Starting phenix.real_space_refine on Mon Jul 6 08:07:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.cif" model { file = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abj_15323/07_2026/8abj_15323.cif" } resolution = 3.7 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 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32548 Number of models: 1 Model: "" Number of chains: 32 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: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "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: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 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: "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 35.274 46.579 24.022 1.00215.57 S ATOM 4207 SG CYS P 187 37.469 45.714 20.914 1.00234.09 S Time building chain proxies: 6.62, per 1000 atoms: 0.20 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.017, 128.898, 165.726, 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=2.06 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 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=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 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 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " 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: 196 helices and 21 sheets defined 61.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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: 3.731A 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 150 Processing helix chain 'C' and resid 151 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: 6.792A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.767A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.817A 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: 4.092A 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: 3.615A 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 101 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: 4.135A 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: 3.586A 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: 3.551A 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: 3.995A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.589A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.528A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.977A 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: 3.654A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.593A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.433A 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: 3.607A 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: 3.597A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.879A 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: 3.582A 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: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.772A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.833A 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: 3.697A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.592A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.944A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.338A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.769A 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: 3.537A 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: 3.548A 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: 3.822A 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: 3.740A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.502A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.777A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.788A 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: 3.775A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.801A 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: 4.085A 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: 3.624A 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: 4.093A 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: 3.594A 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: 3.522A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 4.000A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.065A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.517A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.019A 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: 3.659A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.637A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.345A 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: 3.613A 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: 3.592A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.578A 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: 3.515A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.786A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.841A 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: 3.879A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.585A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 3.953A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 321 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.332A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.540A 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: 3.549A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.824A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.657A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.911A 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: 3.636A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.508A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.309A 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: 3.867A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.109A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.624A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.600A 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: 6.527A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.319A 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: 3.866A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.104A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.647A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.596A 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 1894 hydrogen bonds defined for protein. 5340 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: 6.12 Time building geometry restraints manager: 3.94 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: 13547 1.40 - 1.61: 19598 1.61 - 1.81: 162 1.81 - 2.02: 50 2.02 - 2.23: 18 Bond restraints: 33375 Sorted by residual: bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.619 -0.161 1.90e-02 2.77e+03 7.16e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.486 -0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.608 -0.150 1.90e-02 2.77e+03 6.22e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.475 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.463 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 43300 3.96 - 7.92: 1842 7.92 - 11.88: 189 11.88 - 15.84: 30 15.84 - 19.79: 5 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 91.33 13.00 1.14e+00 7.69e-01 1.30e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.24 13.09 1.20e+00 6.94e-01 1.19e+02 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 92.21 19.79 2.20e+00 2.07e-01 8.10e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.76 -10.10 1.14e+00 7.69e-01 7.85e+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 93.08 18.92 2.20e+00 2.07e-01 7.39e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 18516 31.38 - 62.77: 973 62.77 - 94.15: 98 94.15 - 125.53: 1 125.53 - 156.91: 1 Dihedral angle restraints: 19589 sinusoidal: 7970 harmonic: 11619 Sorted by residual: 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 -106.38 -16.22 0 2.50e+00 1.60e-01 4.21e+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 -106.92 -15.68 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -107.10 -15.50 0 2.50e+00 1.60e-01 3.85e+01 ... (remaining 19586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4765 0.264 - 0.529: 178 0.529 - 0.793: 5 0.793 - 1.058: 2 1.058 - 1.322: 2 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 -1.25 -1.32 2.00e-01 2.50e+01 4.37e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.50 -1.07 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB4 CDL O 402 " pdb=" CB3 CDL O 402 " pdb=" CB6 CDL O 402 " pdb=" OB6 CDL O 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.61 -0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " 0.009 2.00e-02 2.50e+03 2.40e-01 5.78e+02 pdb=" C21 AWB C 506 " -0.395 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.170 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 507 " -0.007 2.00e-02 2.50e+03 2.38e-01 5.65e+02 pdb=" C21 AWB N 507 " 0.390 2.00e-02 2.50e+03 pdb=" N1 AWB N 507 " -0.173 2.00e-02 2.50e+03 pdb=" O5 AWB N 507 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 101 " -0.074 2.00e-02 2.50e+03 3.97e-02 3.15e+01 pdb=" CG TYR G 101 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 101 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR G 101 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR G 101 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR G 101 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 101 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR G 101 " -0.059 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 6 2.23 - 2.90: 12297 2.90 - 3.57: 47057 3.57 - 4.23: 86081 4.23 - 4.90: 137836 Nonbonded interactions: 283277 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.563 3.460 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.048 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.058 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.116 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.187 3.080 ... (remaining 283272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.150 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 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 0.223 33390 Z= 0.721 Angle : 1.931 19.795 45379 Z= 1.199 Chirality : 0.126 1.322 4952 Planarity : 0.009 0.240 5712 Dihedral : 17.932 156.913 12088 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 4.36 % Allowed : 8.39 % Favored : 87.25 % Cbeta Deviations : 2.03 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 3955 helix: -1.22 (0.09), residues: 2139 sheet: -0.11 (0.25), residues: 351 loop : -0.70 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C 283 TYR 0.074 0.009 TYR G 101 PHE 0.055 0.009 PHE B 107 TRP 0.051 0.010 TRP N 30 HIS 0.024 0.005 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01198 / 0.72 (33375) covalent geometry : angle 1.92743 / 1.20 (45366) SS BOND : bond 0.03004 / 1.65 ( 5) SS BOND : angle 2.62708 / 1.37 ( 10) hydrogen bonds : bond 0.18664 / 12.49 ( 1894) hydrogen bonds : angle 7.10676 / 5.09 ( 5340) metal coordination : bond 0.08393 / 4.16 ( 4) metal coordination : angle 13.67792 / 7.51 ( 3) Misc. bond : bond 0.14761 / 7.92 ( 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 428 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 283 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.9105 (mtm) cc_final: 0.8820 (mmm) REVERT: C 272 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8715 (mt-10) REVERT: C 295 MET cc_start: 0.9130 (ttp) cc_final: 0.8792 (tmm) REVERT: P 68 MET cc_start: 0.8592 (mmm) cc_final: 0.8246 (mmt) REVERT: G 17 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7389 (p) REVERT: G 40 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9191 (mm) REVERT: G 50 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: F 113 ASP cc_start: 0.8872 (m-30) cc_final: 0.8605 (t0) REVERT: F 125 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9022 (mp0) REVERT: F 140 ASP cc_start: 0.8933 (m-30) cc_final: 0.8063 (t0) REVERT: A 29 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8641 (mmtt) REVERT: A 59 ASP cc_start: 0.9245 (t0) cc_final: 0.8971 (p0) REVERT: A 94 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 19 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: B 58 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8910 (tm-30) REVERT: B 60 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: D 186 GLN cc_start: 0.8943 (mp10) cc_final: 0.8708 (mp10) REVERT: D 193 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: D 283 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9105 (pm20) REVERT: H 51 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7355 (ptm-80) REVERT: H 75 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8890 (tm-30) REVERT: H 78 GLU cc_start: 0.9127 (tt0) cc_final: 0.8689 (tm-30) REVERT: J 11 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8297 (tmtt) REVERT: J 74 GLU cc_start: 0.8176 (mp0) cc_final: 0.7916 (pm20) REVERT: N 264 VAL cc_start: 0.8384 (t) cc_final: 0.8183 (p) REVERT: N 272 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8663 (mt-10) REVERT: N 369 MET cc_start: 0.9131 (mmm) cc_final: 0.8904 (mtp) REVERT: E 96 ASP cc_start: 0.8933 (p0) cc_final: 0.8710 (p0) REVERT: R 55 MET cc_start: 0.9250 (mmm) cc_final: 0.9006 (tpt) REVERT: R 97 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8694 (mt-10) REVERT: Q 95 LYS cc_start: 0.9351 (tptt) cc_final: 0.8926 (ttpt) REVERT: Q 140 ASP cc_start: 0.9442 (m-30) cc_final: 0.9241 (t0) REVERT: L 51 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8656 (m) REVERT: L 397 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5226 (mt) REVERT: M 292 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8661 (p) REVERT: M 386 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9160 (tp) REVERT: S 51 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7338 (ptm160) REVERT: S 57 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8406 (tp) REVERT: T 31 MET cc_start: 0.9014 (mmp) cc_final: 0.8493 (mmt) outliers start: 145 outliers final: 22 residues processed: 408 average time/residue: 0.2203 time to fit residues: 139.3526 Evaluate side-chains 194 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 109 PRO Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 324 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 332 ASN F 132 HIS ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 177 ASN A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 92 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 HIS N 14 ASN N 332 ASN E 90 ASN L 135 GLN L 371 ASN M 87 HIS M 92 HIS M 215 GLN M 316 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.037633 restraints weight = 164392.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.038866 restraints weight = 78419.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039666 restraints weight = 48520.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040083 restraints weight = 35457.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.040415 restraints weight = 29588.855| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.532 33390 Z= 0.168 Angle : 0.667 17.386 45379 Z= 0.327 Chirality : 0.043 0.226 4952 Planarity : 0.004 0.067 5712 Dihedral : 12.355 128.776 4985 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.77 % Allowed : 10.50 % Favored : 87.73 % 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: 0.74 (0.13), residues: 3955 helix: 0.92 (0.11), residues: 2163 sheet: 0.47 (0.27), residues: 361 loop : 0.01 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 202 TYR 0.023 0.002 TYR H 81 PHE 0.019 0.002 PHE L 334 TRP 0.026 0.002 TRP C 156 HIS 0.007 0.001 HIS N 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (33375) covalent geometry : angle 0.66550 / 0.33 (45366) SS BOND : bond 0.00348 / 0.18 ( 5) SS BOND : angle 0.90669 / 0.48 ( 10) hydrogen bonds : bond 0.04952 / 3.26 ( 1894) hydrogen bonds : angle 4.90189 / 3.54 ( 5340) metal coordination : bond 0.02356 / 1.18 ( 4) metal coordination : angle 5.44592 / 2.98 ( 3) Misc. bond : bond 0.36722 / 18.23 ( 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 235 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8650 (ttp) cc_final: 0.8312 (tmm) REVERT: P 68 MET cc_start: 0.7933 (mmm) cc_final: 0.7671 (mpp) REVERT: G 112 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: G 115 GLU cc_start: 0.8380 (tt0) cc_final: 0.8081 (tt0) REVERT: F 88 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7987 (pp20) REVERT: F 140 ASP cc_start: 0.8262 (m-30) cc_final: 0.7574 (t0) REVERT: A 94 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (tp) REVERT: B 58 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 60 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: B 343 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.9010 (ttmt) REVERT: D 186 GLN cc_start: 0.8686 (mp10) cc_final: 0.8419 (mp10) REVERT: D 283 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: H 78 GLU cc_start: 0.8493 (tt0) cc_final: 0.8238 (tm-30) REVERT: I 31 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: J 11 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8255 (tmtt) REVERT: N 139 MET cc_start: 0.8717 (mmt) cc_final: 0.8423 (tpt) REVERT: N 263 MET cc_start: 0.8161 (mpp) cc_final: 0.7911 (mmp) REVERT: R 31 TYR cc_start: 0.9011 (t80) cc_final: 0.8652 (t80) REVERT: R 112 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: Q 103 GLU cc_start: 0.8871 (pt0) cc_final: 0.8554 (pt0) REVERT: L 51 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8188 (m) REVERT: S 51 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7786 (ptm160) REVERT: T 31 MET cc_start: 0.9188 (mmp) cc_final: 0.8519 (mmt) outliers start: 59 outliers final: 19 residues processed: 226 average time/residue: 0.1998 time to fit residues: 74.0250 Evaluate side-chains 168 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 31 MET 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 88 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 43 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 138 optimal weight: 0.3980 chunk 258 optimal weight: 10.0000 chunk 38 optimal weight: 0.0050 chunk 15 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN P 90 ASN F 96 HIS A 317 GLN B 121 GLN B 316 GLN L 317 GLN M 121 GLN M 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.037699 restraints weight = 163563.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038934 restraints weight = 76992.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.039734 restraints weight = 47140.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040256 restraints weight = 34198.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.040491 restraints weight = 27640.687| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 33390 Z= 0.138 Angle : 0.564 14.326 45379 Z= 0.277 Chirality : 0.041 0.183 4952 Planarity : 0.004 0.041 5712 Dihedral : 11.149 108.790 4919 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.53 % Allowed : 10.86 % Favored : 87.61 % 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: 1.52 (0.13), residues: 3955 helix: 1.59 (0.11), residues: 2158 sheet: 0.69 (0.27), residues: 359 loop : 0.34 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.019 0.001 TYR F 114 PHE 0.016 0.001 PHE B 107 TRP 0.012 0.001 TRP N 142 HIS 0.009 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (33375) covalent geometry : angle 0.56354 / 0.28 (45366) SS BOND : bond 0.00267 / 0.14 ( 5) SS BOND : angle 0.80855 / 0.44 ( 10) hydrogen bonds : bond 0.04214 / 2.77 ( 1894) hydrogen bonds : angle 4.55491 / 3.30 ( 5340) metal coordination : bond 0.01118 / 0.56 ( 4) metal coordination : angle 1.79678 / 1.00 ( 3) Misc. bond : bond 0.36106 / 16.80 ( 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 199 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8640 (ttp) cc_final: 0.8284 (tmm) REVERT: P 68 MET cc_start: 0.7828 (mmm) cc_final: 0.7507 (mpp) REVERT: G 112 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: G 115 GLU cc_start: 0.8355 (tt0) cc_final: 0.8059 (tt0) REVERT: F 88 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7843 (tm-30) REVERT: F 100 GLU cc_start: 0.8826 (pt0) cc_final: 0.8281 (pp20) REVERT: F 140 ASP cc_start: 0.8248 (m-30) cc_final: 0.7780 (t0) REVERT: A 94 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8570 (tp) REVERT: B 58 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: B 60 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: D 186 GLN cc_start: 0.8663 (mp10) cc_final: 0.8303 (mp10) REVERT: H 78 GLU cc_start: 0.8503 (tt0) cc_final: 0.8232 (tm-30) REVERT: J 11 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8311 (tmtt) REVERT: N 139 MET cc_start: 0.8686 (mmt) cc_final: 0.8373 (tpt) REVERT: N 282 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9131 (tp) REVERT: N 374 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7461 (mt-10) REVERT: Q 100 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: Q 103 GLU cc_start: 0.8767 (pt0) cc_final: 0.8348 (pt0) REVERT: L 51 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (m) REVERT: T 31 MET cc_start: 0.9175 (mmp) cc_final: 0.8505 (mmt) outliers start: 51 outliers final: 22 residues processed: 188 average time/residue: 0.2045 time to fit residues: 64.0935 Evaluate side-chains 167 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 90 optimal weight: 9.9990 chunk 241 optimal weight: 0.0370 chunk 111 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN P 90 ASN ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 463 ASN Q 132 HIS L 91 GLN M 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036493 restraints weight = 165516.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037699 restraints weight = 79175.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.038454 restraints weight = 48812.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038946 restraints weight = 35874.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.039231 restraints weight = 29332.063| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.508 33390 Z= 0.222 Angle : 0.609 18.006 45379 Z= 0.293 Chirality : 0.043 0.201 4952 Planarity : 0.004 0.044 5712 Dihedral : 10.727 100.019 4907 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.80 % Allowed : 11.16 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3955 helix: 1.71 (0.11), residues: 2147 sheet: 0.71 (0.28), residues: 351 loop : 0.42 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.017 0.002 TYR F 114 PHE 0.024 0.002 PHE N 77 TRP 0.012 0.001 TRP N 142 HIS 0.009 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (33375) covalent geometry : angle 0.60807 / 0.29 (45366) SS BOND : bond 0.00256 / 0.14 ( 5) SS BOND : angle 0.78602 / 0.41 ( 10) hydrogen bonds : bond 0.04181 / 2.75 ( 1894) hydrogen bonds : angle 4.51768 / 3.28 ( 5340) metal coordination : bond 0.01601 / 0.81 ( 4) metal coordination : angle 2.91947 / 1.70 ( 3) Misc. bond : bond 0.41873 / 20.07 ( 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 199 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8622 (ttp) cc_final: 0.8253 (tmm) REVERT: P 68 MET cc_start: 0.7906 (mmm) cc_final: 0.7607 (mpp) REVERT: G 115 GLU cc_start: 0.8349 (tt0) cc_final: 0.8085 (tt0) REVERT: F 88 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8051 (pp20) REVERT: F 140 ASP cc_start: 0.8371 (m-30) cc_final: 0.7897 (t0) REVERT: A 94 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 212 MET cc_start: 0.8084 (mtm) cc_final: 0.7723 (mpp) REVERT: A 351 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9241 (mt) REVERT: B 58 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: B 60 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: D 186 GLN cc_start: 0.8662 (mp10) cc_final: 0.8322 (mp10) REVERT: H 16 MET cc_start: 0.8405 (tpp) cc_final: 0.7952 (tpp) REVERT: H 78 GLU cc_start: 0.8483 (tt0) cc_final: 0.8275 (tm-30) REVERT: J 11 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (tmtt) REVERT: J 69 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: N 139 MET cc_start: 0.8718 (mmt) cc_final: 0.8411 (tpt) REVERT: N 282 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9180 (tp) REVERT: N 374 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7458 (mt-10) REVERT: R 31 TYR cc_start: 0.8968 (t80) cc_final: 0.8685 (t80) REVERT: Q 100 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: Q 103 GLU cc_start: 0.8820 (pt0) cc_final: 0.8456 (pt0) REVERT: M 357 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8725 (p) REVERT: O 90 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8769 (m-70) REVERT: O 235 MET cc_start: 0.7882 (tpp) cc_final: 0.7623 (tpp) REVERT: T 31 MET cc_start: 0.9170 (mmp) cc_final: 0.8527 (mmt) outliers start: 60 outliers final: 26 residues processed: 191 average time/residue: 0.1811 time to fit residues: 57.7329 Evaluate side-chains 167 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 90 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 159 optimal weight: 0.0370 chunk 226 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.3028 r_free = 0.3028 target = 0.045228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036755 restraints weight = 165689.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.037961 restraints weight = 79544.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.038742 restraints weight = 49277.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.039262 restraints weight = 36068.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039464 restraints weight = 29266.313| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2970 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= 0.166 Angle : 0.551 16.654 45379 Z= 0.266 Chirality : 0.041 0.166 4952 Planarity : 0.004 0.043 5712 Dihedral : 10.311 89.624 4906 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.62 % Allowed : 12.00 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.14), residues: 3955 helix: 1.83 (0.11), residues: 2157 sheet: 0.61 (0.27), residues: 359 loop : 0.52 (0.18), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 43 TYR 0.019 0.001 TYR F 114 PHE 0.014 0.001 PHE B 73 TRP 0.012 0.001 TRP N 142 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (33375) covalent geometry : angle 0.55027 / 0.27 (45366) SS BOND : bond 0.00281 / 0.15 ( 5) SS BOND : angle 0.73952 / 0.39 ( 10) hydrogen bonds : bond 0.03902 / 2.57 ( 1894) hydrogen bonds : angle 4.41552 / 3.21 ( 5340) metal coordination : bond 0.01069 / 0.54 ( 4) metal coordination : angle 2.80605 / 1.65 ( 3) Misc. bond : bond 0.36337 / 17.39 ( 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 189 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 68 MET cc_start: 0.7890 (mmm) cc_final: 0.7586 (mpp) REVERT: G 115 GLU cc_start: 0.8339 (tt0) cc_final: 0.8051 (tt0) REVERT: F 88 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8101 (pp20) REVERT: F 100 GLU cc_start: 0.8829 (pt0) cc_final: 0.8265 (pp20) REVERT: F 140 ASP cc_start: 0.8304 (m-30) cc_final: 0.7860 (t0) REVERT: A 351 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9270 (mt) REVERT: B 357 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.7988 (p) REVERT: D 303 MET cc_start: 0.8898 (mtp) cc_final: 0.8678 (mtp) REVERT: H 16 MET cc_start: 0.8316 (tpp) cc_final: 0.7893 (tpp) REVERT: J 69 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: N 139 MET cc_start: 0.8685 (mmt) cc_final: 0.8436 (tpt) REVERT: N 282 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9159 (tp) REVERT: N 374 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7427 (mt-10) REVERT: R 31 TYR cc_start: 0.8933 (t80) cc_final: 0.8695 (t80) REVERT: Q 99 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8019 (t0) REVERT: Q 100 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: Q 103 GLU cc_start: 0.8738 (pt0) cc_final: 0.8393 (pt0) REVERT: Q 122 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: M 357 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8741 (p) REVERT: O 235 MET cc_start: 0.7828 (tpp) cc_final: 0.7541 (tpp) REVERT: T 31 MET cc_start: 0.9161 (mmp) cc_final: 0.8539 (mmt) outliers start: 54 outliers final: 29 residues processed: 182 average time/residue: 0.1775 time to fit residues: 55.0070 Evaluate side-chains 166 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 348 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS D 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037351 restraints weight = 163907.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.038567 restraints weight = 78609.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.039357 restraints weight = 48760.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039800 restraints weight = 35667.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040162 restraints weight = 29540.599| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.408 33390 Z= 0.119 Angle : 0.514 14.412 45379 Z= 0.250 Chirality : 0.040 0.168 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.806 89.456 4897 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 12.75 % Favored : 85.95 % 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: 1.97 (0.14), residues: 3955 helix: 1.98 (0.11), residues: 2155 sheet: 0.66 (0.27), residues: 361 loop : 0.59 (0.18), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 43 TYR 0.021 0.001 TYR F 114 PHE 0.014 0.001 PHE L 334 TRP 0.014 0.001 TRP P 120 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (33375) covalent geometry : angle 0.51383 / 0.25 (45366) SS BOND : bond 0.00236 / 0.13 ( 5) SS BOND : angle 0.68754 / 0.36 ( 10) hydrogen bonds : bond 0.03648 / 2.40 ( 1894) hydrogen bonds : angle 4.29511 / 3.12 ( 5340) metal coordination : bond 0.00820 / 0.41 ( 4) metal coordination : angle 2.92238 / 1.69 ( 3) Misc. bond : bond 0.28854 / 13.49 ( 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 178 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8836 (ttp) cc_final: 0.8112 (tmm) REVERT: P 68 MET cc_start: 0.7843 (mmm) cc_final: 0.7553 (mpp) REVERT: G 115 GLU cc_start: 0.8327 (tt0) cc_final: 0.8094 (tt0) REVERT: F 88 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8094 (pp20) REVERT: F 100 GLU cc_start: 0.8733 (pt0) cc_final: 0.8190 (pp20) REVERT: A 351 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9268 (mt) REVERT: B 357 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7933 (p) REVERT: H 16 MET cc_start: 0.8238 (tpp) cc_final: 0.7953 (tpp) REVERT: J 69 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: N 139 MET cc_start: 0.8644 (mmt) cc_final: 0.8365 (tpt) REVERT: N 282 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9129 (tp) REVERT: N 374 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7393 (mt-10) REVERT: R 31 TYR cc_start: 0.8882 (t80) cc_final: 0.8656 (t80) REVERT: Q 100 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: Q 103 GLU cc_start: 0.8687 (pt0) cc_final: 0.8373 (pt0) REVERT: M 357 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8721 (p) REVERT: T 31 MET cc_start: 0.9160 (mmp) cc_final: 0.8511 (mmt) outliers start: 43 outliers final: 27 residues processed: 174 average time/residue: 0.2051 time to fit residues: 60.3650 Evaluate side-chains 161 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 90 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 306 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 362 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN O 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036978 restraints weight = 165729.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.038197 restraints weight = 79506.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.038989 restraints weight = 49218.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039422 restraints weight = 35924.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039733 restraints weight = 29806.075| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.420 33390 Z= 0.142 Angle : 0.534 15.869 45379 Z= 0.255 Chirality : 0.040 0.163 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.636 89.932 4897 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 12.93 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.14), residues: 3955 helix: 2.07 (0.11), residues: 2141 sheet: 0.61 (0.27), residues: 361 loop : 0.67 (0.18), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 63 TYR 0.029 0.001 TYR F 114 PHE 0.014 0.001 PHE L 334 TRP 0.011 0.001 TRP P 120 HIS 0.006 0.001 HIS N 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (33375) covalent geometry : angle 0.53346 / 0.25 (45366) SS BOND : bond 0.00273 / 0.15 ( 5) SS BOND : angle 0.67445 / 0.35 ( 10) hydrogen bonds : bond 0.03677 / 2.42 ( 1894) hydrogen bonds : angle 4.28536 / 3.11 ( 5340) metal coordination : bond 0.00920 / 0.46 ( 4) metal coordination : angle 3.10875 / 1.81 ( 3) Misc. bond : bond 0.29928 / 14.29 ( 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 180 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8837 (ttp) cc_final: 0.8130 (tmm) REVERT: G 115 GLU cc_start: 0.8346 (tt0) cc_final: 0.8132 (tt0) REVERT: G 120 ASP cc_start: 0.8252 (t0) cc_final: 0.8011 (m-30) REVERT: F 88 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8084 (pp20) REVERT: F 100 GLU cc_start: 0.8723 (pt0) cc_final: 0.8187 (pp20) REVERT: A 351 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9292 (mt) REVERT: B 357 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7975 (p) REVERT: D 90 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8272 (t-90) REVERT: H 16 MET cc_start: 0.8258 (tpp) cc_final: 0.8032 (tpp) REVERT: J 69 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: N 139 MET cc_start: 0.8644 (mmt) cc_final: 0.8364 (tpt) REVERT: N 282 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9124 (tp) REVERT: N 374 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7464 (mt-10) REVERT: Q 100 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: Q 103 GLU cc_start: 0.8722 (pt0) cc_final: 0.8419 (pt0) REVERT: M 357 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8751 (p) REVERT: T 31 MET cc_start: 0.9143 (mmp) cc_final: 0.8483 (mmt) outliers start: 48 outliers final: 32 residues processed: 176 average time/residue: 0.1958 time to fit residues: 58.6280 Evaluate side-chains 166 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 253 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.044589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.036149 restraints weight = 166917.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037343 restraints weight = 80091.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.038106 restraints weight = 49760.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.038542 restraints weight = 36598.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038880 restraints weight = 30409.553| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.502 33390 Z= 0.222 Angle : 0.600 18.249 45379 Z= 0.286 Chirality : 0.042 0.170 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.685 89.715 4897 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.68 % Allowed : 12.75 % Favored : 85.56 % 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: 1.98 (0.14), residues: 3955 helix: 1.98 (0.11), residues: 2142 sheet: 0.53 (0.27), residues: 361 loop : 0.66 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 63 TYR 0.031 0.002 TYR F 114 PHE 0.016 0.002 PHE N 77 TRP 0.012 0.001 TRP C 142 HIS 0.039 0.001 HIS O 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (33375) covalent geometry : angle 0.59943 / 0.29 (45366) SS BOND : bond 0.00291 / 0.16 ( 5) SS BOND : angle 0.79260 / 0.42 ( 10) hydrogen bonds : bond 0.03936 / 2.59 ( 1894) hydrogen bonds : angle 4.37814 / 3.18 ( 5340) metal coordination : bond 0.01539 / 0.78 ( 4) metal coordination : angle 2.78997 / 1.63 ( 3) Misc. bond : bond 0.38335 / 19.03 ( 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 181 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8835 (ttp) cc_final: 0.8116 (tmm) REVERT: P 68 MET cc_start: 0.8226 (tpp) cc_final: 0.7919 (mpp) REVERT: G 115 GLU cc_start: 0.8331 (tt0) cc_final: 0.8083 (tt0) REVERT: F 88 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8077 (pp20) REVERT: A 212 MET cc_start: 0.8077 (mpp) cc_final: 0.7314 (mpp) REVERT: A 351 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9287 (mt) REVERT: B 357 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 193 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6822 (pp30) REVERT: H 16 MET cc_start: 0.8353 (tpp) cc_final: 0.8095 (tpp) REVERT: J 69 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: N 139 MET cc_start: 0.8650 (mmt) cc_final: 0.8392 (tpt) REVERT: N 282 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9159 (tp) REVERT: R 31 TYR cc_start: 0.8927 (t80) cc_final: 0.8640 (t80) REVERT: Q 99 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.7995 (t0) REVERT: Q 100 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: Q 103 GLU cc_start: 0.8647 (pt0) cc_final: 0.8373 (pt0) REVERT: M 357 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8843 (p) REVERT: T 31 MET cc_start: 0.9138 (mmp) cc_final: 0.8531 (mmt) outliers start: 56 outliers final: 38 residues processed: 177 average time/residue: 0.1891 time to fit residues: 57.4028 Evaluate side-chains 169 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 253 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 82 optimal weight: 20.0000 chunk 278 optimal weight: 0.1980 chunk 128 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036480 restraints weight = 165540.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.037680 restraints weight = 79543.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.038433 restraints weight = 49345.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.038934 restraints weight = 36395.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.039182 restraints weight = 29676.206| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.450 33390 Z= 0.174 Angle : 0.562 17.039 45379 Z= 0.268 Chirality : 0.041 0.163 4952 Planarity : 0.004 0.043 5712 Dihedral : 9.616 88.712 4897 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 1.56 % Allowed : 12.87 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2140 sheet: 0.56 (0.27), residues: 361 loop : 0.67 (0.18), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.031 0.001 TYR F 114 PHE 0.014 0.001 PHE L 334 TRP 0.013 0.001 TRP N 142 HIS 0.007 0.001 HIS O 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (33375) covalent geometry : angle 0.56115 / 0.27 (45366) SS BOND : bond 0.00286 / 0.16 ( 5) SS BOND : angle 0.72086 / 0.38 ( 10) hydrogen bonds : bond 0.03819 / 2.51 ( 1894) hydrogen bonds : angle 4.34616 / 3.16 ( 5340) metal coordination : bond 0.01276 / 0.64 ( 4) metal coordination : angle 2.59952 / 1.51 ( 3) Misc. bond : bond 0.34043 / 16.43 ( 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 179 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8830 (ttp) cc_final: 0.8102 (tmm) REVERT: G 110 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7407 (mm-30) REVERT: G 115 GLU cc_start: 0.8339 (tt0) cc_final: 0.8115 (tt0) REVERT: F 88 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8101 (pp20) REVERT: F 100 GLU cc_start: 0.8614 (pt0) cc_final: 0.8090 (pp20) REVERT: A 212 MET cc_start: 0.8014 (mpp) cc_final: 0.7227 (mpp) REVERT: A 351 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9311 (mt) REVERT: B 357 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8060 (p) REVERT: D 90 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8315 (t-90) REVERT: D 248 MET cc_start: 0.7907 (mmm) cc_final: 0.7418 (tpt) REVERT: H 16 MET cc_start: 0.8306 (tpp) cc_final: 0.8096 (tpp) REVERT: J 69 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: N 139 MET cc_start: 0.8635 (mmt) cc_final: 0.8371 (tpt) REVERT: N 282 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9159 (tp) REVERT: Q 99 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8026 (t0) REVERT: Q 100 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: Q 103 GLU cc_start: 0.8654 (pt0) cc_final: 0.8379 (pt0) REVERT: M 357 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8817 (p) REVERT: T 31 MET cc_start: 0.9134 (mmp) cc_final: 0.8492 (mmt) outliers start: 52 outliers final: 37 residues processed: 174 average time/residue: 0.1919 time to fit residues: 57.5206 Evaluate side-chains 170 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 253 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 317 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 286 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.037380 restraints weight = 164946.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.038598 restraints weight = 78577.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039393 restraints weight = 48372.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039834 restraints weight = 35077.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040187 restraints weight = 28945.242| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.477 33390 Z= 0.112 Angle : 0.526 14.591 45379 Z= 0.252 Chirality : 0.040 0.166 4952 Planarity : 0.004 0.042 5712 Dihedral : 9.343 89.939 4897 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.67 % Favored : 98.28 % Rotamer: Outliers : 1.20 % Allowed : 13.29 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.14), residues: 3955 helix: 2.09 (0.11), residues: 2157 sheet: 0.69 (0.27), residues: 359 loop : 0.71 (0.18), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.030 0.001 TYR F 114 PHE 0.013 0.001 PHE L 334 TRP 0.015 0.001 TRP P 120 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (33375) covalent geometry : angle 0.52508 / 0.25 (45366) SS BOND : bond 0.00324 / 0.18 ( 5) SS BOND : angle 0.73769 / 0.39 ( 10) hydrogen bonds : bond 0.03561 / 2.34 ( 1894) hydrogen bonds : angle 4.24598 / 3.08 ( 5340) metal coordination : bond 0.00913 / 0.46 ( 4) metal coordination : angle 2.67192 / 1.53 ( 3) Misc. bond : bond 0.30988 / 13.54 ( 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 167 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 MET cc_start: 0.8808 (ttp) cc_final: 0.8098 (tmm) REVERT: G 110 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7369 (mm-30) REVERT: G 115 GLU cc_start: 0.8337 (tt0) cc_final: 0.8124 (tt0) REVERT: F 88 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8085 (pp20) REVERT: F 100 GLU cc_start: 0.8589 (pt0) cc_final: 0.8101 (pp20) REVERT: A 212 MET cc_start: 0.7924 (mpp) cc_final: 0.7173 (mpp) REVERT: A 351 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9312 (mt) REVERT: B 357 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8000 (p) REVERT: D 90 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8285 (t-90) REVERT: D 303 MET cc_start: 0.8761 (mtp) cc_final: 0.8343 (mtt) REVERT: J 69 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: N 139 MET cc_start: 0.8623 (mmt) cc_final: 0.8360 (tpt) REVERT: N 282 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9107 (tp) REVERT: R 31 TYR cc_start: 0.8720 (t80) cc_final: 0.8398 (t80) REVERT: R 50 GLU cc_start: 0.7999 (pm20) cc_final: 0.7658 (mp0) REVERT: Q 100 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: Q 103 GLU cc_start: 0.8623 (pt0) cc_final: 0.8359 (pt0) REVERT: M 357 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8829 (p) REVERT: O 248 MET cc_start: 0.7888 (tpp) cc_final: 0.7555 (tpp) REVERT: T 31 MET cc_start: 0.9134 (mmp) cc_final: 0.8476 (mmt) outliers start: 40 outliers final: 27 residues processed: 164 average time/residue: 0.1884 time to fit residues: 52.9931 Evaluate side-chains 157 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 371 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.045685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.037361 restraints weight = 165127.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.038590 restraints weight = 78861.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039381 restraints weight = 48242.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039824 restraints weight = 35024.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.040139 restraints weight = 28935.147| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.417 33390 Z= 0.116 Angle : 0.524 14.570 45379 Z= 0.251 Chirality : 0.040 0.164 4952 Planarity : 0.004 0.043 5712 Dihedral : 9.213 88.372 4897 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 13.47 % Favored : 85.41 % 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: 2.20 (0.14), residues: 3955 helix: 2.14 (0.11), residues: 2157 sheet: 0.72 (0.27), residues: 359 loop : 0.74 (0.18), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.030 0.001 TYR F 114 PHE 0.025 0.001 PHE P 64 TRP 0.013 0.001 TRP P 120 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (33375) covalent geometry : angle 0.52352 / 0.25 (45366) SS BOND : bond 0.00280 / 0.15 ( 5) SS BOND : angle 0.67085 / 0.35 ( 10) hydrogen bonds : bond 0.03519 / 2.31 ( 1894) hydrogen bonds : angle 4.20554 / 3.06 ( 5340) metal coordination : bond 0.00894 / 0.45 ( 4) metal coordination : angle 3.04247 / 1.76 ( 3) Misc. bond : bond 0.29816 / 13.41 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.09 seconds wall clock time: 77 minutes 11.86 seconds (4631.86 seconds total)