Starting phenix.real_space_refine on Mon Jul 6 07:45:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abh_15321/07_2026/8abh_15321.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21039 2.51 5 N 5300 2.21 5 O 6069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32548 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 300 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 129 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "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: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 243 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 86 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.295 50.168 35.049 1.00152.11 S ATOM 4207 SG CYS P 187 32.756 47.305 34.080 1.00117.87 S Time building chain proxies: 6.06, per 1000 atoms: 0.19 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.002, 129.636, 163.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6069 8.00 N 5300 7.00 C 21039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 21 sheets defined 61.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 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: 3.758A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 137 through 151 removed outlier: 3.977A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.814A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.746A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.795A 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: 4.094A 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: 3.632A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 99 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.180A 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: 3.529A 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: 3.997A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.597A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.969A 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: 3.669A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.560A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.612A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.600A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.877A 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: 3.600A 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: 3.527A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.787A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.860A 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: 3.715A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.589A 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: 4.331A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.528A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.539A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.832A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.647A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.756A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.826A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.743A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.791A 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: 4.086A 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: 3.631A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix 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: 4.167A 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: 3.599A 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: 3.509A 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: 3.993A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.059A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.504A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.977A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.662A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.623A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.603A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.594A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.594A 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: 3.529A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.789A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.856A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.839A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.595A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 56 removed outlier: 4.319A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.520A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.559A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.838A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.648A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 removed outlier: 3.526A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.905A 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: 3.611A 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: 6.540A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.839A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.591A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.613A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.541A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.807A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.571A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.623A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1886 hydrogen bonds defined for protein. 5304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13620 1.40 - 1.61: 19543 1.61 - 1.82: 170 1.82 - 2.03: 25 2.03 - 2.24: 17 Bond restraints: 33375 Sorted by residual: bond pdb=" C14 CDL S 701 " pdb=" C15 CDL S 701 " ideal model delta sigma weight residual 1.517 1.790 -0.273 2.70e-02 1.37e+03 1.02e+02 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.609 -0.151 1.90e-02 2.77e+03 6.35e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.606 -0.148 1.90e-02 2.77e+03 6.11e+01 bond pdb=" C76 CDL A3001 " pdb=" C77 CDL A3001 " ideal model delta sigma weight residual 1.517 1.725 -0.208 2.70e-02 1.37e+03 5.94e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.476 -0.148 2.00e-02 2.50e+03 5.45e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 43106 3.68 - 7.36: 1991 7.36 - 11.04: 231 11.04 - 14.72: 29 14.72 - 18.40: 9 Bond angle restraints: 45366 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 94.21 10.12 1.14e+00 7.69e-01 7.89e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 94.03 10.30 1.20e+00 6.94e-01 7.36e+01 angle pdb=" C MET P 100 " pdb=" N ALA P 101 " pdb=" CA ALA P 101 " ideal model delta sigma weight residual 121.54 105.39 16.15 1.91e+00 2.74e-01 7.15e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 93.60 18.40 2.20e+00 2.07e-01 6.99e+01 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 93.95 18.05 2.20e+00 2.07e-01 6.73e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 18574 32.11 - 64.22: 924 64.22 - 96.33: 89 96.33 - 128.45: 1 128.45 - 160.56: 1 Dihedral angle restraints: 19589 sinusoidal: 7970 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -106.05 -16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -106.21 -16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.01e+01 ... (remaining 19586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 4603 0.213 - 0.425: 329 0.425 - 0.638: 16 0.638 - 0.850: 0 0.850 - 1.063: 4 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.51 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB4 CDL D 402 " pdb=" CB3 CDL D 402 " pdb=" CB6 CDL D 402 " pdb=" OB6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.59 -0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.62 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " -0.046 2.00e-02 2.50e+03 2.46e-01 6.06e+02 pdb=" C21 AWB C 506 " -0.382 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.249 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 505 " -0.029 2.00e-02 2.50e+03 2.43e-01 5.93e+02 pdb=" C21 AWB N 505 " 0.403 2.00e-02 2.50e+03 pdb=" N1 AWB N 505 " -0.145 2.00e-02 2.50e+03 pdb=" O5 AWB N 505 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.020 2.00e-02 2.50e+03 3.50e-02 2.75e+01 pdb=" C2A HEC D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.027 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.046 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.052 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.005 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.067 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.018 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.000 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 216 2.61 - 3.18: 28281 3.18 - 3.76: 53680 3.76 - 4.33: 80008 4.33 - 4.90: 123076 Nonbonded interactions: 285261 Sorted by model distance: nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.040 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.062 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.084 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.154 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.211 3.080 ... (remaining 285256 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 504) selection = (chain 'N' and resid 1 through 504) } ncs_group { reference = (chain 'D' and resid 85 through 401) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.630 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.273 33390 Z= 0.717 Angle : 1.851 18.396 45379 Z= 1.154 Chirality : 0.121 1.063 4952 Planarity : 0.009 0.246 5712 Dihedral : 17.870 160.557 12088 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 4.03 % Allowed : 8.06 % Favored : 87.91 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.12), residues: 3955 helix: -1.27 (0.09), residues: 2116 sheet: -0.05 (0.26), residues: 357 loop : -0.70 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.003 ARG B 128 TYR 0.053 0.008 TYR R 101 PHE 0.053 0.008 PHE B 107 TRP 0.039 0.009 TRP L 474 HIS 0.025 0.004 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01186 / 0.72 (33375) covalent geometry : angle 1.84840 / 1.15 (45366) SS BOND : bond 0.02838 / 1.66 ( 5) SS BOND : angle 2.65686 / 1.34 ( 10) hydrogen bonds : bond 0.18689 / 12.39 ( 1886) hydrogen bonds : angle 7.06405 / 5.10 ( 5304) metal coordination : bond 0.08757 / 4.28 ( 4) metal coordination : angle 12.15925 / 6.57 ( 3) Misc. bond : bond 0.14383 / 7.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 412 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9311 (m-30) cc_final: 0.9045 (m-30) REVERT: C 255 ASP cc_start: 0.8516 (m-30) cc_final: 0.8298 (p0) REVERT: C 369 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: P 104 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8955 (tp30) REVERT: P 137 GLU cc_start: 0.9001 (tt0) cc_final: 0.8696 (tt0) REVERT: P 176 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (pp) REVERT: G 66 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8973 (mp0) REVERT: G 123 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: F 84 GLU cc_start: 0.8784 (tt0) cc_final: 0.8329 (tp30) REVERT: F 145 VAL cc_start: 0.9328 (m) cc_final: 0.9110 (p) REVERT: A 91 GLN cc_start: 0.9021 (tp40) cc_final: 0.8806 (tp40) REVERT: A 144 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 31 GLN cc_start: 0.8842 (mt0) cc_final: 0.8508 (mm-40) REVERT: B 334 GLU cc_start: 0.9104 (tp30) cc_final: 0.8676 (pp20) REVERT: D 85 MET cc_start: 0.8360 (mtt) cc_final: 0.8065 (mtt) REVERT: D 164 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8288 (tp30) REVERT: D 166 ASN cc_start: 0.8511 (m110) cc_final: 0.8229 (m110) REVERT: D 235 MET cc_start: 0.8135 (mmt) cc_final: 0.7815 (mmm) REVERT: D 301 SER cc_start: 0.9402 (m) cc_final: 0.9200 (p) REVERT: H 41 VAL cc_start: 0.9046 (t) cc_final: 0.8661 (m) REVERT: H 75 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8355 (tm-30) REVERT: H 87 HIS cc_start: 0.8147 (m-70) cc_final: 0.7842 (m-70) REVERT: I 30 ASP cc_start: 0.8780 (t70) cc_final: 0.8270 (t0) REVERT: I 38 ASP cc_start: 0.8962 (m-30) cc_final: 0.8747 (m-30) REVERT: I 43 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7824 (ptm160) REVERT: J 11 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7766 (tptp) REVERT: J 55 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: N 197 HIS cc_start: 0.9516 (OUTLIER) cc_final: 0.8445 (p-80) REVERT: R 50 GLU cc_start: 0.8916 (pt0) cc_final: 0.8703 (pm20) REVERT: R 94 LYS cc_start: 0.9097 (mttm) cc_final: 0.8880 (mmmt) REVERT: L 164 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9047 (tp30) REVERT: L 228 LEU cc_start: 0.8124 (mt) cc_final: 0.7606 (mp) REVERT: L 397 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6759 (mp) REVERT: L 403 VAL cc_start: 0.8673 (t) cc_final: 0.8472 (m) REVERT: M 19 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: M 31 GLN cc_start: 0.9003 (mt0) cc_final: 0.8585 (mm-40) REVERT: M 170 TYR cc_start: 0.8379 (p90) cc_final: 0.7966 (p90) REVERT: T 35 THR cc_start: 0.9113 (m) cc_final: 0.8716 (p) REVERT: T 38 ASP cc_start: 0.8803 (m-30) cc_final: 0.8489 (m-30) REVERT: U 10 LYS cc_start: 0.9175 (tttm) cc_final: 0.8973 (tptt) REVERT: U 13 SER cc_start: 0.8744 (t) cc_final: 0.8490 (p) REVERT: U 69 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8996 (pp20) outliers start: 134 outliers final: 16 residues processed: 514 average time/residue: 0.6907 time to fit residues: 416.4512 Evaluate side-chains 238 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 332 ASN P 85 GLN G 54 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 222 HIS ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 316 GLN I 39 ASN N 14 ASN N 332 ASN E 90 ASN L 135 GLN L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 215 GLN M 316 GLN M 408 HIS O 102 ASN O 118 GLN O 193 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054277 restraints weight = 107517.277| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.49 r_work: 0.2977 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.496 33390 Z= 0.170 Angle : 0.679 17.222 45379 Z= 0.337 Chirality : 0.043 0.193 4952 Planarity : 0.004 0.048 5712 Dihedral : 12.013 130.203 4937 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.59 % Allowed : 13.11 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 3955 helix: 0.78 (0.11), residues: 2160 sheet: 0.63 (0.27), residues: 355 loop : -0.02 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 55 TYR 0.021 0.002 TYR B 341 PHE 0.020 0.002 PHE L 334 TRP 0.029 0.002 TRP C 156 HIS 0.014 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (33375) covalent geometry : angle 0.67736 / 0.34 (45366) SS BOND : bond 0.00160 / 0.09 ( 5) SS BOND : angle 0.78773 / 0.41 ( 10) hydrogen bonds : bond 0.04975 / 3.29 ( 1886) hydrogen bonds : angle 4.87902 / 3.51 ( 5304) metal coordination : bond 0.02251 / 1.11 ( 4) metal coordination : angle 5.74056 / 3.19 ( 3) Misc. bond : bond 0.35415 / 17.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.8871 (tpt) cc_final: 0.8080 (tpt) REVERT: C 160 ASP cc_start: 0.8605 (m-30) cc_final: 0.8384 (m-30) REVERT: C 374 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8195 (mt-10) REVERT: P 118 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8426 (pp) REVERT: G 110 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8178 (mt-10) REVERT: G 123 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: G 124 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8696 (m) REVERT: F 84 GLU cc_start: 0.8373 (tt0) cc_final: 0.7874 (tp30) REVERT: F 88 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7921 (mm-30) REVERT: F 125 GLU cc_start: 0.8481 (tp30) cc_final: 0.8130 (tp30) REVERT: A 91 GLN cc_start: 0.8712 (tp40) cc_final: 0.8440 (tp40) REVERT: B 334 GLU cc_start: 0.8410 (tp30) cc_final: 0.8104 (tp30) REVERT: D 85 MET cc_start: 0.8270 (mtt) cc_final: 0.8052 (mtt) REVERT: D 164 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7732 (tp30) REVERT: D 166 ASN cc_start: 0.8227 (m110) cc_final: 0.7812 (m110) REVERT: D 235 MET cc_start: 0.8048 (mmt) cc_final: 0.7604 (mmm) REVERT: H 75 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8062 (tm-30) REVERT: H 83 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8392 (mmtp) REVERT: I 43 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7915 (ptm160) REVERT: J 11 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7654 (tptp) REVERT: N 353 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8278 (mm110) REVERT: E 54 LYS cc_start: 0.8865 (tppt) cc_final: 0.8606 (tptm) REVERT: E 62 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7123 (mtm110) REVERT: Q 88 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7724 (mm-30) REVERT: Q 116 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7713 (m-70) REVERT: Q 137 ASN cc_start: 0.7876 (m-40) cc_final: 0.7415 (m-40) REVERT: M 31 GLN cc_start: 0.8600 (mt0) cc_final: 0.8210 (mm-40) REVERT: M 170 TYR cc_start: 0.8106 (p90) cc_final: 0.7843 (p90) REVERT: S 51 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.6979 (ptm160) REVERT: T 31 MET cc_start: 0.8410 (mmm) cc_final: 0.7847 (mmm) outliers start: 86 outliers final: 17 residues processed: 306 average time/residue: 0.6584 time to fit residues: 237.0276 Evaluate side-chains 211 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 43 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 0.0470 chunk 258 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN C 341 GLN P 115 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 379 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 HIS L 317 GLN M 92 HIS O 193 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.064089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051204 restraints weight = 107523.229| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.44 r_work: 0.2897 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 33390 Z= 0.159 Angle : 0.609 15.061 45379 Z= 0.297 Chirality : 0.042 0.259 4952 Planarity : 0.004 0.056 5712 Dihedral : 10.903 109.508 4906 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.38 % Allowed : 13.89 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 3955 helix: 1.41 (0.11), residues: 2148 sheet: 0.71 (0.28), residues: 359 loop : 0.35 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 55 TYR 0.018 0.001 TYR B 341 PHE 0.017 0.002 PHE M 107 TRP 0.014 0.001 TRP N 142 HIS 0.011 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (33375) covalent geometry : angle 0.60748 / 0.30 (45366) SS BOND : bond 0.00144 / 0.08 ( 5) SS BOND : angle 0.66185 / 0.35 ( 10) hydrogen bonds : bond 0.04212 / 2.76 ( 1886) hydrogen bonds : angle 4.55268 / 3.28 ( 5304) metal coordination : bond 0.01814 / 0.89 ( 4) metal coordination : angle 5.45927 / 3.19 ( 3) Misc. bond : bond 0.32276 / 15.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.8717 (m-30) cc_final: 0.8451 (m-30) REVERT: P 118 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8349 (pt) REVERT: G 23 ILE cc_start: 0.8836 (tp) cc_final: 0.8522 (mp) REVERT: G 55 MET cc_start: 0.8665 (tpp) cc_final: 0.8425 (tpp) REVERT: G 110 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8117 (mt-10) REVERT: G 123 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: G 124 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8682 (m) REVERT: F 84 GLU cc_start: 0.8483 (tt0) cc_final: 0.8007 (tp30) REVERT: F 88 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7899 (mm-30) REVERT: F 103 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7923 (tm-30) REVERT: F 104 ARG cc_start: 0.7927 (ptm160) cc_final: 0.7360 (ptm-80) REVERT: F 107 LYS cc_start: 0.8998 (pptt) cc_final: 0.8445 (mmpt) REVERT: F 125 GLU cc_start: 0.8585 (tp30) cc_final: 0.8364 (mp0) REVERT: A 91 GLN cc_start: 0.8742 (tp40) cc_final: 0.8482 (tp40) REVERT: D 166 ASN cc_start: 0.8290 (m110) cc_final: 0.8055 (m110) REVERT: H 83 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: H 88 GLU cc_start: 0.8746 (tp30) cc_final: 0.8267 (tp30) REVERT: I 43 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8056 (ptm160) REVERT: R 12 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8306 (mt-10) REVERT: Q 80 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8313 (pp) REVERT: Q 88 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7802 (mm-30) REVERT: Q 116 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7682 (m-70) REVERT: Q 121 GLU cc_start: 0.7517 (tt0) cc_final: 0.7171 (tp30) REVERT: Q 137 ASN cc_start: 0.7923 (m-40) cc_final: 0.7505 (m-40) REVERT: M 31 GLN cc_start: 0.8752 (mt0) cc_final: 0.8294 (mm-40) REVERT: M 170 TYR cc_start: 0.8190 (p90) cc_final: 0.7962 (p90) REVERT: O 248 MET cc_start: 0.8812 (ttp) cc_final: 0.8486 (ttm) REVERT: T 31 MET cc_start: 0.8460 (mmm) cc_final: 0.8129 (mmm) REVERT: T 34 GLU cc_start: 0.8366 (tt0) cc_final: 0.8081 (mt-10) outliers start: 79 outliers final: 20 residues processed: 272 average time/residue: 0.6471 time to fit residues: 208.8166 Evaluate side-chains 207 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 158 ASP Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 0.2980 chunk 111 optimal weight: 9.9990 chunk 230 optimal weight: 0.4980 chunk 170 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 333 optimal weight: 0.0270 chunk 305 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 136 HIS B 121 GLN H 77 ASN E 90 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN O 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.052238 restraints weight = 106217.050| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.44 r_work: 0.2928 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.418 33390 Z= 0.111 Angle : 0.557 13.414 45379 Z= 0.268 Chirality : 0.040 0.223 4952 Planarity : 0.004 0.057 5712 Dihedral : 10.358 101.508 4896 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.65 % Allowed : 15.19 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3955 helix: 1.70 (0.11), residues: 2147 sheet: 0.75 (0.28), residues: 357 loop : 0.45 (0.18), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 202 TYR 0.021 0.001 TYR B 341 PHE 0.016 0.001 PHE A 334 TRP 0.011 0.001 TRP N 142 HIS 0.009 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (33375) covalent geometry : angle 0.55454 / 0.27 (45366) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.55357 / 0.26 ( 10) hydrogen bonds : bond 0.03755 / 2.46 ( 1886) hydrogen bonds : angle 4.40808 / 3.17 ( 5304) metal coordination : bond 0.01464 / 0.73 ( 4) metal coordination : angle 6.24883 / 3.49 ( 3) Misc. bond : bond 0.26700 / 13.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.8648 (tpt) cc_final: 0.8390 (tpt) REVERT: C 160 ASP cc_start: 0.8739 (m-30) cc_final: 0.8463 (m-30) REVERT: P 118 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8312 (pt) REVERT: G 23 ILE cc_start: 0.8770 (tp) cc_final: 0.8457 (mp) REVERT: G 55 MET cc_start: 0.8590 (tpp) cc_final: 0.8378 (tpp) REVERT: G 110 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8011 (mt-10) REVERT: G 123 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 124 VAL cc_start: 0.9054 (t) cc_final: 0.8522 (m) REVERT: F 84 GLU cc_start: 0.8508 (tt0) cc_final: 0.7982 (tp30) REVERT: F 88 GLU cc_start: 0.8665 (mm-30) cc_final: 0.7981 (mm-30) REVERT: F 103 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7922 (tm-30) REVERT: F 107 LYS cc_start: 0.9010 (pptt) cc_final: 0.8467 (mmpt) REVERT: A 91 GLN cc_start: 0.8711 (tp40) cc_final: 0.8305 (tp40) REVERT: A 103 LEU cc_start: 0.8838 (mp) cc_final: 0.8414 (mm) REVERT: B 268 SER cc_start: 0.8097 (m) cc_final: 0.7666 (p) REVERT: D 85 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: D 166 ASN cc_start: 0.8353 (m110) cc_final: 0.8150 (m110) REVERT: H 88 GLU cc_start: 0.8742 (tp30) cc_final: 0.8247 (tp30) REVERT: I 30 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7880 (t0) REVERT: I 43 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8048 (ptm160) REVERT: E 54 LYS cc_start: 0.8866 (tppt) cc_final: 0.8637 (tptm) REVERT: E 55 ASP cc_start: 0.8012 (p0) cc_final: 0.7760 (p0) REVERT: R 12 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8389 (mt-10) REVERT: R 115 GLU cc_start: 0.8792 (tt0) cc_final: 0.8556 (tt0) REVERT: Q 84 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8604 (mm-30) REVERT: Q 88 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7867 (mm-30) REVERT: Q 121 GLU cc_start: 0.7563 (tt0) cc_final: 0.7234 (tp30) REVERT: Q 131 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: Q 137 ASN cc_start: 0.7857 (m-40) cc_final: 0.7465 (m-40) REVERT: M 31 GLN cc_start: 0.8777 (mt0) cc_final: 0.8283 (mm-40) REVERT: M 170 TYR cc_start: 0.8274 (p90) cc_final: 0.7964 (p90) REVERT: M 357 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8276 (p) REVERT: T 31 MET cc_start: 0.8316 (mmm) cc_final: 0.7960 (mmm) REVERT: T 34 GLU cc_start: 0.8368 (tt0) cc_final: 0.8053 (mt-10) outliers start: 55 outliers final: 19 residues processed: 239 average time/residue: 0.6247 time to fit residues: 177.7760 Evaluate side-chains 211 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 115 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 159 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 90 ASN A 74 HIS A 91 GLN B 63 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN S 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046684 restraints weight = 107511.785| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.40 r_work: 0.2755 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 33390 Z= 0.221 Angle : 0.653 18.730 45379 Z= 0.309 Chirality : 0.043 0.183 4952 Planarity : 0.004 0.059 5712 Dihedral : 10.185 88.625 4889 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.32 % Allowed : 15.22 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.14), residues: 3955 helix: 1.57 (0.11), residues: 2148 sheet: 0.56 (0.28), residues: 358 loop : 0.57 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 55 TYR 0.026 0.002 TYR C 225 PHE 0.021 0.002 PHE C 240 TRP 0.012 0.001 TRP N 156 HIS 0.013 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (33375) covalent geometry : angle 0.64896 / 0.31 (45366) SS BOND : bond 0.00193 / 0.11 ( 5) SS BOND : angle 0.95651 / 0.50 ( 10) hydrogen bonds : bond 0.04256 / 2.80 ( 1886) hydrogen bonds : angle 4.56358 / 3.28 ( 5304) metal coordination : bond 0.02578 / 1.30 ( 4) metal coordination : angle 8.78584 / 5.11 ( 3) Misc. bond : bond 0.39463 / 20.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9004 (m-30) cc_final: 0.8774 (m-30) REVERT: C 295 MET cc_start: 0.8652 (ttt) cc_final: 0.8293 (ttp) REVERT: P 118 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8480 (pt) REVERT: G 23 ILE cc_start: 0.8856 (tp) cc_final: 0.8588 (mp) REVERT: G 55 MET cc_start: 0.8996 (tpp) cc_final: 0.8752 (tpp) REVERT: G 110 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8305 (mt-10) REVERT: G 112 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: G 123 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 124 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8696 (m) REVERT: F 80 ILE cc_start: 0.9052 (mm) cc_final: 0.8786 (pp) REVERT: F 84 GLU cc_start: 0.8818 (tt0) cc_final: 0.8274 (tm-30) REVERT: F 88 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8161 (mm-30) REVERT: F 103 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8102 (tm-30) REVERT: F 104 ARG cc_start: 0.8161 (ptm160) cc_final: 0.7557 (ptm-80) REVERT: F 107 LYS cc_start: 0.9058 (pptt) cc_final: 0.8618 (mmtt) REVERT: A 390 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8584 (mttt) REVERT: B 170 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7139 (p90) REVERT: B 261 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8176 (p) REVERT: D 85 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: D 166 ASN cc_start: 0.8535 (m110) cc_final: 0.8283 (m110) REVERT: H 76 LYS cc_start: 0.8708 (tptm) cc_final: 0.8485 (tppt) REVERT: I 30 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8244 (t0) REVERT: I 43 ARG cc_start: 0.8518 (mtm110) cc_final: 0.8292 (mtp-110) REVERT: J 13 SER cc_start: 0.8645 (t) cc_final: 0.8188 (p) REVERT: N 142 TRP cc_start: 0.8504 (m100) cc_final: 0.8159 (m100) REVERT: N 239 MET cc_start: 0.8722 (ptt) cc_final: 0.8125 (tpt) REVERT: N 272 GLU cc_start: 0.8478 (tp30) cc_final: 0.8128 (mm-30) REVERT: E 62 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7496 (mtm110) REVERT: R 12 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8597 (mt-10) REVERT: Q 88 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8066 (mm-30) REVERT: Q 121 GLU cc_start: 0.7956 (tt0) cc_final: 0.7627 (tp30) REVERT: Q 125 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8316 (mt-10) REVERT: Q 131 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: M 31 GLN cc_start: 0.8932 (mt0) cc_final: 0.8681 (mt0) REVERT: M 292 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8857 (p) REVERT: S 75 GLU cc_start: 0.8835 (pt0) cc_final: 0.8063 (pt0) REVERT: T 34 GLU cc_start: 0.8794 (tt0) cc_final: 0.8581 (mt-10) outliers start: 77 outliers final: 21 residues processed: 247 average time/residue: 0.6402 time to fit residues: 187.8936 Evaluate side-chains 195 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 348 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 361 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.060948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048399 restraints weight = 105779.012| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.39 r_work: 0.2810 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 33390 Z= 0.118 Angle : 0.555 14.703 45379 Z= 0.265 Chirality : 0.040 0.155 4952 Planarity : 0.004 0.058 5712 Dihedral : 9.739 89.952 4889 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.71 % Allowed : 16.60 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3955 helix: 1.78 (0.11), residues: 2147 sheet: 0.64 (0.28), residues: 346 loop : 0.60 (0.18), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 202 TYR 0.015 0.001 TYR C 225 PHE 0.016 0.001 PHE B 302 TRP 0.011 0.001 TRP C 156 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (33375) covalent geometry : angle 0.55281 / 0.26 (45366) SS BOND : bond 0.00276 / 0.14 ( 5) SS BOND : angle 0.91370 / 0.43 ( 10) hydrogen bonds : bond 0.03691 / 2.41 ( 1886) hydrogen bonds : angle 4.41953 / 3.18 ( 5304) metal coordination : bond 0.00813 / 0.41 ( 4) metal coordination : angle 6.21323 / 3.53 ( 3) Misc. bond : bond 0.29618 / 14.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9001 (m-30) cc_final: 0.8757 (m-30) REVERT: C 295 MET cc_start: 0.8633 (ttt) cc_final: 0.8287 (ttp) REVERT: P 118 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8456 (pt) REVERT: G 23 ILE cc_start: 0.8796 (tp) cc_final: 0.8541 (mp) REVERT: G 55 MET cc_start: 0.8926 (tpp) cc_final: 0.8712 (tpp) REVERT: G 110 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8283 (mt-10) REVERT: G 123 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7869 (tm-30) REVERT: G 124 VAL cc_start: 0.9207 (t) cc_final: 0.8711 (m) REVERT: F 80 ILE cc_start: 0.9096 (mm) cc_final: 0.8838 (pp) REVERT: F 84 GLU cc_start: 0.8785 (tt0) cc_final: 0.8261 (tm-30) REVERT: F 88 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8130 (mm-30) REVERT: F 107 LYS cc_start: 0.9072 (pptt) cc_final: 0.8672 (mmtt) REVERT: D 85 MET cc_start: 0.8659 (mtp) cc_final: 0.8325 (mtp) REVERT: D 166 ASN cc_start: 0.8584 (m110) cc_final: 0.8334 (m110) REVERT: H 76 LYS cc_start: 0.8710 (tptm) cc_final: 0.8403 (tppt) REVERT: I 30 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8228 (t0) REVERT: I 43 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8232 (mtp-110) REVERT: J 13 SER cc_start: 0.8568 (t) cc_final: 0.8115 (p) REVERT: N 142 TRP cc_start: 0.8475 (m100) cc_final: 0.8140 (m100) REVERT: N 239 MET cc_start: 0.8659 (ptt) cc_final: 0.8065 (tpt) REVERT: N 272 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: E 54 LYS cc_start: 0.8975 (tptm) cc_final: 0.8713 (tppt) REVERT: E 55 ASP cc_start: 0.8188 (p0) cc_final: 0.7912 (p0) REVERT: E 76 SER cc_start: 0.9196 (m) cc_final: 0.8872 (p) REVERT: R 12 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8619 (mt-10) REVERT: R 115 GLU cc_start: 0.8939 (tt0) cc_final: 0.8723 (tt0) REVERT: Q 88 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8080 (mm-30) REVERT: Q 121 GLU cc_start: 0.8013 (tt0) cc_final: 0.7662 (tp30) REVERT: Q 131 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: L 270 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9219 (mt) REVERT: L 275 MET cc_start: 0.8810 (ttm) cc_final: 0.8555 (ttm) REVERT: M 31 GLN cc_start: 0.8880 (mt0) cc_final: 0.8659 (mt0) REVERT: O 90 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8608 (m-70) REVERT: T 34 GLU cc_start: 0.8715 (tt0) cc_final: 0.8490 (mt-10) outliers start: 57 outliers final: 15 residues processed: 229 average time/residue: 0.5900 time to fit residues: 161.3206 Evaluate side-chains 192 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 306 optimal weight: 0.3980 chunk 368 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 194 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 362 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN E 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048407 restraints weight = 106705.385| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.38 r_work: 0.2811 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.460 33390 Z= 0.117 Angle : 0.549 14.694 45379 Z= 0.259 Chirality : 0.040 0.161 4952 Planarity : 0.004 0.059 5712 Dihedral : 9.524 89.282 4889 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.44 % Allowed : 17.14 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2160 sheet: 0.69 (0.28), residues: 346 loop : 0.59 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 55 TYR 0.026 0.001 TYR M 170 PHE 0.016 0.001 PHE L 334 TRP 0.011 0.001 TRP C 142 HIS 0.009 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (33375) covalent geometry : angle 0.54718 / 0.26 (45366) SS BOND : bond 0.00289 / 0.15 ( 5) SS BOND : angle 0.84422 / 0.39 ( 10) hydrogen bonds : bond 0.03619 / 2.37 ( 1886) hydrogen bonds : angle 4.36061 / 3.14 ( 5304) metal coordination : bond 0.00681 / 0.34 ( 4) metal coordination : angle 5.51451 / 3.21 ( 3) Misc. bond : bond 0.27698 / 13.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9013 (m-30) cc_final: 0.8767 (m-30) REVERT: C 295 MET cc_start: 0.8632 (ttt) cc_final: 0.8290 (ttp) REVERT: P 118 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8455 (pt) REVERT: G 23 ILE cc_start: 0.8764 (tp) cc_final: 0.8518 (mp) REVERT: G 97 GLU cc_start: 0.8783 (tt0) cc_final: 0.8168 (mt-10) REVERT: G 110 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8258 (mt-10) REVERT: G 123 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7811 (tm-30) REVERT: G 124 VAL cc_start: 0.9214 (t) cc_final: 0.8677 (m) REVERT: F 80 ILE cc_start: 0.9110 (mm) cc_final: 0.8857 (pp) REVERT: F 84 GLU cc_start: 0.8794 (tt0) cc_final: 0.8269 (tm-30) REVERT: F 88 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8129 (mm-30) REVERT: F 100 GLU cc_start: 0.8477 (pp20) cc_final: 0.7371 (pt0) REVERT: F 103 GLU cc_start: 0.8738 (pp20) cc_final: 0.8537 (pp20) REVERT: F 107 LYS cc_start: 0.9109 (pptt) cc_final: 0.8732 (mmtt) REVERT: A 390 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8587 (mttt) REVERT: D 85 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8083 (ptp) REVERT: D 166 ASN cc_start: 0.8574 (m110) cc_final: 0.8344 (m110) REVERT: H 76 LYS cc_start: 0.8719 (tptm) cc_final: 0.8411 (tppt) REVERT: I 30 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8276 (t0) REVERT: I 43 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8218 (mtp-110) REVERT: J 13 SER cc_start: 0.8545 (t) cc_final: 0.8066 (p) REVERT: N 142 TRP cc_start: 0.8471 (m100) cc_final: 0.8128 (m100) REVERT: N 239 MET cc_start: 0.8638 (ptt) cc_final: 0.8072 (tpt) REVERT: N 272 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: E 54 LYS cc_start: 0.8987 (tptm) cc_final: 0.8728 (tppt) REVERT: E 55 ASP cc_start: 0.8178 (p0) cc_final: 0.7912 (p0) REVERT: E 62 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7356 (mtm110) REVERT: E 76 SER cc_start: 0.9196 (m) cc_final: 0.8867 (p) REVERT: R 12 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8647 (mt-10) REVERT: R 115 GLU cc_start: 0.8929 (tt0) cc_final: 0.8717 (tt0) REVERT: Q 88 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8078 (mm-30) REVERT: Q 116 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7823 (m170) REVERT: Q 121 GLU cc_start: 0.8090 (tt0) cc_final: 0.7728 (tp30) REVERT: Q 131 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: Q 140 ASP cc_start: 0.8800 (m-30) cc_final: 0.8371 (t70) REVERT: L 270 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9204 (mt) REVERT: L 275 MET cc_start: 0.8852 (ttm) cc_final: 0.8547 (ttm) REVERT: M 31 GLN cc_start: 0.8913 (mt0) cc_final: 0.8656 (mt0) REVERT: T 34 GLU cc_start: 0.8715 (tt0) cc_final: 0.8470 (mt-10) outliers start: 48 outliers final: 16 residues processed: 216 average time/residue: 0.6663 time to fit residues: 170.2707 Evaluate side-chains 197 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 ASN N 332 ASN ** L 50 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 = 0.3234 r_free = 0.3234 target = 0.059140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.046694 restraints weight = 106662.841| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.38 r_work: 0.2760 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.527 33390 Z= 0.170 Angle : 0.595 17.399 45379 Z= 0.280 Chirality : 0.042 0.156 4952 Planarity : 0.004 0.058 5712 Dihedral : 9.592 88.659 4889 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.77 % Allowed : 17.11 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3955 helix: 1.76 (0.11), residues: 2164 sheet: 0.63 (0.28), residues: 354 loop : 0.64 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.022 0.002 TYR C 225 PHE 0.019 0.001 PHE C 240 TRP 0.012 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (33375) covalent geometry : angle 0.59326 / 0.28 (45366) SS BOND : bond 0.00225 / 0.12 ( 5) SS BOND : angle 0.90833 / 0.41 ( 10) hydrogen bonds : bond 0.03869 / 2.53 ( 1886) hydrogen bonds : angle 4.41544 / 3.17 ( 5304) metal coordination : bond 0.01291 / 0.66 ( 4) metal coordination : angle 5.55982 / 3.27 ( 3) Misc. bond : bond 0.33381 / 16.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9072 (m-30) cc_final: 0.8850 (m-30) REVERT: C 295 MET cc_start: 0.8677 (ttt) cc_final: 0.8331 (ttp) REVERT: P 118 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8418 (pt) REVERT: G 23 ILE cc_start: 0.8802 (tp) cc_final: 0.8568 (mp) REVERT: G 110 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8267 (mt-10) REVERT: G 123 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 124 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8716 (m) REVERT: F 80 ILE cc_start: 0.9152 (mm) cc_final: 0.8929 (pp) REVERT: F 84 GLU cc_start: 0.8859 (tt0) cc_final: 0.8363 (tm-30) REVERT: F 88 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8207 (mm-30) REVERT: F 100 GLU cc_start: 0.8531 (pp20) cc_final: 0.7627 (pt0) REVERT: F 103 GLU cc_start: 0.8766 (pp20) cc_final: 0.8537 (pp20) REVERT: F 107 LYS cc_start: 0.9148 (pptt) cc_final: 0.8855 (mmtt) REVERT: F 122 ASP cc_start: 0.7632 (p0) cc_final: 0.7192 (p0) REVERT: A 390 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8586 (mttt) REVERT: D 248 MET cc_start: 0.9102 (ttp) cc_final: 0.8774 (ttm) REVERT: H 76 LYS cc_start: 0.8767 (tptm) cc_final: 0.8516 (tppt) REVERT: I 30 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8290 (t0) REVERT: J 13 SER cc_start: 0.8551 (t) cc_final: 0.8112 (p) REVERT: N 239 MET cc_start: 0.8684 (ptt) cc_final: 0.8103 (tpt) REVERT: N 272 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: E 54 LYS cc_start: 0.9023 (tptm) cc_final: 0.8727 (tppt) REVERT: E 55 ASP cc_start: 0.8193 (p0) cc_final: 0.7942 (p0) REVERT: E 62 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7472 (mtm110) REVERT: E 76 SER cc_start: 0.9229 (m) cc_final: 0.8922 (p) REVERT: R 12 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8702 (mt-10) REVERT: R 115 GLU cc_start: 0.8975 (tt0) cc_final: 0.8744 (tt0) REVERT: Q 88 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8111 (mm-30) REVERT: Q 116 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7731 (m170) REVERT: Q 121 GLU cc_start: 0.8226 (tt0) cc_final: 0.7878 (tp30) REVERT: Q 131 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: Q 140 ASP cc_start: 0.8824 (m-30) cc_final: 0.8431 (t70) REVERT: L 270 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9322 (mt) REVERT: M 31 GLN cc_start: 0.8928 (mt0) cc_final: 0.8662 (mt0) REVERT: M 60 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.8802 (t80) REVERT: M 292 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8990 (p) REVERT: M 339 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8600 (ttp-170) REVERT: O 85 MET cc_start: 0.9019 (pmm) cc_final: 0.8760 (pmm) REVERT: O 90 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8567 (m-70) REVERT: T 34 GLU cc_start: 0.8822 (tt0) cc_final: 0.8584 (mt-10) outliers start: 59 outliers final: 20 residues processed: 226 average time/residue: 0.6367 time to fit residues: 171.4242 Evaluate side-chains 199 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 82 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046810 restraints weight = 106184.956| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.36 r_work: 0.2764 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.500 33390 Z= 0.162 Angle : 0.580 14.945 45379 Z= 0.275 Chirality : 0.041 0.170 4952 Planarity : 0.004 0.084 5712 Dihedral : 9.483 89.871 4889 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.23 % Allowed : 17.77 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3955 helix: 1.79 (0.11), residues: 2160 sheet: 0.56 (0.28), residues: 354 loop : 0.64 (0.18), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 43 TYR 0.018 0.001 TYR C 225 PHE 0.016 0.001 PHE L 334 TRP 0.012 0.001 TRP N 142 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (33375) covalent geometry : angle 0.57872 / 0.28 (45366) SS BOND : bond 0.00139 / 0.08 ( 5) SS BOND : angle 0.84403 / 0.36 ( 10) hydrogen bonds : bond 0.03765 / 2.47 ( 1886) hydrogen bonds : angle 4.41277 / 3.17 ( 5304) metal coordination : bond 0.01029 / 0.52 ( 4) metal coordination : angle 4.60044 / 2.70 ( 3) Misc. bond : bond 0.31279 / 15.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9094 (m-30) cc_final: 0.8886 (m-30) REVERT: C 295 MET cc_start: 0.8682 (ttt) cc_final: 0.8336 (ttp) REVERT: P 118 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8417 (pt) REVERT: G 23 ILE cc_start: 0.8770 (tp) cc_final: 0.8547 (mp) REVERT: G 90 ASN cc_start: 0.9097 (t0) cc_final: 0.8868 (t0) REVERT: G 110 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8296 (mt-10) REVERT: G 123 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 124 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8737 (m) REVERT: F 84 GLU cc_start: 0.8894 (tt0) cc_final: 0.8452 (tm-30) REVERT: F 88 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8239 (mm-30) REVERT: F 100 GLU cc_start: 0.8635 (pp20) cc_final: 0.7890 (pt0) REVERT: F 103 GLU cc_start: 0.8813 (pp20) cc_final: 0.8519 (pp20) REVERT: F 107 LYS cc_start: 0.9173 (pptt) cc_final: 0.8911 (mmtt) REVERT: F 122 ASP cc_start: 0.7889 (p0) cc_final: 0.7413 (p0) REVERT: A 390 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8618 (mttt) REVERT: H 76 LYS cc_start: 0.8780 (tptm) cc_final: 0.8495 (tppt) REVERT: I 30 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8290 (t0) REVERT: J 13 SER cc_start: 0.8546 (t) cc_final: 0.8114 (p) REVERT: N 239 MET cc_start: 0.8671 (ptt) cc_final: 0.8101 (tpt) REVERT: N 272 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: E 54 LYS cc_start: 0.9021 (tptm) cc_final: 0.8747 (tppt) REVERT: E 55 ASP cc_start: 0.8223 (p0) cc_final: 0.7970 (p0) REVERT: E 62 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7474 (mtm110) REVERT: E 76 SER cc_start: 0.9211 (m) cc_final: 0.8918 (p) REVERT: R 12 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8686 (mt-10) REVERT: R 115 GLU cc_start: 0.8992 (tt0) cc_final: 0.8695 (tt0) REVERT: Q 88 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8119 (mm-30) REVERT: Q 121 GLU cc_start: 0.8370 (tt0) cc_final: 0.7950 (tp30) REVERT: Q 126 GLU cc_start: 0.8502 (mp0) cc_final: 0.8232 (mp0) REVERT: Q 131 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: Q 140 ASP cc_start: 0.8814 (m-30) cc_final: 0.8411 (t70) REVERT: L 270 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9316 (mt) REVERT: M 60 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.8946 (t80) REVERT: M 292 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.9018 (p) REVERT: O 85 MET cc_start: 0.9040 (pmm) cc_final: 0.8777 (pmm) REVERT: O 90 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8638 (m-70) REVERT: T 34 GLU cc_start: 0.8838 (tt0) cc_final: 0.8546 (mt-10) outliers start: 41 outliers final: 18 residues processed: 209 average time/residue: 0.6935 time to fit residues: 171.5737 Evaluate side-chains 192 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 249 ILE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 317 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 166 optimal weight: 0.0020 chunk 99 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.059679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047513 restraints weight = 106326.771| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.36 r_work: 0.2784 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.467 33390 Z= 0.125 Angle : 0.572 14.818 45379 Z= 0.272 Chirality : 0.040 0.168 4952 Planarity : 0.004 0.058 5712 Dihedral : 9.330 89.680 4889 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.33 % Rotamer: Outliers : 0.78 % Allowed : 18.38 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2160 sheet: 0.68 (0.28), residues: 342 loop : 0.62 (0.18), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 43 TYR 0.016 0.001 TYR C 225 PHE 0.015 0.001 PHE L 334 TRP 0.011 0.001 TRP C 142 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (33375) covalent geometry : angle 0.57126 / 0.27 (45366) SS BOND : bond 0.00142 / 0.09 ( 5) SS BOND : angle 0.99936 / 0.41 ( 10) hydrogen bonds : bond 0.03632 / 2.37 ( 1886) hydrogen bonds : angle 4.37457 / 3.14 ( 5304) metal coordination : bond 0.00426 / 0.21 ( 4) metal coordination : angle 3.93879 / 2.30 ( 3) Misc. bond : bond 0.28849 / 14.30 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9104 (m-30) cc_final: 0.8901 (m-30) REVERT: C 295 MET cc_start: 0.8642 (ttt) cc_final: 0.8292 (ttp) REVERT: P 118 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8431 (pt) REVERT: G 23 ILE cc_start: 0.8762 (tp) cc_final: 0.8539 (mp) REVERT: G 90 ASN cc_start: 0.9075 (t0) cc_final: 0.8826 (t0) REVERT: G 110 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8284 (mt-10) REVERT: G 123 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 124 VAL cc_start: 0.9279 (t) cc_final: 0.8760 (m) REVERT: F 84 GLU cc_start: 0.8900 (tt0) cc_final: 0.8413 (tm-30) REVERT: F 88 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8236 (mm-30) REVERT: F 100 GLU cc_start: 0.8628 (pp20) cc_final: 0.7897 (pt0) REVERT: F 103 GLU cc_start: 0.8818 (pp20) cc_final: 0.8617 (pp20) REVERT: F 107 LYS cc_start: 0.9173 (pptt) cc_final: 0.8919 (mmtt) REVERT: F 122 ASP cc_start: 0.7831 (p0) cc_final: 0.7413 (p0) REVERT: A 390 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8627 (mttt) REVERT: H 76 LYS cc_start: 0.8851 (tptm) cc_final: 0.8624 (tppt) REVERT: I 30 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8324 (t0) REVERT: J 13 SER cc_start: 0.8513 (t) cc_final: 0.8084 (p) REVERT: N 239 MET cc_start: 0.8640 (ptt) cc_final: 0.8084 (tpt) REVERT: N 272 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: E 54 LYS cc_start: 0.9029 (tptm) cc_final: 0.8750 (tppt) REVERT: E 55 ASP cc_start: 0.8220 (p0) cc_final: 0.7972 (p0) REVERT: E 62 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7423 (mtm110) REVERT: E 76 SER cc_start: 0.9230 (m) cc_final: 0.8910 (p) REVERT: R 12 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8700 (mt-10) REVERT: R 115 GLU cc_start: 0.9008 (tt0) cc_final: 0.8712 (tt0) REVERT: Q 88 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8130 (mm-30) REVERT: Q 121 GLU cc_start: 0.8383 (tt0) cc_final: 0.7955 (tp30) REVERT: Q 125 GLU cc_start: 0.8703 (mp0) cc_final: 0.8249 (mt-10) REVERT: Q 126 GLU cc_start: 0.8506 (mp0) cc_final: 0.8222 (mp0) REVERT: Q 131 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: Q 140 ASP cc_start: 0.8809 (m-30) cc_final: 0.8383 (t70) REVERT: L 270 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9234 (mt) REVERT: M 60 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.8960 (t80) REVERT: O 85 MET cc_start: 0.9031 (pmm) cc_final: 0.8680 (pmm) REVERT: O 90 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8619 (m-70) REVERT: T 34 GLU cc_start: 0.8820 (tt0) cc_final: 0.8594 (mt-10) outliers start: 26 outliers final: 10 residues processed: 197 average time/residue: 0.6854 time to fit residues: 159.4133 Evaluate side-chains 186 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain N residue 272 GLU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047159 restraints weight = 106401.001| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.35 r_work: 0.2774 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.483 33390 Z= 0.142 Angle : 0.577 15.391 45379 Z= 0.273 Chirality : 0.041 0.165 4952 Planarity : 0.004 0.058 5712 Dihedral : 9.285 89.965 4889 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.28 % Rotamer: Outliers : 0.90 % Allowed : 18.35 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2164 sheet: 0.68 (0.28), residues: 342 loop : 0.63 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 43 TYR 0.018 0.001 TYR C 225 PHE 0.016 0.001 PHE L 334 TRP 0.012 0.001 TRP C 142 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (33375) covalent geometry : angle 0.57620 / 0.27 (45366) SS BOND : bond 0.00078 / 0.04 ( 5) SS BOND : angle 0.94546 / 0.42 ( 10) hydrogen bonds : bond 0.03668 / 2.40 ( 1886) hydrogen bonds : angle 4.37147 / 3.14 ( 5304) metal coordination : bond 0.00828 / 0.42 ( 4) metal coordination : angle 4.16171 / 2.44 ( 3) Misc. bond : bond 0.30313 / 15.05 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8314.80 seconds wall clock time: 143 minutes 10.10 seconds (8590.10 seconds total)