mmtm) REVERT: O 173 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7734 (mmmt) REVERT: S 57 LEU cc_start: 0.8273 (mt) cc_final: 0.7796 (tt) REVERT: S 72 GLN cc_start: 0.7765 (mm110) cc_final: 0.7458 (pt0) REVERT: S 88 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6909 (mm-30) REVERT: T 27 PHE cc_start: 0.8085 (t80) cc_final: 0.7605 (t80) REVERT: T 43 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7216 (mtm110) REVERT: T 49 GLN cc_start: 0.7943 (mt0) cc_final: 0.7563 (mt0) REVERT: U 15 LYS cc_start: 0.7837 (pttt) cc_final: 0.7334 (pttt) outliers start: 81 outliers final: 65 residues processed: 523 average time/residue: 0.2010 time to fit residues: 171.9434 Evaluate side-chains 520 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 444 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 203 THR Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 279 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 270 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN B 205 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093825 restraints weight = 47748.970| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.65 r_work: 0.2881 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.389 34536 Z= 0.185 Angle : 0.594 13.494 46932 Z= 0.288 Chirality : 0.043 0.161 5124 Planarity : 0.004 0.049 5896 Dihedral : 10.394 89.397 5088 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 2.45 % Allowed : 17.96 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.31 (0.13), residues: 4080 helix: 1.48 (0.11), residues: 2150 sheet: 0.31 (0.26), residues: 378 loop : 0.31 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.031 0.002 TYR M 47 PHE 0.021 0.002 PHE B 62 TRP 0.026 0.001 TRP B 271 HIS 0.007 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (34514) covalent geometry : angle 0.59168 / 0.29 (46914) SS BOND : bond 0.00349 / 0.18 ( 6) SS BOND : angle 1.24792 / 0.63 ( 12) hydrogen bonds : bond 0.04096 / 2.70 ( 1907) hydrogen bonds : angle 4.66201 / 3.34 ( 5376) metal coordination : bond 0.02518 / 1.19 ( 8) metal coordination : angle 4.21179 / 1.88 ( 6) Misc. bond : bond 0.22460 / 13.59 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 452 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.7759 (tttt) cc_final: 0.7549 (tttp) REVERT: C 250 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7728 (tptp) REVERT: C 289 LEU cc_start: 0.8336 (tp) cc_final: 0.8047 (tp) REVERT: C 369 MET cc_start: 0.8184 (mmm) cc_final: 0.7711 (mmt) REVERT: C 372 THR cc_start: 0.8761 (m) cc_final: 0.8506 (p) REVERT: P 42 THR cc_start: 0.8912 (m) cc_final: 0.8703 (t) REVERT: P 67 PHE cc_start: 0.8291 (t80) cc_final: 0.7933 (t80) REVERT: P 201 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7338 (mmt90) REVERT: G 55 MET cc_start: 0.8458 (tpp) cc_final: 0.8233 (tpp) REVERT: G 56 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7696 (mm-40) REVERT: G 108 ASP cc_start: 0.7698 (m-30) cc_final: 0.7420 (m-30) REVERT: A 32 THR cc_start: 0.7802 (m) cc_final: 0.7262 (p) REVERT: A 59 ASP cc_start: 0.7273 (t0) cc_final: 0.7050 (t0) REVERT: A 148 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6815 (ttm110) REVERT: A 351 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 390 LYS cc_start: 0.7758 (tptt) cc_final: 0.7453 (mtpp) REVERT: A 409 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7666 (ttp80) REVERT: B 168 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: B 197 ASN cc_start: 0.8331 (t0) cc_final: 0.7954 (t0) REVERT: B 335 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6414 (mm-30) REVERT: B 357 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7053 (t) REVERT: B 379 GLN cc_start: 0.6535 (tt0) cc_final: 0.5963 (mp10) REVERT: B 385 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6002 (mm-30) REVERT: B 392 GLN cc_start: 0.7368 (mt0) cc_final: 0.7116 (mm110) REVERT: D 154 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7020 (mt-10) REVERT: D 166 ASN cc_start: 0.7087 (m110) cc_final: 0.6770 (m-40) REVERT: D 173 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7785 (mmmt) REVERT: D 283 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7938 (mp0) REVERT: H 57 LEU cc_start: 0.8314 (mt) cc_final: 0.7893 (tt) REVERT: H 72 GLN cc_start: 0.7893 (mm110) cc_final: 0.7604 (pt0) REVERT: H 88 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6930 (mm-30) REVERT: I 27 PHE cc_start: 0.8124 (t80) cc_final: 0.7575 (t80) REVERT: I 43 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7234 (mtm110) REVERT: I 49 GLN cc_start: 0.7910 (mt0) cc_final: 0.7612 (mt0) REVERT: N 217 ASP cc_start: 0.7092 (t0) cc_final: 0.6803 (t70) REVERT: N 250 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7704 (tptp) REVERT: N 295 MET cc_start: 0.8035 (ttp) cc_final: 0.7599 (ttp) REVERT: N 369 MET cc_start: 0.8053 (mmm) cc_final: 0.7595 (mmt) REVERT: N 372 THR cc_start: 0.8793 (m) cc_final: 0.8523 (p) REVERT: E 67 PHE cc_start: 0.8336 (t80) cc_final: 0.7990 (t80) REVERT: E 86 ASP cc_start: 0.8420 (m-30) cc_final: 0.8205 (m-30) REVERT: E 201 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7323 (mmt90) REVERT: R 51 GLU cc_start: 0.7980 (mp0) cc_final: 0.7707 (mp0) REVERT: R 55 MET cc_start: 0.8390 (mmm) cc_final: 0.8137 (tpp) REVERT: L 32 THR cc_start: 0.7843 (m) cc_final: 0.7320 (p) REVERT: L 59 ASP cc_start: 0.7311 (t0) cc_final: 0.7058 (t0) REVERT: L 390 LYS cc_start: 0.7890 (tptt) cc_final: 0.7548 (mtpt) REVERT: L 409 ARG cc_start: 0.7328 (tmm160) cc_final: 0.6819 (ttp80) REVERT: M 60 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8843 (t80) REVERT: M 95 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8535 (mt) REVERT: M 197 ASN cc_start: 0.8127 (t0) cc_final: 0.7863 (t0) REVERT: M 198 VAL cc_start: 0.8727 (t) cc_final: 0.8511 (p) REVERT: M 271 TRP cc_start: 0.7763 (m100) cc_final: 0.7456 (m100) REVERT: M 356 ASP cc_start: 0.6495 (t70) cc_final: 0.6104 (m-30) REVERT: M 357 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.7005 (p) REVERT: M 379 GLN cc_start: 0.6535 (tt0) cc_final: 0.6029 (pm20) REVERT: M 406 GLN cc_start: 0.7209 (mm110) cc_final: 0.6681 (mm-40) REVERT: O 154 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7016 (mt-10) REVERT: O 166 ASN cc_start: 0.7097 (m110) cc_final: 0.6785 (m-40) REVERT: O 169 LYS cc_start: 0.7438 (mmtp) cc_final: 0.7229 (mptt) REVERT: O 173 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7809 (mmmt) REVERT: S 57 LEU cc_start: 0.8305 (mt) cc_final: 0.7880 (tt) REVERT: S 72 GLN cc_start: 0.7858 (mm110) cc_final: 0.7574 (pt0) REVERT: S 88 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6933 (mm-30) REVERT: T 27 PHE cc_start: 0.8131 (t80) cc_final: 0.7573 (t80) REVERT: T 43 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7300 (mtm110) REVERT: T 49 GLN cc_start: 0.7877 (mt0) cc_final: 0.7589 (mt0) REVERT: U 15 LYS cc_start: 0.7853 (pttt) cc_final: 0.7391 (pttt) REVERT: U 20 PHE cc_start: 0.7970 (t80) cc_final: 0.7761 (t80) outliers start: 84 outliers final: 63 residues processed: 517 average time/residue: 0.2123 time to fit residues: 179.0554 Evaluate side-chains 504 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 203 THR Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain L residue 119 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 261 ASP Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 237 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 391 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094326 restraints weight = 47729.161| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.66 r_work: 0.2855 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.389 34536 Z= 0.160 Angle : 0.570 13.340 46932 Z= 0.277 Chirality : 0.042 0.153 5124 Planarity : 0.004 0.049 5896 Dihedral : 10.291 89.561 5088 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Rotamer: Outliers : 2.36 % Allowed : 18.08 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.36 (0.13), residues: 4080 helix: 1.54 (0.11), residues: 2148 sheet: 0.29 (0.26), residues: 378 loop : 0.31 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.028 0.002 TYR M 47 PHE 0.033 0.002 PHE N 74 TRP 0.030 0.001 TRP B 271 HIS 0.007 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (34514) covalent geometry : angle 0.56803 / 0.28 (46914) SS BOND : bond 0.00267 / 0.14 ( 6) SS BOND : angle 1.22169 / 0.62 ( 12) hydrogen bonds : bond 0.03986 / 2.61 ( 1907) hydrogen bonds : angle 4.61583 / 3.30 ( 5376) metal coordination : bond 0.01949 / 0.92 ( 8) metal coordination : angle 3.47833 / 1.58 ( 6) Misc. bond : bond 0.22792 / 13.69 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8811.39 seconds wall clock time: 152 minutes 5.18 seconds (9125.18 seconds total)