Starting phenix.real_space_refine on Mon Jul 6 07:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.map" model { file = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abi_15322/07_2026/8abi_15322.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21039 2.51 5 N 5300 2.21 5 O 6069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 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: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 339 Unusual residues: {'AWB': 1, 'CDL': 3, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 190 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 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: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 293 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 136 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "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 31.387 47.893 26.800 1.00345.56 S ATOM 4207 SG CYS P 187 33.675 46.143 24.220 1.00298.67 S Time building chain proxies: 6.45, per 1000 atoms: 0.20 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.833, 129.636, 165.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6069 8.00 N 5300 7.00 C 21039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 21 sheets defined 61.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 3.734A 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: 6.800A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.760A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.813A 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: 3.630A 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: 4.171A 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: 3.552A 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: 3.998A 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: 3.590A 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: 3.521A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.963A 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: 3.659A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.594A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.447A 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: 3.622A 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: 3.578A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.878A 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: 3.581A 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: 3.517A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.774A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.836A 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: 3.703A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.582A 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: 3.948A 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 56 removed outlier: 4.344A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 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: 3.534A 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: 3.502A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.816A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.661A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.742A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.806A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.757A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.805A 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: 4.099A 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: 3.633A 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: 4.146A 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: 3.595A 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: 3.994A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.585A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 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: 3.525A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.984A 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: 3.658A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.650A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.448A 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: 3.615A 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: 3.575A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.589A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 removed outlier: 3.522A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.785A 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: 3.951A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 56 removed outlier: 4.331A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.530A 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: 3.552A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.819A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.652A 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: 3.894A 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: 3.622A 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: 6.526A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.293A 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: 3.937A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.782A 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: 4.110A 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: 6.642A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.601A 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: 6.521A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.301A 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: 3.960A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.799A 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: 4.096A 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: 6.641A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.581A 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 1892 hydrogen bonds defined for protein. 5334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 3.40 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: 13579 1.40 - 1.61: 19582 1.61 - 1.82: 170 1.82 - 2.03: 26 2.03 - 2.24: 18 Bond restraints: 33375 Sorted by residual: bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.607 -0.149 1.90e-02 2.77e+03 6.13e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.601 -0.143 1.90e-02 2.77e+03 5.64e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.462 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.461 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C4 XP4 A3003 " pdb=" O5 XP4 A3003 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 43136 3.64 - 7.28: 1966 7.28 - 10.91: 223 10.91 - 14.55: 31 14.55 - 18.19: 10 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 91.84 12.49 1.14e+00 7.69e-01 1.20e+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 91.92 12.41 1.20e+00 6.94e-01 1.07e+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 93.81 18.19 2.20e+00 2.07e-01 6.84e+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 85.06 -9.40 1.14e+00 7.69e-01 6.80e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 98.38 12.76 1.56e+00 4.11e-01 6.69e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 18566 31.96 - 63.92: 933 63.92 - 95.87: 88 95.87 - 127.83: 1 127.83 - 159.79: 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 -105.29 -17.31 0 2.50e+00 1.60e-01 4.80e+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 -105.41 -17.19 0 2.50e+00 1.60e-01 4.73e+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 -106.34 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 19586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 4726 0.235 - 0.469: 216 0.469 - 0.704: 6 0.704 - 0.938: 2 0.938 - 1.173: 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 -1.40 -1.17 2.00e-01 2.50e+01 3.44e+01 chirality pdb=" CB4 CDL C 508 " pdb=" CB3 CDL C 508 " pdb=" CB6 CDL C 508 " pdb=" OB6 CDL C 508 " both_signs ideal model delta sigma weight residual False -2.57 -1.53 -1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB4 CDL N 507 " pdb=" CB3 CDL N 507 " pdb=" CB6 CDL N 507 " pdb=" OB6 CDL N 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.66 -0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 506 " -0.007 2.00e-02 2.50e+03 2.44e-01 5.95e+02 pdb=" C21 AWB N 506 " 0.400 2.00e-02 2.50e+03 pdb=" N1 AWB N 506 " -0.176 2.00e-02 2.50e+03 pdb=" O5 AWB N 506 " -0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " 0.023 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C21 AWB C 506 " -0.402 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.153 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC D 401 " -0.001 2.00e-02 2.50e+03 3.03e-02 2.07e+01 pdb=" C1B HEC D 401 " 0.020 2.00e-02 2.50e+03 pdb=" C2B HEC D 401 " 0.030 2.00e-02 2.50e+03 pdb=" C3B HEC D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C4B HEC D 401 " 0.005 2.00e-02 2.50e+03 pdb=" CAB HEC D 401 " -0.056 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " -0.051 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " 0.023 2.00e-02 2.50e+03 pdb=" CMB HEC D 401 " 0.027 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 287 2.63 - 3.19: 28778 3.19 - 3.76: 54097 3.76 - 4.33: 79539 4.33 - 4.90: 122376 Nonbonded interactions: 285077 Sorted by model distance: nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.058 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.067 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.100 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.165 3.080 nonbonded pdb=" NE2 HIS C 197 " pdb="FE HEM C 502 " model vdw 2.207 3.080 ... (remaining 285072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 503 or resid 506 through 507)) selection = (chain 'N' and (resid 1 through 503 or resid 506 through 507)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.720 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 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 0.208 33390 Z= 0.701 Angle : 1.828 18.191 45379 Z= 1.139 Chirality : 0.120 1.173 4952 Planarity : 0.009 0.244 5712 Dihedral : 17.778 159.790 12088 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 3.82 % Allowed : 8.45 % Favored : 87.73 % Cbeta Deviations : 1.55 % 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: -1.54 (0.12), residues: 3955 helix: -1.18 (0.09), residues: 2122 sheet: 0.13 (0.26), residues: 347 loop : -0.76 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG C 283 TYR 0.056 0.009 TYR G 101 PHE 0.053 0.008 PHE B 107 TRP 0.046 0.009 TRP A 474 HIS 0.026 0.005 HIS Q 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01147 / 0.70 (33375) covalent geometry : angle 1.82511 / 1.14 (45366) SS BOND : bond 0.02525 / 1.48 ( 5) SS BOND : angle 2.34161 / 1.18 ( 10) hydrogen bonds : bond 0.18624 / 12.24 ( 1892) hydrogen bonds : angle 7.06602 / 5.08 ( 5334) metal coordination : bond 0.08802 / 4.33 ( 4) metal coordination : angle 13.16436 / 7.00 ( 3) Misc. bond : bond 0.14133 / 7.26 ( 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 552 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 425 time to evaluate : 0.914 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: C 160 ASP cc_start: 0.9311 (m-30) cc_final: 0.8967 (m-30) REVERT: P 126 PHE cc_start: 0.7837 (m-10) cc_final: 0.6916 (m-10) REVERT: P 147 ARG cc_start: 0.4721 (OUTLIER) cc_final: 0.3563 (mtp180) REVERT: P 196 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7005 (mt) REVERT: G 50 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: F 138 THR cc_start: 0.7409 (m) cc_final: 0.7057 (m) REVERT: A 91 GLN cc_start: 0.8922 (tp40) cc_final: 0.8518 (tp40) REVERT: A 144 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 205 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: B 251 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8462 (pm20) REVERT: B 268 SER cc_start: 0.7696 (m) cc_final: 0.7284 (p) REVERT: B 306 ILE cc_start: 0.8833 (mt) cc_final: 0.8535 (mp) REVERT: D 164 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8623 (pm20) REVERT: I 35 THR cc_start: 0.9051 (m) cc_final: 0.8778 (p) REVERT: I 38 ASP cc_start: 0.8821 (m-30) cc_final: 0.8541 (m-30) REVERT: J 10 LYS cc_start: 0.9201 (tttm) cc_final: 0.8987 (tptt) REVERT: J 13 SER cc_start: 0.8632 (t) cc_final: 0.8355 (p) REVERT: N 197 HIS cc_start: 0.9490 (OUTLIER) cc_final: 0.8647 (p-80) REVERT: N 250 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8173 (ttpt) REVERT: R 123 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8363 (tm-30) REVERT: Q 109 GLN cc_start: 0.8369 (mt0) cc_final: 0.7914 (mp10) REVERT: Q 126 GLU cc_start: 0.7762 (mp0) cc_final: 0.7433 (tp30) REVERT: Q 140 ASP cc_start: 0.9027 (m-30) cc_final: 0.8626 (m-30) REVERT: L 91 GLN cc_start: 0.8647 (tp40) cc_final: 0.8346 (tp40) REVERT: O 164 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8813 (pm20) REVERT: O 223 ASP cc_start: 0.8437 (m-30) cc_final: 0.8217 (p0) REVERT: S 71 THR cc_start: 0.8767 (m) cc_final: 0.8458 (p) REVERT: S 87 HIS cc_start: 0.8315 (m-70) cc_final: 0.7686 (m-70) REVERT: U 55 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8079 (ttm170) outliers start: 127 outliers final: 9 residues processed: 521 average time/residue: 0.6871 time to fit residues: 420.1563 Evaluate side-chains 235 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 173 ASN C 332 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 92 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN D 90 HIS D 118 GLN H 42 HIS N 14 ASN N 332 ASN Q 131 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN M 215 GLN O 90 HIS O 118 GLN T 49 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055359 restraints weight = 108813.279| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.54 r_work: 0.3025 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.493 33390 Z= 0.163 Angle : 0.689 19.235 45379 Z= 0.336 Chirality : 0.043 0.220 4952 Planarity : 0.004 0.042 5712 Dihedral : 11.819 131.243 4920 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.17 % Allowed : 13.35 % Favored : 84.48 % 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: 0.69 (0.13), residues: 3955 helix: 0.87 (0.11), residues: 2173 sheet: 0.54 (0.27), residues: 357 loop : -0.02 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 146 TYR 0.023 0.002 TYR P 194 PHE 0.019 0.002 PHE A 334 TRP 0.032 0.002 TRP C 156 HIS 0.014 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (33375) covalent geometry : angle 0.68786 / 0.34 (45366) SS BOND : bond 0.00149 / 0.08 ( 5) SS BOND : angle 0.77383 / 0.41 ( 10) hydrogen bonds : bond 0.04896 / 3.26 ( 1892) hydrogen bonds : angle 4.90188 / 3.57 ( 5334) metal coordination : bond 0.01244 / 0.63 ( 4) metal coordination : angle 5.09344 / 2.60 ( 3) Misc. bond : bond 0.35252 / 17.57 ( 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 305 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 233 time to evaluate : 1.152 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: C 1 MET cc_start: 0.8812 (ttp) cc_final: 0.8560 (ttm) REVERT: C 160 ASP cc_start: 0.8721 (m-30) cc_final: 0.8485 (m-30) REVERT: C 369 MET cc_start: 0.8563 (mmm) cc_final: 0.8284 (mmm) REVERT: P 126 PHE cc_start: 0.7245 (m-10) cc_final: 0.6983 (m-10) REVERT: P 147 ARG cc_start: 0.3992 (OUTLIER) cc_final: 0.2076 (ttt180) REVERT: P 202 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7733 (ttm170) REVERT: P 222 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8429 (tp) REVERT: G 110 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8457 (mt-10) REVERT: G 115 GLU cc_start: 0.9036 (tt0) cc_final: 0.8809 (tt0) REVERT: F 80 ILE cc_start: 0.8748 (mm) cc_final: 0.8496 (mp) REVERT: F 125 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8549 (mm-30) REVERT: A 231 LYS cc_start: 0.8938 (tttt) cc_final: 0.8734 (tppt) REVERT: A 275 MET cc_start: 0.8625 (ttm) cc_final: 0.8314 (ttm) REVERT: B 58 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: B 306 ILE cc_start: 0.8552 (mt) cc_final: 0.8220 (mp) REVERT: D 166 ASN cc_start: 0.8261 (m110) cc_final: 0.7450 (m110) REVERT: J 13 SER cc_start: 0.8303 (t) cc_final: 0.7923 (p) REVERT: J 74 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: E 55 ASP cc_start: 0.8215 (p0) cc_final: 0.7877 (p0) REVERT: E 96 ASP cc_start: 0.8478 (p0) cc_final: 0.8218 (p0) REVERT: R 94 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8804 (mtmm) REVERT: R 123 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7843 (tm-30) REVERT: Q 126 GLU cc_start: 0.7442 (mp0) cc_final: 0.7019 (tp30) REVERT: Q 130 LEU cc_start: 0.9235 (tp) cc_final: 0.8973 (tp) REVERT: Q 141 LYS cc_start: 0.8846 (mppt) cc_final: 0.8626 (mppt) REVERT: L 91 GLN cc_start: 0.8471 (tp40) cc_final: 0.8096 (tp40) REVERT: M 334 GLU cc_start: 0.8829 (tp30) cc_final: 0.8459 (mm-30) REVERT: M 373 ILE cc_start: 0.5915 (tp) cc_final: 0.5175 (tt) REVERT: S 51 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.6462 (ptm-80) REVERT: U 59 ASP cc_start: 0.7834 (m-30) cc_final: 0.7515 (m-30) REVERT: U 73 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6877 (ptt-90) outliers start: 72 outliers final: 15 residues processed: 284 average time/residue: 0.6547 time to fit residues: 219.3020 Evaluate side-chains 211 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain Q residue 144 ARG Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 43 optimal weight: 8.9990 chunk 292 optimal weight: 0.2980 chunk 384 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 138 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN P 85 GLN F 132 HIS A 317 GLN B 121 GLN B 316 GLN D 102 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN N 177 GLN N 341 GLN Q 132 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 317 GLN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN M 379 GLN S 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047757 restraints weight = 109119.769| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.45 r_work: 0.2806 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.475 33390 Z= 0.241 Angle : 0.689 16.630 45379 Z= 0.338 Chirality : 0.045 0.268 4952 Planarity : 0.005 0.078 5712 Dihedral : 10.743 97.138 4897 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.85 % Rotamer: Outliers : 2.56 % Allowed : 13.29 % Favored : 84.15 % 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: 1.25 (0.13), residues: 3955 helix: 1.34 (0.11), residues: 2160 sheet: 0.62 (0.27), residues: 357 loop : 0.26 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 130 TYR 0.026 0.002 TYR M 341 PHE 0.019 0.002 PHE B 107 TRP 0.018 0.002 TRP C 156 HIS 0.027 0.002 HIS N 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (33375) covalent geometry : angle 0.68684 / 0.34 (45366) SS BOND : bond 0.00332 / 0.21 ( 5) SS BOND : angle 1.08653 / 0.53 ( 10) hydrogen bonds : bond 0.04500 / 2.99 ( 1892) hydrogen bonds : angle 4.71321 / 3.45 ( 5334) metal coordination : bond 0.03184 / 1.61 ( 4) metal coordination : angle 6.61897 / 3.48 ( 3) Misc. bond : bond 0.39490 / 19.45 ( 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 286 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 201 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8816 (ttp) cc_final: 0.8540 (ttm) REVERT: C 160 ASP cc_start: 0.8786 (m-30) cc_final: 0.8448 (m-30) REVERT: C 369 MET cc_start: 0.8607 (mmm) cc_final: 0.8353 (mmm) REVERT: P 126 PHE cc_start: 0.7750 (m-10) cc_final: 0.7016 (m-10) REVERT: P 202 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7875 (ttp80) REVERT: P 222 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8096 (tp) REVERT: G 16 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8865 (pptt) REVERT: G 112 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: G 123 GLU cc_start: 0.8585 (tt0) cc_final: 0.8382 (tt0) REVERT: F 80 ILE cc_start: 0.9129 (mm) cc_final: 0.8616 (mp) REVERT: F 125 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8654 (mm-30) REVERT: F 126 GLU cc_start: 0.7962 (mp0) cc_final: 0.7336 (mm-30) REVERT: A 397 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7582 (pp) REVERT: B 58 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 269 MET cc_start: 0.8092 (ttm) cc_final: 0.7888 (ttt) REVERT: D 164 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: D 166 ASN cc_start: 0.8756 (m110) cc_final: 0.8116 (m-40) REVERT: N 341 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8553 (pp30) REVERT: E 54 LYS cc_start: 0.9052 (tppt) cc_final: 0.8791 (tttt) REVERT: E 55 ASP cc_start: 0.8468 (p0) cc_final: 0.8016 (p0) REVERT: R 123 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7896 (tm-30) REVERT: Q 99 ASP cc_start: 0.8086 (m-30) cc_final: 0.7683 (p0) REVERT: Q 100 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7858 (pp20) REVERT: Q 141 LYS cc_start: 0.9051 (mppt) cc_final: 0.8778 (mppt) REVERT: S 51 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.6489 (ptm-80) REVERT: S 76 LYS cc_start: 0.8758 (tptm) cc_final: 0.8412 (tppt) REVERT: U 59 ASP cc_start: 0.8206 (m-30) cc_final: 0.7845 (m-30) outliers start: 85 outliers final: 17 residues processed: 267 average time/residue: 0.7059 time to fit residues: 219.5495 Evaluate side-chains 200 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 90 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 388 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 ASN N 341 GLN L 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047952 restraints weight = 108008.476| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.43 r_work: 0.2814 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.457 33390 Z= 0.151 Angle : 0.569 15.273 45379 Z= 0.277 Chirality : 0.041 0.156 4952 Planarity : 0.004 0.047 5712 Dihedral : 10.396 89.018 4892 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.65 % Allowed : 14.74 % Favored : 83.61 % 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: 1.56 (0.14), residues: 3955 helix: 1.61 (0.11), residues: 2158 sheet: 0.63 (0.27), residues: 353 loop : 0.42 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 70 TYR 0.016 0.001 TYR S 81 PHE 0.018 0.001 PHE P 216 TRP 0.011 0.001 TRP C 156 HIS 0.005 0.001 HIS M 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33375) covalent geometry : angle 0.56834 / 0.28 (45366) SS BOND : bond 0.00186 / 0.10 ( 5) SS BOND : angle 0.71294 / 0.36 ( 10) hydrogen bonds : bond 0.03920 / 2.60 ( 1892) hydrogen bonds : angle 4.57678 / 3.35 ( 5334) metal coordination : bond 0.00606 / 0.30 ( 4) metal coordination : angle 4.41802 / 2.32 ( 3) Misc. bond : bond 0.31584 / 15.78 ( 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 238 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8841 (ttp) cc_final: 0.8558 (ttm) REVERT: C 160 ASP cc_start: 0.8781 (m-30) cc_final: 0.8449 (m-30) REVERT: C 369 MET cc_start: 0.8599 (mmm) cc_final: 0.8374 (mmm) REVERT: G 115 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8903 (tp30) REVERT: G 123 GLU cc_start: 0.8567 (tt0) cc_final: 0.8317 (tt0) REVERT: F 80 ILE cc_start: 0.9170 (mm) cc_final: 0.8842 (mm) REVERT: F 84 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8776 (mm-30) REVERT: F 95 LYS cc_start: 0.8245 (tptt) cc_final: 0.7737 (tppt) REVERT: F 126 GLU cc_start: 0.8171 (mp0) cc_final: 0.7440 (mm-30) REVERT: B 58 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: D 90 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8732 (m-70) REVERT: D 164 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: J 13 SER cc_start: 0.8494 (t) cc_final: 0.8280 (t) REVERT: N 341 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8257 (pp30) REVERT: E 55 ASP cc_start: 0.8509 (p0) cc_final: 0.8075 (p0) REVERT: R 123 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7806 (tm-30) REVERT: Q 141 LYS cc_start: 0.9066 (mppt) cc_final: 0.8782 (mppt) REVERT: M 197 ASN cc_start: 0.8404 (t0) cc_final: 0.7149 (t0) REVERT: M 334 GLU cc_start: 0.9011 (tp30) cc_final: 0.8591 (mm-30) REVERT: O 248 MET cc_start: 0.9028 (ttp) cc_final: 0.8521 (ttm) REVERT: S 76 LYS cc_start: 0.8866 (tptm) cc_final: 0.8538 (tppt) REVERT: S 78 GLU cc_start: 0.8088 (tt0) cc_final: 0.7670 (tm-30) REVERT: U 59 ASP cc_start: 0.8254 (m-30) cc_final: 0.7746 (m-30) REVERT: U 73 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7299 (ptt-90) outliers start: 55 outliers final: 15 residues processed: 226 average time/residue: 0.6674 time to fit residues: 177.5048 Evaluate side-chains 186 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 226 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN R 45 ASN R 84 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047356 restraints weight = 108493.047| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.42 r_work: 0.2798 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.470 33390 Z= 0.150 Angle : 0.564 15.530 45379 Z= 0.272 Chirality : 0.041 0.166 4952 Planarity : 0.004 0.046 5712 Dihedral : 9.950 89.873 4889 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.83 % Allowed : 14.80 % Favored : 83.37 % 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: 1.72 (0.14), residues: 3955 helix: 1.75 (0.11), residues: 2152 sheet: 0.53 (0.27), residues: 359 loop : 0.52 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 70 TYR 0.020 0.001 TYR M 341 PHE 0.017 0.001 PHE L 334 TRP 0.011 0.001 TRP N 142 HIS 0.006 0.001 HIS N 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33375) covalent geometry : angle 0.56276 / 0.27 (45366) SS BOND : bond 0.00189 / 0.11 ( 5) SS BOND : angle 0.66892 / 0.32 ( 10) hydrogen bonds : bond 0.03824 / 2.53 ( 1892) hydrogen bonds : angle 4.47872 / 3.28 ( 5334) metal coordination : bond 0.01146 / 0.57 ( 4) metal coordination : angle 5.18384 / 2.77 ( 3) Misc. bond : bond 0.31411 / 15.88 ( 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 238 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8867 (ttp) cc_final: 0.8599 (ttm) REVERT: C 160 ASP cc_start: 0.8771 (m-30) cc_final: 0.8413 (m-30) REVERT: C 369 MET cc_start: 0.8606 (mmm) cc_final: 0.8377 (mmt) REVERT: G 16 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (pptt) REVERT: G 115 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8925 (tp30) REVERT: G 123 GLU cc_start: 0.8611 (tt0) cc_final: 0.8386 (tt0) REVERT: F 80 ILE cc_start: 0.9230 (mm) cc_final: 0.8903 (mm) REVERT: F 95 LYS cc_start: 0.8242 (tptt) cc_final: 0.8040 (tppt) REVERT: F 125 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8383 (mt-10) REVERT: F 126 GLU cc_start: 0.8245 (mp0) cc_final: 0.7515 (mm-30) REVERT: A 223 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7913 (OUTLIER) REVERT: B 58 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: B 180 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: B 269 MET cc_start: 0.8115 (ttm) cc_final: 0.7895 (tmm) REVERT: D 164 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7542 (pp20) REVERT: J 13 SER cc_start: 0.8481 (t) cc_final: 0.8255 (t) REVERT: N 341 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: E 54 LYS cc_start: 0.8960 (tppt) cc_final: 0.8739 (tttm) REVERT: E 55 ASP cc_start: 0.8517 (p0) cc_final: 0.8071 (p0) REVERT: R 123 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7869 (tm-30) REVERT: Q 116 HIS cc_start: 0.7360 (m-70) cc_final: 0.6774 (m-70) REVERT: Q 125 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8098 (tt0) REVERT: Q 141 LYS cc_start: 0.9103 (mppt) cc_final: 0.8789 (mppt) REVERT: M 119 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (mtpp) REVERT: M 197 ASN cc_start: 0.8564 (t0) cc_final: 0.7217 (t0) REVERT: M 364 MET cc_start: 0.8718 (mmm) cc_final: 0.8436 (mmt) REVERT: O 248 MET cc_start: 0.9211 (ttp) cc_final: 0.8456 (ttm) REVERT: S 76 LYS cc_start: 0.8985 (tptm) cc_final: 0.8709 (tppt) REVERT: S 78 GLU cc_start: 0.8161 (tt0) cc_final: 0.7746 (tm-30) REVERT: U 59 ASP cc_start: 0.8352 (m-30) cc_final: 0.7813 (m-30) REVERT: U 69 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7535 (pm20) outliers start: 61 outliers final: 22 residues processed: 229 average time/residue: 0.6746 time to fit residues: 182.3175 Evaluate side-chains 189 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 348 optimal weight: 0.0870 chunk 53 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 341 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 361 optimal weight: 0.0770 chunk 82 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047452 restraints weight = 107827.539| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.39 r_work: 0.2802 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.459 33390 Z= 0.143 Angle : 0.556 15.446 45379 Z= 0.267 Chirality : 0.041 0.163 4952 Planarity : 0.004 0.046 5712 Dihedral : 9.695 89.706 4887 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.74 % Allowed : 15.46 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3955 helix: 1.83 (0.11), residues: 2153 sheet: 0.50 (0.27), residues: 359 loop : 0.58 (0.18), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 54 TYR 0.016 0.001 TYR C 225 PHE 0.016 0.001 PHE L 334 TRP 0.012 0.001 TRP N 142 HIS 0.007 0.001 HIS N 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (33375) covalent geometry : angle 0.55433 / 0.27 (45366) SS BOND : bond 0.00162 / 0.09 ( 5) SS BOND : angle 0.59346 / 0.28 ( 10) hydrogen bonds : bond 0.03728 / 2.47 ( 1892) hydrogen bonds : angle 4.43344 / 3.25 ( 5334) metal coordination : bond 0.00561 / 0.28 ( 4) metal coordination : angle 4.91809 / 2.62 ( 3) Misc. bond : bond 0.30087 / 15.20 ( 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 229 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.251 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: C 1 MET cc_start: 0.8797 (ttp) cc_final: 0.8510 (ttm) REVERT: C 160 ASP cc_start: 0.8934 (m-30) cc_final: 0.8557 (m-30) REVERT: C 369 MET cc_start: 0.8820 (mmm) cc_final: 0.8530 (mmt) REVERT: G 115 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.9060 (tp30) REVERT: G 123 GLU cc_start: 0.8844 (tt0) cc_final: 0.8626 (tt0) REVERT: F 80 ILE cc_start: 0.9260 (mm) cc_final: 0.8951 (mm) REVERT: F 95 LYS cc_start: 0.8274 (tptt) cc_final: 0.8037 (tppt) REVERT: F 125 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8491 (mt-10) REVERT: F 126 GLU cc_start: 0.8451 (mp0) cc_final: 0.7637 (mm-30) REVERT: A 214 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9020 (tm) REVERT: A 223 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 58 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: B 180 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: D 164 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: J 13 SER cc_start: 0.8535 (t) cc_final: 0.8288 (t) REVERT: N 341 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8223 (pp30) REVERT: E 54 LYS cc_start: 0.9052 (tppt) cc_final: 0.8744 (mtpt) REVERT: E 55 ASP cc_start: 0.8719 (p0) cc_final: 0.8317 (p0) REVERT: R 123 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8136 (tm-30) REVERT: Q 116 HIS cc_start: 0.7459 (m-70) cc_final: 0.6847 (m-70) REVERT: Q 122 ASP cc_start: 0.6658 (p0) cc_final: 0.6417 (p0) REVERT: Q 125 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8174 (tt0) REVERT: Q 141 LYS cc_start: 0.9146 (mppt) cc_final: 0.8924 (mppt) REVERT: L 99 MET cc_start: 0.8918 (ttp) cc_final: 0.8542 (pp-130) REVERT: L 390 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (ptpp) REVERT: M 197 ASN cc_start: 0.8706 (t0) cc_final: 0.7554 (t0) REVERT: O 85 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (pmm) REVERT: S 76 LYS cc_start: 0.9048 (tptm) cc_final: 0.8734 (tppt) REVERT: S 78 GLU cc_start: 0.8325 (tt0) cc_final: 0.7874 (tm-30) REVERT: S 88 GLU cc_start: 0.8596 (mp0) cc_final: 0.8390 (mm-30) REVERT: U 59 ASP cc_start: 0.8586 (m-30) cc_final: 0.8027 (m-30) REVERT: U 69 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7637 (pm20) outliers start: 58 outliers final: 23 residues processed: 222 average time/residue: 0.7012 time to fit residues: 182.9976 Evaluate side-chains 193 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 306 optimal weight: 0.9980 chunk 368 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 350 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 362 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN M 184 GLN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047408 restraints weight = 108792.534| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.39 r_work: 0.2803 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.452 33390 Z= 0.137 Angle : 0.552 15.254 45379 Z= 0.264 Chirality : 0.040 0.190 4952 Planarity : 0.004 0.045 5712 Dihedral : 9.525 89.664 4887 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.29 % Allowed : 16.00 % Favored : 82.71 % 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: 1.92 (0.14), residues: 3955 helix: 1.91 (0.11), residues: 2141 sheet: 0.46 (0.27), residues: 359 loop : 0.68 (0.18), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 54 TYR 0.018 0.001 TYR S 27 PHE 0.016 0.001 PHE L 334 TRP 0.024 0.001 TRP P 185 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (33375) covalent geometry : angle 0.54977 / 0.26 (45366) SS BOND : bond 0.00146 / 0.08 ( 5) SS BOND : angle 0.54943 / 0.25 ( 10) hydrogen bonds : bond 0.03675 / 2.44 ( 1892) hydrogen bonds : angle 4.40280 / 3.22 ( 5334) metal coordination : bond 0.02230 / 1.12 ( 4) metal coordination : angle 5.48849 / 3.04 ( 3) Misc. bond : bond 0.33248 / 16.28 ( 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 213 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.087 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: C 1 MET cc_start: 0.8813 (ttp) cc_final: 0.8522 (ttm) REVERT: C 160 ASP cc_start: 0.8937 (m-30) cc_final: 0.8554 (m-30) REVERT: C 369 MET cc_start: 0.8820 (mmm) cc_final: 0.8495 (mmt) REVERT: G 115 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.9028 (tp30) REVERT: G 123 GLU cc_start: 0.8837 (tt0) cc_final: 0.8635 (tt0) REVERT: F 80 ILE cc_start: 0.9263 (mm) cc_final: 0.8952 (mp) REVERT: F 95 LYS cc_start: 0.8292 (tptt) cc_final: 0.7904 (tppt) REVERT: F 125 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8553 (mt-10) REVERT: F 126 GLU cc_start: 0.8533 (mp0) cc_final: 0.7745 (mm-30) REVERT: A 223 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8044 (t0) REVERT: B 58 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: B 60 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8504 (t80) REVERT: B 364 MET cc_start: 0.8651 (mmm) cc_final: 0.8397 (mmp) REVERT: D 164 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: J 13 SER cc_start: 0.8529 (t) cc_final: 0.8272 (t) REVERT: N 341 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: E 55 ASP cc_start: 0.8706 (p0) cc_final: 0.8322 (p0) REVERT: R 123 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8072 (tm-30) REVERT: Q 99 ASP cc_start: 0.8262 (m-30) cc_final: 0.7792 (p0) REVERT: Q 116 HIS cc_start: 0.7380 (m-70) cc_final: 0.6791 (m-70) REVERT: Q 122 ASP cc_start: 0.6856 (p0) cc_final: 0.6604 (p0) REVERT: Q 125 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8216 (tt0) REVERT: Q 141 LYS cc_start: 0.9137 (mppt) cc_final: 0.8932 (mppt) REVERT: L 99 MET cc_start: 0.8887 (ttp) cc_final: 0.8421 (pp-130) REVERT: L 390 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8583 (mtpm) REVERT: M 119 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8292 (mtpp) REVERT: M 197 ASN cc_start: 0.8722 (t0) cc_final: 0.7676 (t0) REVERT: M 364 MET cc_start: 0.8913 (mmm) cc_final: 0.8595 (mmt) REVERT: O 85 MET cc_start: 0.8824 (mpp) cc_final: 0.8608 (pmm) REVERT: S 76 LYS cc_start: 0.9062 (tptm) cc_final: 0.8751 (tppt) REVERT: S 78 GLU cc_start: 0.8331 (tt0) cc_final: 0.7882 (tm-30) REVERT: S 88 GLU cc_start: 0.8602 (mp0) cc_final: 0.8398 (mm-30) REVERT: U 59 ASP cc_start: 0.8610 (m-30) cc_final: 0.8042 (m-30) REVERT: U 69 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7661 (pm20) outliers start: 43 outliers final: 22 residues processed: 210 average time/residue: 0.7130 time to fit residues: 175.9430 Evaluate side-chains 192 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN R 56 GLN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.045132 restraints weight = 109830.165| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.38 r_work: 0.2726 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.548 33390 Z= 0.250 Angle : 0.650 18.216 45379 Z= 0.309 Chirality : 0.043 0.195 4952 Planarity : 0.004 0.045 5712 Dihedral : 9.761 88.393 4887 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.47 % Allowed : 15.91 % Favored : 82.62 % 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: 1.73 (0.14), residues: 3955 helix: 1.72 (0.11), residues: 2158 sheet: 0.42 (0.27), residues: 359 loop : 0.63 (0.18), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 54 TYR 0.021 0.002 TYR F 114 PHE 0.019 0.002 PHE L 334 TRP 0.015 0.002 TRP P 185 HIS 0.015 0.001 HIS N 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (33375) covalent geometry : angle 0.64814 / 0.31 (45366) SS BOND : bond 0.00172 / 0.09 ( 5) SS BOND : angle 0.61683 / 0.32 ( 10) hydrogen bonds : bond 0.04151 / 2.75 ( 1892) hydrogen bonds : angle 4.55661 / 3.33 ( 5334) metal coordination : bond 0.02857 / 1.41 ( 4) metal coordination : angle 6.43456 / 3.48 ( 3) Misc. bond : bond 0.40801 / 20.85 ( 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 217 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8804 (ttp) cc_final: 0.8536 (ttm) REVERT: C 139 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8042 (tpt) REVERT: C 160 ASP cc_start: 0.8939 (m-30) cc_final: 0.8579 (m-30) REVERT: C 369 MET cc_start: 0.8852 (mmm) cc_final: 0.8508 (mmt) REVERT: G 115 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8997 (tt0) REVERT: G 123 GLU cc_start: 0.8936 (tt0) cc_final: 0.8700 (tt0) REVERT: F 80 ILE cc_start: 0.9311 (mm) cc_final: 0.9058 (mp) REVERT: F 95 LYS cc_start: 0.8485 (tptt) cc_final: 0.8066 (tppt) REVERT: F 99 ASP cc_start: 0.7986 (m-30) cc_final: 0.7754 (m-30) REVERT: F 125 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8659 (mt-10) REVERT: F 126 GLU cc_start: 0.8713 (mp0) cc_final: 0.8487 (mp0) REVERT: A 223 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8175 (t0) REVERT: A 390 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: B 58 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: B 60 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8538 (t80) REVERT: B 180 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8674 (tp30) REVERT: B 364 MET cc_start: 0.8691 (mmm) cc_final: 0.8437 (mmp) REVERT: D 164 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: N 255 ASP cc_start: 0.8578 (p0) cc_final: 0.8335 (p0) REVERT: E 54 LYS cc_start: 0.9032 (tppt) cc_final: 0.8759 (tttm) REVERT: E 55 ASP cc_start: 0.8794 (p0) cc_final: 0.8474 (p0) REVERT: R 123 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8206 (tm-30) REVERT: Q 84 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8948 (mm-30) REVERT: Q 99 ASP cc_start: 0.8383 (m-30) cc_final: 0.7978 (p0) REVERT: Q 100 GLU cc_start: 0.8212 (pp20) cc_final: 0.7947 (pp20) REVERT: Q 122 ASP cc_start: 0.7337 (p0) cc_final: 0.7009 (p0) REVERT: Q 125 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8311 (tt0) REVERT: Q 141 LYS cc_start: 0.9156 (mppt) cc_final: 0.8900 (mppt) REVERT: L 99 MET cc_start: 0.8839 (ttp) cc_final: 0.8564 (pp-130) REVERT: L 390 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8677 (ttpp) REVERT: M 119 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: M 197 ASN cc_start: 0.8919 (t0) cc_final: 0.8081 (t0) REVERT: S 76 LYS cc_start: 0.9133 (tptm) cc_final: 0.8859 (tppt) REVERT: S 78 GLU cc_start: 0.8477 (tt0) cc_final: 0.8068 (tm-30) REVERT: U 59 ASP cc_start: 0.8739 (m-30) cc_final: 0.8095 (m-30) outliers start: 49 outliers final: 19 residues processed: 208 average time/residue: 0.7016 time to fit residues: 170.8089 Evaluate side-chains 188 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE 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: 0.3980 chunk 128 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 332 ASN L 135 GLN U 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.058955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046116 restraints weight = 108577.214| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.37 r_work: 0.2757 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.498 33390 Z= 0.162 Angle : 0.586 15.595 45379 Z= 0.280 Chirality : 0.041 0.172 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.621 89.955 4887 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.20 % Allowed : 16.33 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3955 helix: 1.78 (0.11), residues: 2159 sheet: 0.30 (0.27), residues: 359 loop : 0.74 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 54 TYR 0.017 0.001 TYR M 341 PHE 0.016 0.001 PHE L 334 TRP 0.014 0.001 TRP N 142 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (33375) covalent geometry : angle 0.58420 / 0.28 (45366) SS BOND : bond 0.00174 / 0.10 ( 5) SS BOND : angle 0.53542 / 0.26 ( 10) hydrogen bonds : bond 0.03852 / 2.56 ( 1892) hydrogen bonds : angle 4.48247 / 3.28 ( 5334) metal coordination : bond 0.01596 / 0.79 ( 4) metal coordination : angle 5.38004 / 2.95 ( 3) Misc. bond : bond 0.37355 / 18.50 ( 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 208 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8861 (ttp) cc_final: 0.8591 (ttm) REVERT: C 160 ASP cc_start: 0.8924 (m-30) cc_final: 0.8550 (m-30) REVERT: C 369 MET cc_start: 0.8828 (mmm) cc_final: 0.8529 (mmt) REVERT: G 97 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8451 (mt-10) REVERT: G 115 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9025 (tp30) REVERT: F 80 ILE cc_start: 0.9328 (mm) cc_final: 0.8966 (mp) REVERT: F 95 LYS cc_start: 0.8474 (tptt) cc_final: 0.8196 (tppt) REVERT: F 125 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8645 (mt-10) REVERT: F 126 GLU cc_start: 0.8784 (mp0) cc_final: 0.8366 (mp0) REVERT: A 223 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8207 (t0) REVERT: A 390 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8459 (mtmm) REVERT: B 58 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: B 60 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8504 (t80) REVERT: B 180 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8692 (tp30) REVERT: B 364 MET cc_start: 0.8745 (mmm) cc_final: 0.8543 (mmp) REVERT: D 164 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: E 54 LYS cc_start: 0.9014 (tppt) cc_final: 0.8722 (mtpt) REVERT: E 55 ASP cc_start: 0.8737 (p0) cc_final: 0.8368 (p0) REVERT: R 123 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8190 (tm-30) REVERT: Q 84 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8966 (mm-30) REVERT: Q 99 ASP cc_start: 0.8400 (m-30) cc_final: 0.8003 (p0) REVERT: Q 100 GLU cc_start: 0.8253 (pp20) cc_final: 0.7988 (pp20) REVERT: Q 122 ASP cc_start: 0.7375 (p0) cc_final: 0.7084 (p0) REVERT: Q 125 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8321 (tt0) REVERT: L 390 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: M 119 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8352 (mtpp) REVERT: M 197 ASN cc_start: 0.8899 (t0) cc_final: 0.8019 (t0) REVERT: M 350 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8507 (tm-30) REVERT: M 364 MET cc_start: 0.8860 (mmm) cc_final: 0.8485 (mmt) REVERT: S 76 LYS cc_start: 0.9117 (tptm) cc_final: 0.8853 (tppt) REVERT: S 78 GLU cc_start: 0.8455 (tt0) cc_final: 0.8015 (tm-30) REVERT: U 59 ASP cc_start: 0.8749 (m-30) cc_final: 0.8091 (m-30) outliers start: 40 outliers final: 18 residues processed: 203 average time/residue: 0.7026 time to fit residues: 167.2920 Evaluate side-chains 185 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 317 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 286 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 HIS R 45 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046771 restraints weight = 108319.260| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.34 r_work: 0.2782 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.472 33390 Z= 0.137 Angle : 0.567 14.996 45379 Z= 0.269 Chirality : 0.040 0.174 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.384 88.931 4887 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.96 % Allowed : 16.75 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.95 (0.14), residues: 3955 helix: 1.88 (0.11), residues: 2151 sheet: 0.35 (0.27), residues: 357 loop : 0.82 (0.18), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 54 TYR 0.017 0.001 TYR M 341 PHE 0.016 0.001 PHE L 334 TRP 0.013 0.001 TRP P 185 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (33375) covalent geometry : angle 0.56516 / 0.27 (45366) SS BOND : bond 0.00189 / 0.11 ( 5) SS BOND : angle 0.52880 / 0.25 ( 10) hydrogen bonds : bond 0.03691 / 2.45 ( 1892) hydrogen bonds : angle 4.41067 / 3.23 ( 5334) metal coordination : bond 0.01226 / 0.60 ( 4) metal coordination : angle 4.85441 / 2.70 ( 3) Misc. bond : bond 0.34214 / 16.03 ( 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 201 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8918 (ttp) cc_final: 0.8624 (ttm) REVERT: C 160 ASP cc_start: 0.8905 (m-30) cc_final: 0.8499 (m-30) REVERT: C 369 MET cc_start: 0.8816 (mmm) cc_final: 0.8503 (mmt) REVERT: G 97 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8468 (mt-10) REVERT: G 115 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.9043 (tp30) REVERT: F 80 ILE cc_start: 0.9327 (mm) cc_final: 0.9076 (mt) REVERT: F 95 LYS cc_start: 0.8496 (tptt) cc_final: 0.8097 (tppt) REVERT: F 99 ASP cc_start: 0.8030 (m-30) cc_final: 0.7819 (m-30) REVERT: F 125 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8626 (mt-10) REVERT: F 126 GLU cc_start: 0.8821 (mp0) cc_final: 0.8427 (mp0) REVERT: A 390 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8491 (mtmm) REVERT: B 58 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: B 60 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8556 (t80) REVERT: D 164 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: E 54 LYS cc_start: 0.9058 (tppt) cc_final: 0.8742 (mtpt) REVERT: E 55 ASP cc_start: 0.8769 (p0) cc_final: 0.8429 (p0) REVERT: R 123 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8155 (tm-30) REVERT: Q 84 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8964 (mm-30) REVERT: Q 99 ASP cc_start: 0.8413 (m-30) cc_final: 0.7994 (p0) REVERT: Q 100 GLU cc_start: 0.8187 (pp20) cc_final: 0.7933 (pp20) REVERT: Q 122 ASP cc_start: 0.7451 (p0) cc_final: 0.7100 (p0) REVERT: Q 125 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8339 (tt0) REVERT: M 119 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8321 (mtpp) REVERT: M 197 ASN cc_start: 0.8904 (t0) cc_final: 0.8147 (t0) REVERT: M 350 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8477 (pp20) REVERT: M 364 MET cc_start: 0.8837 (mmm) cc_final: 0.8433 (mmt) REVERT: O 85 MET cc_start: 0.8811 (pmm) cc_final: 0.8482 (pmm) REVERT: S 76 LYS cc_start: 0.9139 (tptm) cc_final: 0.8886 (tppt) REVERT: S 78 GLU cc_start: 0.8453 (tt0) cc_final: 0.8065 (tm-30) outliers start: 32 outliers final: 15 residues processed: 200 average time/residue: 0.6718 time to fit residues: 159.9281 Evaluate side-chains 179 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 196 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 HIS R 45 ASN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN U 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.045591 restraints weight = 109196.039| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.35 r_work: 0.2742 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.534 33390 Z= 0.203 Angle : 0.616 16.749 45379 Z= 0.289 Chirality : 0.042 0.224 4952 Planarity : 0.004 0.044 5712 Dihedral : 9.514 89.933 4887 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.90 % Allowed : 17.08 % Favored : 82.02 % 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: 1.86 (0.14), residues: 3955 helix: 1.77 (0.11), residues: 2171 sheet: 0.34 (0.27), residues: 357 loop : 0.83 (0.18), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 54 TYR 0.022 0.002 TYR F 114 PHE 0.019 0.002 PHE L 334 TRP 0.015 0.001 TRP N 142 HIS 0.006 0.001 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (33375) covalent geometry : angle 0.61496 / 0.29 (45366) SS BOND : bond 0.00174 / 0.09 ( 5) SS BOND : angle 0.53375 / 0.26 ( 10) hydrogen bonds : bond 0.03940 / 2.61 ( 1892) hydrogen bonds : angle 4.47431 / 3.27 ( 5334) metal coordination : bond 0.01797 / 0.88 ( 4) metal coordination : angle 4.86405 / 2.68 ( 3) Misc. bond : bond 0.42140 / 20.64 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8236.68 seconds wall clock time: 141 minutes 58.37 seconds (8518.37 seconds total)